Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms.
Abstract: P681R/H, T732A), and at the basis of the protein, V1176F, raising concerns about the lack of phenotypic and clinical data available for the variants of interest we postulate: 20B/478K.V1 (B.1.1.222 or B.1.1.519) and 20B/P.4 (B.1.1.28.4).
Introduction: For instance, 20J/501Y.V3 or P.1 evolved in parallel with the 20B/S.484K or P.2 variant in Brazil, and they share the spike protein mutations E484K and V1176F, but not N501Y.
Result: As expected from independently evolving VOC, mutation V1176F is absent from the two sequences from the State of San Luis Potosi.
Result: Overall, we found that most of the genomic variants (SNVs+indels) occur in low frequencies, except for a few point
Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants.
Introduction: The Gamma P.1 variant encodes an S protein with 12 mutations (L18F, T20N, P26S, D138Y, R190S, K417N/T, E484K, N501Y, D614G, H655Y, T1027I, and V1176F), two of which are in the RBD (E484K, and N501Y).
Analysis of Immune Escape Variants from Antibody-Based Therapeutics against COVID-19: A Systematic Review.
PMID: 35008446
2021
International journal of molecular sciences
Discussion: Among 33 patients having positive NPS PCR for an average of 18 days, Voloch et al., observed a distinguishing pattern of mutations over the course of the infection mainly driven by increasing A U and decreasing G A signatures, including spike mutations (V362L, T553I, H655Y, A688V, S691F, S884F, V1176F).
Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India.
PMID: 35017872
2021
Journal of global infectious diseases
Discussion: A recent study has reported that L54F, D614G and V1176F of S-protein, identified in the study, are correlated with severe clinical outcome.
Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants.
Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week.
Result: Given these results with viruses encoding E484K mutations, we performed separate studies with human convalescent serum (n =10) and a chimeric SARS-CoV-2 WA1/2020 strain encoding a Brazilian variant spike gene (Wash BR-B.1.1.248; L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I, and V1176F [Extended Data Fig 5a]).
Figure: Substitutions seen in the B.1.1.248 Brazilian variant (L18F, T20N,
Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines.
SARS_CoV_2 mutation literature information.
PMID: 
2021
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