Fig. 3.

Maximum clade credibility molecular clock phylogeny, estimated from the whole genome alignment. Branch lengths represent time (see scale bar at the bottom of the figure). Posterior clade probabilities are shown next to each node. Sequences are labelled with their subtype and accession number. Subtypes are indicated on the right side of the diagram. The three intra-genotypic lineages discussed in the main text are labelled L1, L2, and L3.