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The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages
Cell  (IF41.582),  Pub Date : 2021-09-07, DOI: 10.1016/j.cell.2021.09.003
Darren P. Martin, Steven Weaver, Houriiyah Tegally, James Emmanuel San, Stephen D. Shank, Eduan Wilkinson, Alexander G. Lucaci, Jennifer Giandhari, Sureshnee Naidoo, Yeshnee Pillay, Lavanya Singh, Richard J. Lessells, Ravindra K. Gupta, Joel O. Wertheim, Anton Nekturenko, Ben Murrell, Sergei L. Kosakovsky Pond

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.