Fig 2.

Phylogenetic tree topology classes (based on gag sequences) between mother and infant transmission pairs. Maximum-likelihood phylogenetic trees for two paired mother and infant sequences exemplifying the two different tree topologies observed. The red tips represent mother sequences whereas the green tips represent sequences of the paired infant. In the PP class, the infant sequences were nested in more than one cluster among the mother sequences (infant 258). In the PM class, the infant sequences were nested in one cluster among the mother sequences (infant 135). Relevant branches supported by an approximate likelihood ratio test (aLRT-SH) score of 1 are indicated by “1” in the trees. The scale bar represents substitutions per site. All mother-to-child-transmission trees are presented in Fig. S2. Abbreviations: p32, 32 weeks of pregnancy; del, delivery; pn1, 1 month after delivery.