Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein.
PMID: 34419160
2021
Infectious diseases of poverty
Abstract: In more than ten countries, the frequencies of the isolates with E484K and S477N increased significantly.
Abstract: Of all predicted mutants, the number of E484K was the largest one with 86 585 sequences, followed by S477N with 55 442 sequences worldwide.
Table: S477N
Discussion: S477N enhance the binding affinity.
Discussion: S477N, a mutation mainly identified in the USA, Australia, and some European countries, also had a large number of uploaded sequences.
Discussion: Thus, rapid identification of emerging mutants with immune evasion including E484K and those with increased binding affinity such as S477N is important in tracing S
Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York.
Introduction: 2b shows the localization of signature B.1.526-E484K and B.1.526-S477N mutations within the spike protein.
Introduction: B.1.526-E484K and B.1.526-S477N share the characteristic spike protein mutations L5F, T95I, D253G, D614G and either A701V or Q957R, along with either E484K or S477N.
Introduction: Isolates subsequently branched into four sub-lineages, with two major groups B.1.526-E484K and B.1.526-S477N contai
Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics.
Figure: (C) S477N has been observed beyond clades 20 F and 20A.EU2.
Discussion: In this case, the opposite effect of the RBD S477N mutation on its affinity for ACE2 S19P (decreased), compared with ACE2 WT (increased), suggests that this RBD variant may have a selective disadvantage amongst carriers of the ACE2 S19P variant, in contrast to those with ACE2 WT, where it appears to be advantageous.
Discussion: Our finding that the N501Y, E484K, and S477N all increase the binding affinity of RBD for ACE2 raises the question as to whether this contributed to their selection.
Discussion: Taken together, these findings suggest that the WT
Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling.
PMID: 34438144
2021
The Science of the total environment
Abstract: We identify four signature mutations in the surface glycoprotein (spike) gene that are associated with the following variants of interest or concern, VOI or VOC (listed in parenthesis): S477N (B.1.526, Iota), T478K (B.1.617.2, Delta), D614G (present in all VOC as of May 2021), and H655Y (P.1, Gamma).
Result: Four mutations in the spike gene were detected that are present in one or more variants of interest (VOI) or variants of concern (VOC), which are listed in parenthesis: S477N (B.1.526, Iota), T478K (B.1.617.2, Delta), D614G (present in all VOC as of May 2021), H655Y (P.1, Gamma).
Table:
Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico.
Introduction: These SARS-CoV-2 VOCs have acquired some of the same spike protein mutations independently, particularly E484K, N501Y, S477N, and K417T, which have been associated with increased viral transmission and/or decreased sensitivity to antibody neutralization.
Myxobacterial depsipeptide chondramides interrupt SARS-CoV-2 entry by targeting its broad, cell tropic spike protein.
PMID: 34463219
2021
Journal of biomolecular structure & dynamics
Introduction: The top-binding ligands were additionally screened against biologically significant SARS-CoV-2 mutations occurring in the RBD of the S protein such as N501Y, E484K, K417N/T, A475V, I472V, L452R, V483A, F490L, S477N and N439K along with the United Kingdom, South African and Brazilian SARS-CoV-2 variants.
Method: Using the same PDB ID, the SARS-CoV-2 variants (N501Y, E484K, K417N/T, A475V,
Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2.
PMID: 34478710
2021
The Journal of biological chemistry
Result: S1), notably mutations L452R (8.8%), E484K (7.7%), T478K (5.9%), S477N (2.2%), and N439K (1.2%), which are also found in other various VOCs and were shown to either increase infectivity or promote the evasion of antibody responses.
Crucial Mutations of Spike Protein on SARS-CoV-2 Evolved to Variant Strains Escaping Neutralization of Convalescent Plasmas and RBD-Specific Monoclonal Antibodies.
Figure: Eight mutations (Y453F, L455F, F456L, A475V, A475S, T500S, N501Y, and Y505H) were in the RBD and hACE2 interaction region (RBD/hACE2); 10 mutations (V367I, V382L, R408G, N438K, L452Q, S477N, T478K, E484Q, S494P, and A520S) were in the RBD region but no
Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines.
Result: On the other hand, only 10 variants have destabilized the spike protein (e.g., E484K, K417 N, V1176F, E484Q, Q675P, G1167V, E553D, L5F, Y453F and Q675H) meanwhile, 18 variants (e.g., A262S, D080A, Q677P, N501T, A701V, Q677H, L452R, N501Y, D614G, P681R, L18F
Result: First, the 10 most observed or fast-growing RBD mutations are N501Y, L452R, T478K, E484K, K417T, S477N, N439K, K417N, F490S, and S494P, as shown in Table 1.
Result: Note that high-frequency mutation S477N does not significantly weaken any antibody and RBD binding, and thus does not appear in any prevailing variants.
SARS_CoV_2 mutation literature information.
PMID: 
2021
Infectious diseases of poverty
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