Fig. 3

A Temporally-resolved phylogenetic tree showing the farm-associated outbreak clade. Viruses collected from individuals reporting an epidemiologic link to the farm are indicated as yellow squares, individuals with an indirect link to the farm are shown as blue circles, and individuals testing positive within the community with no reported connection with the farm are shown as grey circles. The indirect linkages are labeled A through F, and the nature of the link is described in text. B Maximum likelihood genetic divergence tree of the same clade as shown in panel A. Genome sequences that are identical are dispersed along the y-axis at the same location along the x-axis. Twenty identical sequences collected from employees at the farm are indicated as a single collapsed node on the tree