Abstract: To build an investigative framework, we have applied an unsupervised machine learning approach to 4296 Omicron viral genomes collected and deposited to GISAID as of December 14, 2021, and have identified a core haplotype of 28 polymutants (A67V, T95I, G339D, R346K, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H,
Age-Specific Changes in Virulence Associated with SARS-CoV-2 Variants of Concern.
Introduction: As such, it has been challenging to determine with certainty whether infection with the Delta VOC is more virulent in children than non-VOC SARS-CoV-2 or other VOCs, such as those with the N501Y mutation.
Introduction: In the Canadian province of Ontario, the VOC carrying the N501Y mutation (including the Alpha/B.1.1.7, Beta/B.1.351, and Gamma/P.1 VOC) replaced earlier SARS-CoV-2 lineages by April 2021 but were, in turn, replaced by the Delta (B.1.617.2) variant, which has been the dominant variant in the province since July 2021.
Introduction: Our objectives were to estimate age-specific risks of severe illness in individuals infected with the Delta or N501Y-positive VOC relative to non-VOC SARS-CoV-2 infection, determine whether there is heterogeneity in differential risk by age group, and explore the possible sources of an
Human serum from SARS-CoV-2-vaccinated and COVID-19 patients shows reduced binding to the RBD of SARS-CoV-2 Omicron variant.
Discussion: S477N, T478K, and E484A were initially at ~47% (status 2021-12-14, 2146 sequences), now instead above 88%, as N501Y (status 2022-02-07, 873.492 sequences).
Discussion: Several Omicron RBD mutations are assumed to increase the binding to ACE2: G339D, S477N, T478K, Q493K, and N501Y; others are proposed to be neutral: S371L, S373P, G446S, E484A, Q493R, and Q498R, or are assumed to reduce the binding to ACE2: PMID: 35240804
2022
Mathematical biosciences and engineering
Abstract: The variant of concern (VOC) 202012/01 (B.1.1.7, also known as the alpha variant) bearing the N501Y mutation emerged in late 2020.
Antibody escape and global spread of SARS-CoV-2 lineage A.27.
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
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.
Tetra-primer ARMS-PCR combined with dual-color fluorescent lateral flow assay for the discrimination of SARS-CoV-2 and its mutations with a handheld wireless reader.
Abstract: Herein, we report a low-cost, facile, and highly sensitive diagnostic platform that can simultaneously distinguish wild-type (WT) SARS-CoV-2 and its two mutations, namely, D614G and N501Y, within 2 h.
Abstract: The WT and M viruses were indicated and were strictly discriminated by the presence of a green or red band on test line 1 for the D614G site and test line 2 for the N501Y site.
Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion.
Introduction: In addition, spike with the N501Y mutation has gained the ability to utilize mouse ACE2 as the receptor to infect the mouse, expanding its host range.
Introduction: Subsequently, the N501Y mutation found in the B.1.1.7, B.1.351, and B.1.1.28.1 spike proteins has increased the binding affinity between the receptor-binding domain (RBD) and ACE2, increasing viral fitness and infectivity.
Result: In addition, the N501Y mutation in the spike has been demonstrated to have gained the ability to utilize mouse ACE2 for cell entry, and our data suggested that the N501Y mutant specifically gained the ability to utilize mouse ACE2 for cell entry, with an efficiency approximately 4-fold higher than that o
SARS_CoV_2 mutation literature information.
PMID: 
2022
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