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

Fitness effects estimated from observed versus predicted counts as predicted by a general linear model.

Analysis described in Haddox H.K. et al. (2024).

Interactive plots for gisaid_2024-04-24 dataset:

• 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

• Correlations among effect estimates

  • correlation of fitness estimates for different clusters of viral clades
  • correlation of naive fitness estimates for different clusters of viral clades
  • correlation between novel and naive fitness estimates for different clusters of viral clades

See Haddox H.K. et al. (2024) for a paper describing the work.

See https://github.com/neherlab/SARS2-mut-fitness-v2 for full computer code, data and a short summary of the theoretical framework.

See https://neherlab.github.io/SARS2-mut-fitness-v2/ for links to all interactive plots.