Figure 1.

A. Overview of the PyR₀ analysis pipeline. After clustering UShER’s mutation annotated tree, sequence data are used to construct spatio-temporal lineage prevalence counts y_tpc and amino acid substitution covariates X_cf. Pyro is used to fit a Bayesian multivariate logistic multinomial regression model to y_tpc and X_cf.

B. Relative fitness versus date of lineage emergence. Circle size is proportional to cumulative case count inferred from lineage proportion estimates and confirmed case counts. Inset table lists the 10 fittest lineages inferred by the model. R/R_A is the fold increase in relative fitness over the Wuhan (A) lineage, assuming a fixed generation time of 5.5 days.