Phylogenetic analysis of viral populations in the index and partner.

<p>The program BEAST was used to recreate phylogeny (Bayesian skyline) of the viral <i>env</i> sequences generated from the index (black) and partner (red) for Case A (Panel A) and Case B (Panel B). Each tip (with dot) of the tree is an individual sequence. For Case A, sequences from the partner are dispersed among the sequences from the index, indicating the transmission of at least four variants (seen as four discrete positions in the tree where one or more red dots occur). For Case B, the sequences from the partner represent a single lineage/cluster, indicative of transmission of a single variant. The tree structure moves back in time from right to left as indicated by the arrow at the bottom and with the scale shown for 100 days. The tips of the tree are displaced to correspond to the date the sample was taken that gave rise to those sequences. Each internal node/branch point in the tree represents the inferred most recent common ancestor (MRCA) of all sequences that appear to the right of the node, with the position of each node given an estimated date from the date the partner's infection was detected. The dates (in days) of the MRCA within each partner (interpreted as the date expansion of the virus population started after the transmission event) are indicated (40 days for Case A; 84 days for Case B), and the relevant nodes circled. The numbers in small font indicate the estimated error in the dating of each node. The time to MRCA was estimated from two independent runs which were combined, the HKY substitution model, estimated base frequencies, Gamma site heterogeneity model with 4 gamma categories, a strict clock with a fixed mutation rate of 1.5×10⁻⁵, partner tip dating, and the Bayesian skyline tree model.