Fig. 4: Future adaptive RBD mutations forecasted by chronic-like clades.

a Timeline of the study data indicating the last date of sampling (dashed) line, projected onto a phylogeny of SARS-CoV-2 derived from nextstrain.org³. b Convergent RBD mutations that occurred in sub-lineages of Omicron circulating since the summer or fall of 2022. Mutations are color-coded based on their maximal association with the group of chronic-like clades, with stronger shades of orange indicating a stronger association. X marks a mutation not detected. c All RBD mutations found in BA.1/BA.2 chronic like clades with LIME scores >0.05 are listed. The three right columns are measures of future global success of these mutations. Max global prevalence refers to the maximal global proportion at which this mutation was observed, at any time point in the pandemic (Fig. S4), fitness effect range is based on inferences derived from mutation abundance across all globally circulating sequences⁴³, and convergence is described in the main text. b, c When several mutations are listed (e.g., N460K/S) the color coding is based on the maximal LIME score obtained. d The probability of detecting RBD convergent mutations in chronic clades compared to their probability of detection in increasingly large sample sizes of control clades.