Figure 1.

Description of the partially-observed transmission networks (POTN) algorithm. (A) Example sampled pair with candidate parent case at time t­₁ and candidate child at time t­₂. The time to the most recent common ancestor (tMRCA) is ${\mathit{t}}_1-\mathrm{\Delta }\mathit{t}$, and so the cumulative time elapsed for genetic evolution between the cases is ${\mathit{t}}_2-{\mathit{t}}_1+2\mathrm{\Delta }\mathit{t}$, as in Equation (1). (B) Example phylogenetic tree describing the genetic relationships among six cases sampled at different times. For each pair of the blue cases, $\mathrm{\Delta }\mathit{t}\to 0$, while for each pair of the red cases and each pair consisting of one red and one blue case, $\mathrm{\Delta }\mathit{t}$ is greater than zero. (C) The POTN corresponding to the phylogenetic tree in panel B. The POTN algorithm identifies ancestral links between the blue cases where $\mathrm{\Delta }\mathit{t}\to 0$, while it leaves the red cases disconnected because there are no observed direct ancestors of the red cases. For the blue cases, the dashed link indicates a redundant grandparent-child link that is removed by the triangle pruning algorithm.