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

NGS-SA, The COVID-19 Genomics UK (COG-UK) Consortium, 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, Gordon W. Harkins, Philippe LemeyOscar A. MacLean, David L. Robertson, Tulio de Oliveira, Sergei L. Kosakovsky Pond, Matthew Bashton, Andrew Nelson, Clare McCann, Greg Young, Darren Smith

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

49 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)5189-5200.e7
Number of pages20
Issue number20
Early online date7 Sept 2021
Publication statusPublished - 30 Sept 2021


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