Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations.
PMID: 34801754
2022
Infection, genetics and evolution
Figure: 1 associated with the Alpha variant of concern first detected in the United Kingdom are H69_V70del, Y144del (identified as Y145del by alignment software), N501Y, A570D, D614G, P681H, T716I, S982A, and D1118H.
Figure: L18F, E484K, N501Y, D614G, H655Y, and V1176F are associated with the Gamma variant of concern, and S13I, W152C, L452R are associated
Functional Antibodies Against SARS-CoV-2 Receptor Binding Domain Variants with Mutations N501Y or E484K in Human Milk from COVID-19-Vaccinated, -Recovered, and -Unvaccinated Women.
Abstract: Results: The titers of human milk IgG against N501Y were higher in the COVID-19 vaccine group than in the no-vaccine group but comparable with the COVID-19 PCR group.
Abstract: The titers and NAbs of secretory IgA (SIgA)/IgA, secretory IgM (IgM)/IgM, and IgG against SARS-CoV-2 RBD with mutations N501Y or E484K were measured by using ELISA and a surrogate virus neutralization assay.
Abstract: The titers of SIgM/IgM and the inhibition of NAbs were higher against the mutation E484K than N501Y.
Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination.
Abstract: As suggested by its convergent evolution in Brazil, South Africa and elsewhere2,3, our results indicate that N501Y substitution is an adaptive spike mutation of major concern.
Abstract: Here, using a reverse genetics approach, we show that of the 8 individual spike protein substitutions, only N501Y resulted in consistent fitness gains for replication in the upper airway in a hamster model as well as in primary human airway epithelial cells.
Abstract: Mechanistically, the N501Y substitution increased the affinity of the viral spike protein for cellular receptors.
Abstract: The N501Y substitution recapitulated the enhanced viral transmission phenotype of the eight mutations in the Alpha spike
Surveillance of SARS-CoV-2 variants of concern by identification of single nucleotide polymorphisms in the spike protein by a multiplex real-time PCR.
PMID: 34822912
2022
Journal of virological methods
Method: Details of the primers and duel labelled probes used are previously described and used to detect the presence of the following spike protein mutations: N501Y, E484 K and L452R wi
Discussion: However, in situations where there is a dominant variant with L452R or N501Y, confirmed by whole genomic sequencing, this would be an easy to use, low-cost assay to rapidly identify the prevalence of VOCs such as delta.
Discussion: Therefore, this multiplex real-time PCR approach would not be useful to identify emergence of new SARS-CoV-2 variants or to differentiate between the variants which have L425R, N501Y or E484 K, which again is seen in different SARS-CoV-2 variants.
Occurrence of a substitution or deletion of SARS-CoV-2 spike amino acid 677 in various lineages in Marseille, France.
Introduction: The variants recently considered to be of greatest concern are those carrying amino acid substitutions N501Y and/or E484K within the spike protein, as they have increased affinity for the ACE2 cellular receptor, decreased sensitivity to neutralising antibodies, and may escape the immune responses elicited by the vaccines currently used in Western countries.
Result: Therefore, the spike Q677H substitution should be considered as another example of convergent evolution, in addition to spike amino acid substitutions N501Y, L452R, and L18F which also independently appeared in various lineages.
A year living with SARS-CoV-2: an epidemiological overview of viral lineage circulation by whole-genome sequencing in Barcelona city (Catalonia, Spain).
Result: The D614G (96.4%) substitution was observed in most viral genomes, in addition to multiple mutations defining lineages, such as the mutation set Delta69-70, Delta144, N501Y, A570D, P681H, T716I, S982A, and D1118H for B.1.1.7 viruses.
Discussion: Therefore, one of the substitutions of interest and shared by the new variants is N501Y, located at the RBD of Spike, which increases ACE2 binding affinity, and improves the human-to-human transmission.
Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021.
PMID: 34848355
2022
Infection, genetics and evolution
Abstract: In addition, the profiling of sub-haplotypes indicated that sub-haplotype 2A_1 with the mutations at N501Y, A570D, D614G, P681H, T716I, S982A, and D118H in Spike was over 58% in May 2021 in the high partly vaccinated rate group (US, Canada, and Germany).
Introduction: The B.1.1.7 lineage harbors three amino acid deletions and seven missense mutations in spike protein, including D614G and N501Y in the ACE2 receptor-binding domain.
Result: Among the sub-haplotypes of haplotype 2A variants, sub-haplotype 2A_1 was the most prevalent sub-
Table: N501Y
The significant immune escape of pseudotyped SARS-CoV-2 variant Omicron.
Introduction: These mutations cover almost all the key mutations of the previous VOCs (Alpha, Beta, Gamma, and Delta), including K417N, E484A, and N501Y and other known mutations which are proved to change the sensitivity of the virus to neutralization by protective antibodies.
Result: There are 32 mutations on the Spike of Omicron, including the following sites: A67V, H69del-V70del, T95I, G142D-V143del-Y144del-Y145del, N211del-L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K,
Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform.
Result: 4C and D), higher than observed for N501Y detection and in a previous study.
Result: Because CRISPR/Cas12a has been reported to differentiate SNPs with single-base resolution, we used Cas12a to identify SARS-CoV-2 N501Y, D614G, and 69/70 deletion mutations; these are the key mutations of SARS-CoV-2 VOC (Table S1).
Result: Furthermore, five samples carrying the N501Y mutation and two samples carrying the 69/70 deletion were identified.
Result: Notably, kinetic analyses showed N501Y and 69/70 deletion can be identified in as small duration as 5-10 min, indicating a shorter reaction time for mutation tracking.
Result: RT-CORDS fluorescence assay for 69/70 deletion identification showed a sensitivity of 10-17 M, the same value as that achieved for N501Y
SARS_CoV_2 mutation literature information.
PMID: 
2022
Infection, genetics and evolution
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