Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2.
PMID: 34121839
2021
Bioinformatics and biology insights
Table: S13I
Estimation of secondary household attack rates for emergent SARS-CoV-2 variants detected by genomic surveillance at a community-based testing site in San Francisco.
Abstract: Certain viral lineages bearing spike mutations, defined in part by L452R, S13I, and W152C, comprised 54.9% of the total sequences from January, compared to 15.7% in November.
Result: We observed SARS-CoV-2 genome sequences that belonged to PANGO lineages B.1.427 and B.1.429, both of which share a trio of recent mutations in the spike protein (S13I, W152C, and L452R) (Figure 2).
Coding-Complete Genome Sequences and Mutation Profiles of Nine SARS-CoV-2 Strains Detected from COVID-19 Patients in Bangladesh.
Introduction: The E484K substitution was observed in a cluster containing D614G, P681H, and S13I changes (GRBL_S1), while the S359T amino acid substitution was observed in a cluster containing D614G and A942V changes (GRBL_S9).
Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines.
Result: Both lineages share a triad of coding mutations in the Discussion: An alternative (but not mutually exclusive) possibility is that the additional mutations in B.1.427/B.1.429, especially the W152C and S13I mutations in the spike protein, may contribute to increased infectivity of the variant relative to lineages carrying the L452R mutation alone.
Discussion: In the current study, we describe the spread of a novel B.1.427/B.1.429 variant in California carrying a characteristic triad of spike protein mutations (S13I, W152C, and L452R) that is predicted to have emerged in May 2020 and increased in frequency from 0% to >50% of sequenced cases from September 2020 to January 2021.
SARS-CoV-2 immune evasion by variant B.1.427/B.1.429.
Abstract: Furthermore, we observed a complete loss of B.1.427/B.1.429 neutralization for a panel of mAbs targeting the N-terminal domain due to a large structural rearrangement of the NTD antigenic supersite involving an S13I-mediated shift of the signal peptide cleavage site.
Abstract: It is unclear whether antibody responses to SARS-CoV-2 infection or to the prototypic Wuhan-1 isolate-based vaccines will be impacted by the three B.1.427/B.1.429 S mutations: S13I, W152C and L452R.
Assessment of basic reproduction number (R0), spatial and temporal epidemiological determinants, and genetic characterization of SARS-CoV-2 in Bangladesh.
PMID: 33930563
2021
Infection, genetics and evolution
Result: In case of S protein, we found 20 predominant mutation sites, among which 13 were in N-terminal domain (NTD) fragment (T95I, Q14H, S13I, T75I, H49Y, N211Y, D138H, V127F, P26, G75V, S255, Y248H, and S95F).
Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K.
Introduction: 11 Virtually all variants of concern contain mutations in the SARS-CoV-2 Spike protein, such as variant B.1.351 (Spike mutations K417N, E484K, N501Y, D614G, and A701V) and variants B.1.427/B.1.429 (Spike mutations S13I, W152C, L452R, and D614G), and many of these reside on the receptor-binding domain (RBD), a region located between residues 350-550 of Spike and directly binding to the human ACE2.
The Spike of Concern-The Novel Variants of SARS-CoV-2.
SARS_CoV_2 mutation literature information.
PMID: 
2021
Bioinformatics and biology insights
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