NGS-SA: Publications and pre-prints of our genomics surveillance work

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

Authors: Martin DP, Weaver S, Tegally H, San EJ, Shank SD, Wilkinson E, Lucaci AG, Giandhari J, Naidoo S, Pillay Y, Singh L, Lessells RJ; NGS-SA; COVID-19 Genomics UK (COG-UK), Gupta RK, Wertheim JO, Nekturenko A, Murrell B, Harkins GW, Lemey P, MacLean OA, Robertson DL, de Oliveira T, Kosakovsky Pond SL.

Journal: Cell, 2021. DOI:


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 favoured 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.


- Detected a major global shift in the SARS-CoV-2 selective landscape in late 2020

- Identified ongoing convergent evolution between the alpha, beta and gamma lineages

- Defined the mutational meta-signature upon which these lineages are converging