a, Root-to-tip plot showing genetic divergence of all 792 genomes as a function of their sampling date. The regression line indicates the average substitution rate across this outbreak (1.17 × 10−3 substitutions per site per year, as annotated). b, Temporally resolved phylogenetic tree showing patient’s June sample (MAN4194) and December sample (MAN12309). c, Phylogenetic tree showing nucleotide divergence from the root of this clade. The June infection (MAN4194) and December infection (MAN12309) are diverged by only two substitutions, T5587C and A6867G.