Fig. 6: CoVFit-based in silico DMS on the BA.2.86.1 lineage.

a Association between the fitness gain [per site] score and the mutation frequency at each site in the BA.2.86.1 lineage. Points represent amino acid sites, while dashed lines indicate the 98th percentile (top 2%) for both the fitness gain score and mutation frequency. Statistical measures quantifying the degree of overlap between data points within the top 2% for these two metrics are shown. The p value was calculated using a two-sided Fisher’s exact test. b Temporal trend in mutation frequency at individual amino acid sites within the BA.2.86.1 population. The genome surveillance data from October 1, 2023, to July 31, 2024, was used. Frequencies were calculated using 7-day bins. c Temporal trends in viral lineage frequencies within the BA.2.86.1 population. Each viral lineage category includes its descendant lineages unless those descendant lineages are explicitly defined as separate categories. Mutations in the S protein relative to BA.2.86.1 are indicated, with emphasis on those with higher fitness gain [per site] scores. Source data are provided as a Source Data file.