Cell Host & Microbe
Volume 30, Issue 4, 13 April 2022, Pages 545-555.e4
Journal home page for Cell Host & Microbe

Article
Rapid and parallel adaptive mutations in spike S1 drive clade success in SARS-CoV-2

https://doi.org/10.1016/j.chom.2022.03.018Get rights and content
Under an Elsevier user license
open archive

Highlights

  • SARS-CoV-2 is evolving adaptively in multiple regions of the genome

  • The spike S1 subunit is the focus of adaptive evolution on a per-site basis

  • S1 adaptation in the first 1.5 years was 2.5× greater than in the 2009 H1N1 pandemic

Summary

The SARS-CoV-2 pandemic has resulted in numerous virus variants, some of which have altered receptor-binding or antigenic phenotypes. Here, we quantify the degree to which adaptive evolution is driving the accumulation of mutations across the genome. We correlate clade growth with mutation accumulation, compare rates of nonsynonymous to synonymous divergence, assess temporal clustering of mutations, and evaluate the evolutionary success of individual mutations. We find that spike S1 is the focus of adaptive evolution but also identify positively selected mutations in other proteins (notably Nsp6) that are sculpting the evolutionary trajectory of SARS-CoV-2. Adaptive changes in S1 accumulated rapidly, resulting in a remarkably high ratio of nonsynonymous to synonymous divergence that is 2.5× greater than that observed in influenza hemagglutinin HA1 at the beginning of the 2009 H1N1 pandemic. These findings uncover a high degree of adaptation in S1 and suggest that SARS-CoV-2 might undergo antigenic drift.

Keywords

viral evolution
adaptation
SARS-CoV-2

Data and code availability

  • This paper analyzes existing, publicly accessible data. The accession numbers are listed in Table S1, which is available from Mendeley Data: 10.17632/mxjt9nhgmj.1.

  • Source code for all analyses presented in this manuscript is available at https://github.com/blab/sarscov2-adaptive-evolution. This repository has been archived at Zenodo: 10.5281/zenodo.6126495 and is publicly available as of the date of publication.

  • Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.

Cited by (0)

4

Lead contact