Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms.
Discussion: A hypothesis - yet to be tested - is that mutations P323L-D614G reinforce the asymptomatic phenotype, at least in a Mexican genetic background.
Discussion: In this case, mutation Q613H defining the emerging lineage A.23.1, from Uganda, may have taken the role of the mutation D614G in B lineages during evolution of A lineages.
Discussion: The discrete association of both D614G and P323L to an asymptomatic phenotype could mean that those fixed mutations enhance transmissibility by bypassing an immune response.
Discussion: The other hotspot is within S1-S2 subdomains, and which includes the furin-like protease cleavage site, and contains D614G, P681H/R and PMID: 34848718
2021
Nature communications
Introduction: In this regard, some mutations in SARS-CoV-2 are responsible for large conformational changes that may enhance infection, such as those located in the distal region of the spike protein and near the fusion region as the well-known D614G.
Rapid Identification of SARS-CoV-2 Variants of Concern Using a Portable peakPCR Platform.
Introduction: For example, the D614G variant has been shown to increase the viral load of infected patients and has replaced the original variant since June 2020 around the globe.
Niclosamide shows strong antiviral activity in a human airway model of SARS-CoV-2 infection and a conserved potency against the Alpha (B.1.1.7), Beta (B.1.351) and Delta variant (B.1.617.2).
Abstract: Furthermore, niclosamide remains its potency against the D614G, Alpha (B.1.1.7), Beta (B.1.351), and Delta (B.1.617.2) variants.
Method: Briefly, human bronchial epithelial cells were apically infected with the European D614G strain of SARS-CoV-2 (BavPat1 D614G) at a multiplicity of infection (MOI) of 0.1 and cult
Result: Importantly, niclosamide also blocked the replication of the European BavPat D614G, B.1.1.7, B.1.351 and B.1.617.2 variant with an IC50 of 0.06 muM, 0.08 muM, 0.07 muM, and 0.08 muM respectively (Fig 2).
Result: We then tested the activity of niclosamide against several variants of concern of SARS-CoV-2, including the BavPat1 strain (D614G), SARS-CoV-2 lineage B.1.1.7 (Alpha), SARS-CoV-2 Wuhan D614, SARS CoV-2 lineage B.1.351 (Beta) and SARS-CoV-2 lineage B.1.617.2 (Delta).
Differential Interactions between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern.
PMID: 34856802
2021
Journal of chemical theory and computation
Result: Although our results are accordant with recently published studies, the reason why Kappa/Delta and Epsilon behaviors are distinctive remained to be further studied, and it might stem from the limitation in our model, as we only employed the L452R mutation in RBD for the Epsilon variant without a D614G mutation.
Recognition of Variants of Concern by Antibodies and T Cells Induced by a SARS-CoV-2 Inactivated Vaccine.
Result: In order to further corroborate whether these antibodies were also able to neutralize viral infection in a cell culture, we performed cVNT for lineage B SARS-CoV2 (D614G) and the Alpha, Gamma, and Delta variants.
Result: The GMT values obtained by cVNT for D614G strain and the Alpha, Gamma, and Delta variants were 74.8 (95% CI 59.8-93.6), 32.1(95% CI 20.1-51.1), 15.8 (95% CI 9.5-26.2) and 7.9 (95% CI 5.2-12), respectively.
Result: The results obtained showed that, as compared to the D614G strain, there was a 2.33-fold decrease in neutralizing antibodies against the Alpha variant, a 4.73-fold reduction against the Gamma variant and a 9.46-fold reduction against the Delta variant ( Figure 2A ).
Result: The seropositivity rates of neutralizing antibodies for the Alpha, Gamma and Delta variants were 84.62%, 65.38% and 55.76% respectively, while for the COVID-19 outbreak in Malaysia: Decoding D614G mutation of SARS-CoV-2 virus isolated from an asymptomatic case in Pahang.
Result: A total of 34 nonsynonymous mutations were observed, with the spike D614G having the highest occurrence in 2400 genomes followed by the nsp12 P4715L mutation observed in 2254 genomes (Figure 1A).
Result: After D614G, P681R occurred in 1455 of the analyzed sequences.
Result: All, except D614G, from the 9 non-synonymous mutations observed, had rel
Figure: (A) Pangolin-CoV, (B) SARS-CoV-2 (D614G) Variant, (C) Reference sequence at 614 position in spike glycoprotein sequence.
Figure: (B) Amino acid sequence alignment of spike protein encompassing the D614G position.
Production, Titration, Neutralisation, Storage and Lyophilisation of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Lentiviral Pseudotypes.
Abstract: This protocol details a rapid and reliable method for the production and titration of high-titre viral pseudotype particles with the SARS-CoV-2 spike protein (and D614G or other variants of concern, VOC) on a lentiviral vector core, and use for neutralisation assays in target cells expressing angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2).
Characterization of altered genomic landscape of SARS-CoV-2 variants isolated in Saudi Arabia in a comparative in silico study.
PMID: 34866979
2021
Saudi journal of biological sciences
Abstract: The most frequently changed nucleotide was C3037T (silent mutation) and A23403G (D614G), each of which occurred in 57 variants out of 58 followed by C14408T (P4715L) and C241T (5'UTR) which were found in 56 and 55 variants respectively.
Result: Our analysis showed that the most frequently changed nucleotide were C3037T (silent mutation) and A23403G (D614G) each of which occurred in 57 variants out of 58, followed by C14408T (P4715L) and C241T (5'UTR) which were found in 56
COVID-19 outbreak in Malaysia: Decoding D614G mutation of SARS-CoV-2 virus isolated from an asymptomatic case in Pahang.
Abstract: Comparison of the whole cell-derived WA1 and D614G spike proteins revealed that N-glycosites local to the mutation site appeared to be more readily detected, hinting that these sites are more exposed to glycosylation machinery.
Abstract: Moreover, recombinant HEK293-derived S1 was occupied almost completely with complex glycan, while both WA1 and D614G derived from the Vero E6 cell whole virus were predominantly high-mannose glycans.
Abstract: The Vero cell-derived spike from the WA1 strain and a D614G variant was analyzed.
C
Conclusion: Glycan modification at most N-glycosites is very similar between WA1 and D614G and primarily high-mannose, with significant differences at N343.
SARS_CoV_2 mutation literature information.
PMID: 
2021
Microbial genomics
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