High genetic diversity of HIV-1 was found in men who have sex with men in Shijiazhuang, China

► This is the first report on genetic characterization and drug resistance of HIV-1 strains prevalent in the MSM in Shijiazhuang, China, basing on the HIV-1 full-length gag, pol, and partial env gene. ► Multiple HIV subtypes were found in the population, including CRF01_AE (52.9%), subtype B (35.3%) and CRF07_BC (11.8%). ► No close phylogenetic relationship between our strains with those prevalent in paid blood donors from Hebei local area was found. ► Very low level of drug-resistance was found in the drug-naïve HIV-1 infected MSMs in Shijiazhuang. Men who have sex with men (MSM) have become one of the populations with severely HIV prevalence in China. However, very few genetic studies have been done on HIV-1 spreading in this population. In this study, the genetic characterization of HIV-1 strains prevalent in the MSM in Shijiazhuang, China, was analyzed basing on the HIV-1 full-length gag, pol, and partial env gene. 21 drug-naïve HIV-1 sero-positive patients were enrolled into the study. Full length gag, pol, partial env genes and some near full length genomes were amplified with nest RT-PCR followed by sequencing. Multiple subtypes, including CRF01_AE (52.9%), subtype B (35.3%) and CRF07_BC (11.8%), were found in the population. Phylogenetic analysis showed close relationship between our strains with those from Beijing MSM but not those from paid blood donors of local area. Drug resistance surveillance evaluation showed no transmitted drug resistance (TDR). However, some drug-resistance related polymorphism sites (V181I and V106I) were popularly found in B subtype strains. The findings will contribute to understanding the distribution and evolution of HIV-1 in MSM and also help the behavior change intervention.