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. 2023 Aug 28;14:5105. doi: 10.1038/s41467-023-40706-y

Fig. 4. Evolutionary rate of SARS-CoV-2 in humans and white-tailed deer.

Fig. 4

a The posterior distributions of evolutionary rates (substitutions per site per year) for five partitions of the SARS-CoV-2 genome (ORF1a, ORF1b, ORF3–ORF8 plus envelope (E) and membrane (M), spike (S), and nucleocapsid (N)) are presented for human (pink) and WTD (blue) for the delta variant (Fig. S4). Alpha results (similar) are provided in Fig. S11. b Mutations in spike protein that were found in delta WTD clusters (orange), L18F is shown in red, alpha WTD clusters (green), and T29I found in both alpha and delta WTD clusters (yellow). Characteristic mutations for delta lineages (mutations present in human and WTD viruses belonging to delta compared to Wuhan reference genome) are shown in dark orange, while characteristic mutations for alpha lineages are shown in dark green. All recurrent mutations from WTD clusters are documented in Supplementary Data 2. The log deviation (random-effect) from HKY model relative rates is presented for c alpha, humans, d alpha, WTD, e alpha, WTD-to-human ratio, f delta, humans, g delta, WTD, and h delta, WTD-to-human ratio, inferred independently for alpha (n = 786) and delta (n = 1094). Box midlines indicate the median, the box limits show the upper and lower quartiles, and the whiskers extend to 1.5 times the interquartile range. Asterisks indicate transversions. WTD-to-human ratios that significantly differ from zero are highlighted.