SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes

Nat Commun. 2021 May 11;12(1):2642. doi: 10.1038/s41467-021-22905-7.

Abstract

Despite its clinical importance, the SARS-CoV-2 gene set remains unresolved, hindering dissection of COVID-19 biology. We use comparative genomics to provide a high-confidence protein-coding gene set, characterize evolutionary constraint, and prioritize functional mutations. We select 44 Sarbecovirus genomes at ideally-suited evolutionary distances, and quantify protein-coding evolutionary signatures and overlapping constraint. We find strong protein-coding signatures for ORFs 3a, 6, 7a, 7b, 8, 9b, and a novel alternate-frame gene, ORF3c, whereas ORFs 2b, 3d/3d-2, 3b, 9c, and 10 lack protein-coding signatures or convincing experimental evidence of protein-coding function. Furthermore, we show no other conserved protein-coding genes remain to be discovered. Mutation analysis suggests ORF8 contributes to within-individual fitness but not person-to-person transmission. Cross-strain and within-strain evolutionary pressures agree, except for fewer-than-expected within-strain mutations in nsp3 and S1, and more-than-expected in nucleocapsid, which shows a cluster of mutations in a predicted B-cell epitope, suggesting immune-avoidance selection. Evolutionary histories of residues disrupted by spike-protein substitutions D614G, N501Y, E484K, and K417N/T provide clues about their biology, and we catalog likely-functional co-inherited mutations. Previously reported RNA-modification sites show no enrichment for conservation. Here we report a high-confidence gene set and evolutionary-history annotations providing valuable resources and insights on SARS-CoV-2 biology, mutations, and evolution.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural

MeSH terms

  • Betacoronavirus / classification
  • Betacoronavirus / genetics
  • COVID-19 / virology*
  • Codon
  • Evolution, Molecular
  • Genes, Viral
  • Genetic Fitness
  • Genetic Variation
  • Genome, Viral / genetics*
  • Mutation*
  • Open Reading Frames
  • Phylogeny
  • SARS-CoV-2 / genetics*
  • Spike Glycoprotein, Coronavirus / genetics
  • Viral Proteins / genetics

Substances

  • Codon
  • Spike Glycoprotein, Coronavirus
  • Viral Proteins
  • spike protein, SARS-CoV-2