Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds.
Abstract: The concordance and rigidity ratios of multiple mutation strains such as B.1.617.2 against the wild-type one at the receptor-binding domain (RBD) and receptor-binding motif (RBM) regions provide a good indication of the transmissibility and neutralization escape ability except for binding affinity of mutation sites such as N501Y.
Introduction: Although the high binding affinity of the mutation site such as N501Y in B.1.1.7 (alpha) expanded from UK and in B.1.351 (beta) circulated from South Africa, which was measured by the quantitative deep mutational scanning, can rationalize the increased infections, identifying the fundamental cause of vaccine nullification is difficult in general, and is a source of significant concern.
Introduction: B.1.1.7 is prevalent all over the world, but the N501Y frequency of phylogeny is about 60-70% ().
Differential Interactions Between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern.
Introduction: As shown in Figure 2B,C, Alpha and Beta variants include N501Y mutation, while Beta variant involves two additional mutations, K417N and E484K.
Introduction: However, only the N501Y mutation was examined in their study, although other potentially important mutations have emerged.
Introduction: Such contacts are decreased or even lost in the case of RBDWT or RBDEpsilon lacking the N501Y mutation (Figure 2A,D).
Introduction: The weakened interactions of RBDBeta N417 and RBDGamma T417 could make them less contagious than the Alpha variant, while the N501Y mutation still allow
Introduction: conducted an experimental and computational study to capture the role of N501Y mutation in Alpha, Beta, and Gamma variants.
Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach.
PMID: 34346317
2021
Computers in biology and medicine
Abstract: Further, the molecular dynamics simulation (MDS) approach reveals the structural transition of mutants (N501Y and D614G) S-protein.
Abstract: Using the extensive bioinformatics pipeline, we screened the destabilizing (L8V, L8W, L18F, Y145H, M153T, F157S, G476S, L611F, A879S, C1247F, and C1254F) and stabilizing (H49Y, S50L, N501Y, D614G,
Transformations, Lineage Comparisons, and Analysis of Down-to-Up Protomer States of Variants of the SARS-CoV-2 Prefusion Spike Protein, Including the UK Variant B.1.1.7.
Abstract: For the B.1.1.7 variant, we demonstrated the critical importance of mutations D614G and N501Y on the structure and binding, respectively, of the Spike protein.
Introduction: We are able to demonstrate dynamic changes in the B.1.1.7 spike protein that can be traced to two key mutations, resulting in a more accessible Result: Note that both D614G and N501Y are also present in the South African variant (B.1.351).
Result: The N501Y mutation may demonstrate a significant increase in binding to hACE2 due to the highly favorable Y-Y hydrophobic interaction pair in the new mutant state (Table S3); however, this remains to be concretely verified.
Table: N501Y
Near-Complete Genome Sequences of Nine SARS-CoV-2 Strains Harboring the D614G Mutation in Malaysia.
Introduction: Of the nine strains sequenced, six were classified as the B.1.351 variant, which harbors the E484K and N501Y mutations commonly associated with increased transmission rate.
Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants.
Abstract: We predict the same effect for several mutations on glycine residues (404, 416, 504, 252) as well as residues K417, D467 and N501, including the N501Y mutation recently observed within the B.1.1.7, 501.V2 and P1 strains.
Result: 501.V2 includes the mutations L18F, D80A, D215G, R246I, K417N, E484K, N501Y, D614G, A701V.
Result: According to our calculations, the N501Y mutant shows DeltaSvib (open) = -1.60x10-2 J.K-1 and DeltaSvib (closed) = 2.37x10-1 J.K-1, with VDS = 2.53x10-1 J.K-1.
Result: COG-UK recently detected a strain containing the mutation N501Y
Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies.
Abstract: Using the already circulating mutation S494P, we found that it reduces antibody neutralization of convalescent and post-immunization sera, particularly when combined with E484K and with mutations able to increase binding to ACE2, such as N501Y.
Abstract: We confirmed that E484K evades antibody neutralization elicited by infection or vaccination, a capacity augmented when
Figure: (F, H) Paired analysis of neutralizing activity of convalescent sera (F) or post-vaccination sera (H) against WT vs S494P, S494P/N501Y, E484K/S494P or E484K/S494P/N501Y mutants.
Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021.
Neutralizing Activity of Sera from Sputnik V-Vaccinated People against Variants of Concern (VOC: B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.617.3) and Moscow Endemic SARS-CoV-2 Variants.
Result: The RBD variability data obtained for SARS-CoV-2 variants from Moscow patients (Figure 2, dashed lines) are generally consistent with the variability data for Russian sequences available in GISAID (Figure 2, solid lines and Figure S1) showing increasing prevalence of S477N, A522S, E484K, N501Y, T385I, S494P, N439K, K417N, T487K, N501T, and Y508H mutations.
Discussion: A significant percentage of the substitution variants that are becoming common is recorded: S477N + A522S (27.8%),
ViMRT
SARS_CoV_2 mutation literature information.
PMID: 
2021
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