HIV-1 genetic diversity and recombinant forms among men who have sex with men at a sentinel surveillance site in Xi'an City, China

Abstract HIV-1 genetic distribution and recombinant patterns are important in understanding the HIV epidemic among men who have sex with men (MSM). In this study, 83 HIV-positive MSM infections were confirmed at a sentinel surveillance site in Xi'an city, China in 2018. HIV-1 genotypes were determined by phylogenetic analyses of HIV-1 gag, pol and env gene fragments, including CRF07_BC (51.8%), CRF01_AE (30.1%), subtype B (3.6%), CRF55_01B (3.6%), CRF104_0107 (1.2%) and unique recombinant forms (URFs) (9.6%). Transmitted drug resistance mutations were detected in 2.4% (2/82) of HIV-infected MSM individuals. The phylogenetic analyses of near full-length genome (NFLG) of HIV-1 URFs were performed. A new circulating recombinant form (CRF), designated as CRF104_0107, was found in three epidemiologically unlinked individuals in Shaanxi province, China. The CRF104_0107 is composed of genomes CRF01_AE and CRF07_BC, with six recombinant breakpoints in the gag, pol, vif and vpr genes. This second-generation CRF has a breakpoint (HXB2 nt 3011) in common with CRF07_BC. The emergence of novel CRF and multiple URFs reflected HIV-1 genetic complexity among the local key populations in Xi'an city, China.