- Martin, Darren P;
- Weaver, Steven;
- Tegally, Houriiyah;
- San, James Emmanuel;
- Shank, Stephen D;
- Wilkinson, Eduan;
- Lucaci, Alexander G;
- Giandhari, Jennifer;
- Naidoo, Sureshnee;
- Pillay, Yeshnee;
- Singh, Lavanya;
- Lessells, Richard J;
- NGS-SA;
- UK, COVID-19 Genomics;
- Gupta, Ravindra K;
- Wertheim, Joel O;
- Nekturenko, Anton;
- Murrell, Ben;
- Harkins, Gordon W;
- Lemey, Philippe;
- MacLean, Oscar A;
- Robertson, David L;
- de Oliveira, Tulio;
- Pond, Sergei L Kosakovsky
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.