The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages

Martin DP, Weaver S, Tegally H, San JE, Shank SD, Wilkinson E, Lucaci AG, Giandhari J, Naidoo S, Pillay Y, Singh L, Lessells RJ, Gupta RK, Wertheim JO, Nekturenko A, Murrell B, Harkins GW, Lemey P, MacLean OA, Robertson DL, de Oliveira T, Kosakovsky Pond SL

Cell - (-) - [2021-09-00; online 2021-09-00]

The independent emergence late in 2020 of the B.1.1.7, B.1.351, and P.1 lineages of SARS-CoV-2 prompted renewed concerns about the evolutionary capacity of this virus to overcome public health interventions and rising population immunity. Here, by examining patterns of synonymous and non-synonymous mutations that have accumulated in SARS-CoV-2 genomes since the pandemic began, we find that the emergence of these three "501Y lineages" coincided with a major global shift in the selective forces acting on various SARS-CoV-2 genes. Following their emergence, the adaptive evolution of 501Y lineage viruses has involved repeated selectively favored convergent mutations at 35 genome sites, mutations we refer to as the 501Y meta-signature. The ongoing convergence of viruses in many other lineages on this meta-signature suggests that it includes multiple mutation combinations capable of promoting the persistence of diverse SARS-CoV-2 lineages in the face of mounting host immune recognition.

Category: Genomics & transcriptomics

Category: Health

Type: Journal article

PubMed 34537136

DOI 10.1016/j.cell.2021.09.003

Crossref 10.1016/j.cell.2021.09.003

pii: S0092-8674(21)01050-3
pmc: PMC8421097
Initial release of SARS-CoV2 variation data
Visualizing selection analysis results for evolution of the B.1.351 clade
Frequency trends and selection detection of subsets of sites in SARS-CoV-2 genes
Temporal evolution of selective pressures on SARS-CoV-2 genes
Collection of result files and underlying sequence alignments processed by the RASCL SARS-CoV-2 clade analysis pipeline

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