Interactive plots of estimated fitness effects of SARS-CoV-2 amino-acid mutations

Fitness effects estimated from observed versus expected counts of mutations.

Analysis described in Bloom and Neher (2023).

Interactive plots:

• Heatmaps of effects of mutations

  • nsp1 amino-acid fitnesses
  • nsp2 amino-acid fitnesses
  • nsp3 amino-acid fitnesses
  • nsp4 amino-acid fitnesses
  • nsp5 (Mpro) amino-acid fitnesses
  • nsp6 amino-acid fitnesses
  • nsp7 amino-acid fitnesses
  • nsp8 amino-acid fitnesses
  • nsp9 amino-acid fitnesses
  • nsp10 amino-acid fitnesses
  • nsp12 (RdRp) amino-acid fitnesses
  • nsp13 (helicase) amino-acid fitnesses
  • nsp14 (ExoN) amino-acid fitnesses
  • nsp15 amino-acid fitnesses
  • nsp16 amino-acid fitnesses
  • S (spike) amino-acid fitnesses
  • ORF3a amino-acid fitnesses
  • E (envelope) amino-acid fitnesses
  • M (membrane) amino-acid fitnesses
  • ORF6 amino-acid fitnesses
  • ORF7a amino-acid fitnesses
  • ORF7b amino-acid fitnesses
  • ORF8 amino-acid fitnesses
  • ORF9b amino-acid fitnesses
  • N (nucleocapsid) amino-acid fitnesses
  • ORF10 amino-acid fitnesses

• Expected counts per site

  • neutral mutation rates for each clade
  • average per-site counts of each nucleotide mutation type

• Distribution of estimated mutation fitness effects

  • distribution of fitness effects of mutations
  • mutation fitness effects for each gene

• Correlations among effect estimates

  • correlation of fitness estimates for different viral clades
  • correlation of fitness estimates for different countries
  • average correlation of fitness estimates for spike and non-spike proteins
  • clade correlations of fitness estimates versus protein divergence

• Correlations of estimates with deep mutational scanning

  • correlation of fitness estimates with spike deep mutational scanning
  • correlation of fitness estimated with spike deep mutational scanning (all phenotypes)
  • correlation of fitness estimates with Mpro (nsp5) deep mutational scanning
  • correlation of fitness estimates with Mpro (nsp5) deep mutational scanning (all phenotypes)

• Effects of fixed mutations

  • fitness effects of mutations fixed in at least one clade
  • fitness effects of mutations fixed in a clade versus all mutations

• Effects of mutations versus number of descendants

  • fitness effects versus number of descendant sequences

See Bloom and Neher (2023) for a paper describing the work.

See https://github.com/jbloomlab/SARS2-mut-fitness for full computer code and data.

See https://jbloomlab.github.io/SARS2-mut-fitness/ for links to all interactive plots.