Abstract: We applied the primer set and wet-laboratory protocol to sequence 222 samples that were missing positions with key mutations K417N, E484K, and N501Y due to poor coverage after NGS sequencing.
Abstract: We successfully sequenced 153 samples of 222 (69 %) using Sanger sequencing and confirmed the occurrence of key beta variant mutations (K417N, E484K, N501Y) in the S genes of 142 of 153 (93 %) samples.
Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity.
Result: Additionally, the mouse-adapted mutants N501Y, Q493K, and Q498H of the SARS-CoV-2 RBD also showed significantly increased binding affinity towards mouse ACE2.
Result: Notably, similar as K417N, N501Y, and E484K in the B.1.351 variant, RBD mutations in the B.1.617 variants also showed enhanced infectivity in mouse cells.
[Detection SARS-CoV-2 (Coronaviridae: Coronavirinae: Betacoronavirus: Sarbecovirus) in children with acute intestinal infection in Nizhny Novgorod during 2020-2021].
Abstract: Analysis of the S-protein amino acid sequence of the strains studied showed the absence of the N501Y mutation in the 2020 samples, which is a marker for variants with a high epidemic potential, called variants of concern (VOC) according to the World Health Organization (WHO) definition (lines Alpha B.1.1.7, Beta B.1.351, Gamma P.1).
Design of SARS-CoV-2 Variant-Specific PCR Assays Considering Regional and Temporal Characteristics.
PMID: 35285246
2022
Applied and environmental microbiology
Result: To further confirm whether the RT-qPCR results were correct, we conducted NGS analysis to examine eight mutation markers for the Alpha variant (S:Delta69/70, S:Delta144, S:N501Y, S:A570D, S:P681H, S:T716I, S:S982A, and S:D1118H) and six mutation markers for the Delta variant (S:T19R, S:Delta156/157, S:L452R,
SARS-CoV-2 infection after vaccination in Italian health care workers: a case report.
PMID: 35283546
2022
National Academy science letters. National Academy of Sciences, India
Abstract: Their genotyping performed on RNA extracts highlighted the presence of del69/70, N501Y, A570D, and 1841A > G (D614G) sequence variants, all indicative of VOC 202012/01-lineage B.1.1.7, suggesting a common source of infection.
Result: The genotyping performed first by Real-time PCR and then confirmed by direct sequencing proved the presence of del69/70, N501Y, A570D, and 1841A > G (D614G) variants, indicative of VOC 202,012/01-lineage B.
Figure: Sections from the electropherograms showing the 69/70, N501Y, A570D, and D614G (a., b., c., d.) associated with SARS-CoV-2 Alfa Variant B.1.1.7.
Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections.
Introduction: B.1.1.7, which was firstly detected in the United Kingdom, has an N501Y mutation in the receptor binding domain (RBD) of S protein.
Introduction: B.1.351, which was found in South Africa, has three mutations (K417N, E484K, and N501Y) in the RBD.
Introduction: Finally, B.1.1.529, which was detected in Botswana on November 11, 2021 and South Africa on November 14, 2021, has 15 mutations (G339D, S371L, S373P, S375F, K417N, N440K, G446S,
Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations.
Abstract: In addition, GB-1 inhibited the binding between ACE2 and RBD with a single mutation (E484K or N501Y), except the K417N mutation.
Abstract: In the compositions of GB-1, glycyrrhizic acid can inhibit the binding between ACE2 and RBD with Wuhan type, except K417N-E484K-N501Y mutation.
Abstract: In this study, we discovered that GB-1, developed from Chiehyuan herbal formula which obtained from Tian Shang Sheng Mu of Chiayi Puzi Peitian Temple, can inhibit the binding between ACE2 and RBD with Wuhan type, K417N-E484K-N501Y and
Omicron variant (B.1.1.529) of SARS-CoV-2: understanding mutations in the genome, S-glycoprotein, and antibody-binding regions.
Figure: In the figure, red arrows in a, c, e, and g show the K417N, T478K, E484A, and N501Y mutations found in the Omicron variant.
Figure: Red box in b, d, f, and h represents the county of origin of the K417N, T478K, E484A
Discussion: The significant mutations and features are N501Y (augments the binding between of S-protein and ACE2); D614G (increase infectivity); H655Y (accelerate transmission); N679K (increase viral transmission); and P681H (enhance binding affinity of S-protein) (Table 2).
Evolution of the SARS-CoV-2 spike protein in the human host.
Abstract: Spikes of both variants have the same mutation, N501Y, in the receptor-binding domains.
Method: The following variant spikes were made (SA, Alpha and mink) (all mutations listed with reference to the NCBI sequence YP_009724390.1): 2P Alpha (Delta69-70, Delta144, N501Y, A570D, D614G, P681H, T716A, S982A, D1118H, and K986P, V987P), FUR2P Alpha (Delta69-70, Delta144,
Figure: d The N501Y substitution present in both the Beta and Alpha variants allows formation of a new hydrogen bond or a salt bridge.
Using genomic epidemiology of SARS-CoV-2 to support contact tracing and public health surveillance in rural Humboldt County, California.
5Result: Notably, N501Y is present in three ""variant of concern"" lineages: B.1.1.7, B.1.351, and P.1."
Result: Detection of de novo N501Y emergence within a skilled nursing facility outbreak.
Result: Genomic surveillance of the outbreak in Facility A also revealed the emergence and eradication of a lineage that had a de novo asparagine to tyrosine substitution in site 501 of the Spike protein (N501Y).
Result: Of 89 samples sequenced during this outbreak, 16 samples shared this N501Y substitution.
Result: The first sample containing this N501Y substitution was collected on November 29, 2020.
Result: Within this clade, 14 of the 16 sequences differed from the primary outbreak strain in Facility A by only the
SARS_CoV_2 mutation literature information.
PMID: 
2022
Microbial genomics
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