literature

SARS_CoV_2 mutation literature information.

Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach.

PMID: 34700382 2021 mBio

Result: Dual mutants containing D614G and other amino acid changes, including those under positive selection or observed in VOCs (L5F, L18F, S98F, W152L/C, E154K, L222V, and A262S in S1-NTD; N439K, L452Q/R, S477N, L478R/K, E484K/Q, N501Y, and A570D within S1-RBD; Q677H/P and P681H/R in S1-CTD; T716I,

A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features.

PMID: 34806033 2021 Current research in structural biology

Result: Further, for the characteristic RBD mutations across VoCs (K417 T/N, L452R, S477N, T478K, E484K, and N501Y), we observed MTR scores between 0.68 and 0.91, suggesting these substitutions to be tolerant.

Result: Interestingly, five out of eight mutations of RBD are present in the epitope region, where L452Rand N501Y substitutions map to the RBD-loop epitope and S477N, T478K, and E484K are harboured in the RBD-ridge epitope.

Discussion: studied the effect of five prevalent

Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants.

PMID: 34649620 2021 Genome medicine

Result: N501Y, L452R, and S477N mutants exhibited high affinity for ACE2 and exhibited 9.24- to 14.66-fold higher binding affinity than wildtype RBD.

Result: Notably, the most frequent RBD variants seen in clinical isolates, N501Y and S477N, remained similarly sensitive to the majority of the selected NAbs; only 24-1L failed to neutralize N501Y.

Result: Unlike N501Y, which induced tighter binding with ACE2, S477N and L452R occurred at sites that were likely not in the ACE2 contact region.

Result: We observed that the substitution N501Y and

PMID: 34688034 2021 EBioMedicine

Result: Sera from participants who were naive prior to vaccination (N=20, 8 viruses) neutralized WT WA1/USA (GMT: 356) and Iota (parental, GMT: 289, P: not significant) to comparable levels followed by - in decreasing order - Iota+E484K (GMT: 233, P: 0.0019), Gamma (GMT: 120, P: 0.0004), Iota+S477N (GMT: 197, P: 0.0009), Alpha+484K (GMT: 99, P: 0.0001), Beta (GMT: 91, P: < 0.0001) and Lambda subvariant (GMT: 84, P: < 0.0001).

Result: There was, however, a small but statistically significant reduction in neutralization activity against the Iota variant with the S477N substitution (GMT: 298, 1.9-fold reduction; P < 0.5) and the Delta (GMT: 218, 2.6-fold, P < 0.01).

Result: These isolates represent the three sublineages found in the NYC variants of interest: Iota (no change in RBD), Iota+E484K, Iota+

PMID: 34696404 2021 Viruses

Result: During this period, N501Y, L452R and T478K mutations increased by 15.39, 23.06 and 26.75% points, respectively, while E484K, S477N, K417T and S494P mutations decreased by 1.35, 3.09, 0.37 and 0.88% points, respectively.

Result: Further, we observed a considerable prevalence of other adaptive mutations in the RBD, namely L452R, T478K, E484K, S477N, K417T, N439K and S494P.

Result: In T3, mutations N439K,

PMID: 34790342 2021 Journal of market access & health policy

Abstract: The average proportion of EU2 variant (S:477 N) was a significant predictor of cumulative COVID-19 deaths in the pre-peak period.

Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission.

PMID: 34733263 2021 Frontiers in microbiology

Result: R6997P and V30L co-occurred and rapidly increased starting in July 2020; M3087I, X5167Y, K4576N, N5542D, A376T, and S5585I co-occurred and gradually increased; and S477N started to rise in June but decreased again in July (Figure 3B).

Table: S477N

Genomic diversity of SARS-CoV-2 in Malaysia.

PMID: 34760404 2021 PeerJ

Result: None of our D614G mutations were accompanied by the S477N substitution noted to be frequently alongside D614G in the S protein.

Prediction of the Effects of Variants and Differential Expression of Key Host Genes ACE2, TMPRSS2, and FURIN in SARS-CoV-2 Pathogenesis: An In Silico Approach.

PMID: 34720581 2021 Bioinformatics and biology insights

Result: We also analyzed the effect of 27 missense variants of SARS-CoV-2 spike protein (RBD) on the binding interaction of spike protein with ACE2 and observed that L452Q, T478K, L455F, F456L, S459F, A475V, N439K, L452R, T470N, E484D, E484A, E484K, E484Q, F486L, S494P, S494L, N501T,

PMID: 34655895 2021 Computers in biology and medicine

Result: According to the MM/GBSA analysis, the reported mutations (N439K, S477 N, and T478K) enhanced the binding affinity toward the ACE2 receptor compared with the wild-type RBD complex.

Result: Conversely, the RMSD remained slightly higher for the S477 N than for the wild type, but the system exhibited a dynamically stable behavior, thus achieving stable binding of the mutant RBD.

Result: Due to the high credibility of this method, we analyzed the effect of the reported mutations in the RBD domain (N439K, S477 N, and T478K) on the interaction network with the human receptor ACE2.

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