Maximum likelihood phylogenetic trees and full-length gag sequences. (A) Maximum likelihood phylogenetic trees of SM cohort p17 sequences (black circles) shown with length-matched publicly available sequences derived from plasma donation-associated HIV-1 infection from other cities in Henan as described in Zhang et al²²  (gray circles), a subtype B′ reference sequence (open circle), injecting drug user–associated p17 sequences also generated²⁰  (triangles of different colors from 3 different regions in China) and sexual-transmission sequences from Beijing (open diamonds). (B) Full-length gag sequences from SM cohort subjects (black circles) are shown in a maximum likelihood phylogenetic tree with matched-length gag sequences sampled from a subtype B-infected population in the United States (open triangles). Because of the sample size, a bootstrap value from 500 replications was only obtained for the nef maximum likelihood tree and was found to be 87% for the SM cluster. We obtained bootstrap values for gag and pol clusters using neighbor-joining trees, which shared the same topology as maximum likelihood trees, and these were both > 80%.