Frequent HIV-1 recombination among MSM in Beijing revealed by subtyping and near full-length genome analyses

The high mutation and recombination rates of HIV-1 drive extensive genetic diversity. Co-infection with different subtypes or recombinant forms facilitates the emergence of new recombinants, complicating transmission networks and posing challenges for molecular surveillance. Although antiretroviral therapy (ART) coverage is high among diagnosed individuals in China, ongoing HIV-1 transmission-including from undiagnosed infections-likely contributes to the continued circulation and accumulation of recombinant lineages. We retrospectively analyzed 1006 plasma samples from 993 individuals diagnosed with HIV-1 at Beijing Ditan Hospital between January 2022 and August 2023. Subtyping of the pol region was conducted using seven tools. For seven cases with discordant results, near full-length genome (NFLG) sequencing and phylogenetic analysis were performed. The study cohort included a significantly higher proportion of male infected individuals (n = 932, 93.86%) than female (n = 57, 5.74%), with a higher proportion of homosexual transmission (n = 570, 57.40%) compared to heterosexual transmission (n = 168, 16.92%). The most prevalent genotypes were CRF01_AE and CRF07_BC, accounting for 23.76% (239/1006) and 11.03% (111/1006), respectively. Among seven NFLG-analyzed samples, four were identified as second-generation URFs composed of CRF01_AE and CRF07_BC, and three as CRF121_0107. Bayesian analysis provided a broad temporal context for the emergence of CRF121_0107. Single-genome amplification did not identify the pre-recombination parental strains in the four URF samples. The URF detection rate was 0.4% (4/1006), which may be underestimated due to limitations of partial-genome genotyping. Together, these findings highlight the importance of continued molecular surveillance to monitor novel recombinants and inform HIV-1 prevention and treatment strategies.