Evaluation of phylogenetic methods for inferring the direction of HIV transmission: HPTN 052

We inferred the direction of HIV transmission using whole-genome HIV sequences from couples with known linked infection and known transmission direction. Complete next generation sequencing (NGS) data were obtained for 105 unique index-partner sample pairs from 32 index-partner pairs (couples) enrolled in the HIV Prevention Trials Network (HPTN) 052 trial (up to two samples/person) Index samples were obtained up to 5.5 years before partner infection; partner samples were obtained near the time of seroconversion.