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Molecular Infectious Disease Epidemiology: Survival Analysis and Algorithms Linking Phylogenies to Transmission Trees

Fig 1

Two possible transmission trees and three possible pathogen phylogenies for a household outbreak.

A, B, and C were infected in alphabetical order such that their infectious sets are , , and . We have a single pathogen sequence from each person. The top shows the two possible transmission trees within the household: either A infected B and B infected C (left) or A infected B and C (right). The bottom shows the three rooted, bifurcating phylogenies linking pathogen sequences from A, B, and C. In each phylogeny, the possible hosts are written underneath each interior node and arrows indicate how each assignment of interior node hosts determines a transmission tree via Assumption 5.

doi: https://doi.org/10.1371/journal.pcbi.1004869.g001