Fig. 3: SARS-CoV-2 lineage prevalence and mutation accumulation in S1 subunit of spike.

a, Frequency of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages over time. b,c, Accumulation of amino acid mutations in the S1 subunit over time (panel b) and as a function of their relative mutational fitness (panel c) shown for 3,055 globally representative genome samples of SARS-CoV-2 between December 2019 and December 2022 generated by nextstrain.org¹⁸². Mutational fitness is calculated using results from ref. ¹⁰⁵ that computes the relative impact of each mutation in the growth advantage of a lineage using a hierarchical Bayesian regression model. The model estimates the exponential growth advantage of each SARS-CoV-2 lineage (proxy for measuring relative fitness) as a linear combination of the effect of individual mutations. Each Pango lineage (World Health Organization (WHO) label, Nextstrain clade) is given a unique colour. VOC, variant of concern.