Molecular Transmission Clustering and Pretreatment Drug Resistance Among Men Infected With HIV-1 Who Have Sex With Men in Baotou, China: A Cross-Sectional Subgroup Analysis

Background In the Inner Mongolia Autonomous Region, men who have sex with men (MSM) have become a high-risk group for HIV transmission due to their complex, secretive sexual relationships, posing challenges to HIV-1 prevention. Objective We analyzed factors associated with molecular transmission clustering and pretreatment drug resistance (PDR) among newly reported HIV-1–infected MSM in Baotou, China, and to provide locally relevant evidence for targeted public health interventions. Methods We conducted a subgroup cross-sectional molecular epidemiological analysis of all newly reported HIV-1 cases attributed to homosexual transmission in Baotou between January 2022 and December 2024. The sample comprised 213 treatment-naïve MSM, from whom plasma samples were obtained. A 1.3-kb fragment of the HIV-1 pol gene was amplified and sequenced using next-generation sequencing. Inclusion criteria were a newly reported HIV-1 infection, no antiretroviral therapy at the time of this writing, and self-reported same-sex sexual behavior. Primary outcomes were clustering in a genetic distance–based molecular transmission network and the presence of PDR according to the Stanford HIV Drug Resistance Database. Results In total, 176 pol gene sequences were successfully obtained, with circulating recombinant form (CRF)–07_BC being the most prevalent subtype, accounting for 56.82% of the total sequences. The molecular transmission network was constructed using a pairwise genetic distance of 1.30%, with 52 of 176 (29.55%) sequences forming 19 clusters within the network. The network exhibited significant assortative mixing by age (ra=0.41; P =.001), marital status (ra=0.408; P =.002), and educational attainment (ra=0.385; P =.001), rather than random mixing. Multivariate logistic regression analysis revealed that CRF07_BC subtype–infected individuals had a significantly higher risk of clustering (AOR 4.98; 95% CI 1.92‐12.94; P <.01). Compared to never-married individuals, divorced or widowed individuals were less likely to have clustered cases (AOR 0.27; 95% CI 0.08‐0.92; P <.05). The prevalence of PDR was 6.57% (n=14). Nonnucleoside reverse transcriptase inhibitor resistance was the most common (n=8, 3.76%), followed by protease inhibitor resistance (n=5, 2.35%), and nucleoside reverse transcriptase inhibitor resistance (n=3, 1.14%). Drug-resistant strains were more frequently detected among individuals infected with the CRF07_BC subtype ( χ 2 8 =90.44; P< .001). Conclusions Unlike previous studies primarily focused on high-burden southeastern coastal regions of China, we investigated the molecular transmission characteristics of HIV-1 among MSM in the Inner Mongolia Autonomous Region. Our findings demonstrate that transmission clustering and drug resistance patterns previously observed are also present in northern border areas. This study integrated HIV-1 molecular transmission network analysis with next-generation sequencing technologies to identify key populations involved in local HIV transmission, thereby supporting targeted public health interventions. In addition, surveillance of PDR among high-risk populations may facilitate the development of evidence-based antiretroviral treatment strategies and improve the efficient allocation of limited health care resources.