Within each genetic cluster parsimony-based ancestral host state reconstruction was done with Phyloscanner (Grabowski et al., 2018; Ratmann et al., 2019; Wymant et al., 2018b) to identify probable transmission pairs and resolve the probable order of transmission events. Thereafter, within each identified genetic cluster, the median subgraph distance and most frequent subgraph topology between each pair of individuals were determined across all deep-sequence phylogenies along the genome where the pair had sufficient mapped reads for phylogenetic inference. A subgraph refers to all tips and internal nodes of a phylogeny assigned to an individual through parsimony-based ancestral state reconstruction. Subgraph distances were standardized to the mean rate of evolution for HIV-1 group-specific antigen (GAG) and polymerase (POL) genes to account for variation in mutation rates along the genome. The three panels show median subgraph distance distributions of pairs in the union (A) of genetic clusters detected with HIV-TRACE (B) and Cluster Picker (C) algorithms. Within each panel, phylogenetically linked pairs with an inferred direction of transmission are summarized into same-sex (male-male and female-female) and opposite-sex pairs (male-female). The subgraphs of deep-sequenced HIV-1 viral genomes of most phylogenetically linked directed pairs were separated by a patristic distance below 0.035 (3.5%). Same-sex pairs were presumed to be members of transmission chains with missing intermediates.