Abstract: Variant A.27 is characterized by a mutational pattern in the spike gene that includes the L18F, L452R and N501Y spike amino acid substitutions found in various variants of concern but lacks the globally dominant D614G.
Result: L18F is present in the VOCs B.1.351 and P.1, the L452R substitution is found in high frequencies in B.1.617.2 and related AY lineages, and N501Y is known from B.1.1.7, B.1.351 and P.1.
Result: Furthermore, N501Y was suggested to enhance the binding affinity to ACE2.
Result: Lineage A.27 has two mutations in its Table: N501Y
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
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).
Identifying SARS-CoV-2 Variants of Concern through saliva-based RT-qPCR by targeting recurrent mutation sites.
Introduction: However, neutralization of the Wuhan strain was reduced when a variant vaccine was used that contained the K417N, E484K, N501Y and D614G mutations, which agrees well with our results.
Method: Pre-fusion spike protein ectodomain DNA constructs were designed containing the following mutations compared to the Wuhan variant (Wuhan Hu-1; GenBank: MN908947.3): deletion of H69, V70 and Y144, N501Y, A570D, D614G, P681H, T716I, S982A and D1118H in Alpha; L18F, D80A, D21
A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay.
PMID: 35271889
2022
Journal of virological methods
Table: N501Y
Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm.
PMID: 35266951
2022
Genetics and molecular biology
Introduction: Currently, the WHO has identified the Gamma lineage (B.1.1.28.1, P.1 or Gamma; Nextstrain clade 20J/V3) with the following key S mutations: L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I, and V1176F.
Introduction: Nine key mutations involving the S glycoprotein have been
Table: N501Y
Discussion: Other derived lineages also harbor the N501Y mutation, signaling its recurrence.
The SARS-CoV-2 Alpha variant exhibits comparable fitness to the D614G strain in a Syrian hamster model.
Introduction: In late 2020, three SARS-CoV-2 variants sharing the N501Y spike mutation located in the receptor-binding motif (RBM) emerged almost simultaneously in the United Kingdom (Alpha variant from lineage B.1.1.7; initially named VOC 202012/01), in South Africa (Beta variant from lineage B.1.351) and in Brazil (P.1 variant from lineage B.1.1.28.1).
Discussion: In another study that used engineered rescued viruses derived from the USA_WA1/2020 strain, the hamster model appeared useful to detect weak fitness advantages and increases in transmissibility of viruses that carry the N501Y and A570D spike mutations.
SARS_CoV_2 mutation literature information.
PMID: 
2022
Mathematical biosciences and engineering
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