Abstract: Specifically, we employ a recently developed phylogeographic workflow to infer the regional dispersal history of viral lineages associated with three specific mutations on the spike protein (S98F, A222V and S477N) and to quantify their relative importance through time.
Method: In particular, we targeted three specific mutations in the spike protein (S98F,
Figure: We report the estimated temporal evolution of the frequency of the main spike mutations in the province of Liege (A), as well as the cartography of phylogenetic nodes and branches associated with the target mutations S98F (B), A222V (C), and S477N (D).
Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan.
Result: Overall, A222V had the highest ratio of nonsynonymous and synonymous site (dN/dS ratio) substitutions (FUBAR [fast, unconstrained Bayesian approximation] test, omega=37.06), with a GCT (A) to GTT (V) change at the second codon position commonly observed in B.1.177, followed by residues 5 (omega=28.91), 477 (omega=28.22), and 98 (omega=28.05).
Table: A222V
Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617.
Result: Additionally, six of these 22 sites were led by C-to-U transition (R134N in nsp10, A394V in nsp14, A222V and H1101D/Y in S, and P13T and T135I in N).
Table: A222V
Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model.
Introduction: The variant GV or lineage B.1.177 featured an A222V mutation in the S protein and other mutations of the clade G.
Result: The GV strains featuring an A222V mutation in the S protein have probably no effect on the viral transmission, severity, and antibody escape due to its structural position; rather, super-spreading founder events might be the reason behind its faster spreading.
Spike protein evolution in the SARS-CoV-2 Delta variant of concern: a case series from Northern Lombardy.
Discussion: K77T and T95I (typical of B.1.617 v.1), L216F, A222V, and G1124V have also been rarely reported.
Discussion: AY.2 additionally harbours V70F (unique among delta lineages), A222V (shared with AY.9, AY.10, AY.11, AY.19 and AY.24) and K417N (as for AY.1) K356N and V1228L have also been rarely reported.
Discussion: AY.3.1 never harbours T95I nor A222V, and harbours F157C and R158G at about 10% frequencies.
Genomic reconstruction of the SARS-CoV-2 epidemic in England.
Introduction: However, the underlying biological mechanism is unclear as the characteristic A222V spike variant is not believed to confer a growth advantage.
Genomic epidemiological analysis of SARS-CoV-2 household transmission.
Discussion: These include D614G, associated with the B.1 lineage observed in this family cluster, which is now ubiquitous and appears to have a moderate effect on SARS-CoV-2 transmissibility; A222V, present in the 20A.EU1 (B.1.177) cluster which has spread quickly across Europe from Spain and become dominant in Irish sequences; and N439K, a variant for which there is evidence to suggest increased ACE2 receptor binding affinity and immune-escape from neutralising antibodies.
Clinical Characterization and Genomic Analysis of Samples from COVID-19 Breakthrough Infections during the Second Wave among the Various States of India.
Abstract: Sub-lineage I had mutations in ORF1ab A1306S, P2046L, P2287S, V2930L, T3255I, T3446A, G5063S, P5401L, and A6319V, and in N G215C; Sub-lineage II had mutations in ORF1ab P309L, A3209V, V3718A, G5063S, P5401L, and ORF7a L116F; Sub-lineage III had m
AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus.
PMID: 34512928
2021
Computational and structural biotechnology journal
SARS_CoV_2 mutation literature information.
PMID: 
2021
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