HIV-1 molecular transmission networks among MSM in Ningxia, China (2018–2024): insights into local transmission dynamics and drug resistance

Objectives Men who have sex with men (MSM) remain a high-risk group for HIV infection, accounting for nearly half of new HIV cases worldwide—a persistent global public health concern. This study investigated HIV-1 molecular transmission networks among MSM in Ningxia Hui Autonomous Region (NHAR), China. The aim was to characterize transmission dynamics within. Methods Plasma samples were collected from HIV-positive MSM in Ningxia between 2018 and 2024. HIV-1 RNA was extracted and sequenced for genotyping and drug resistance analysis. Genetic distances were calculated using the TN93 model in HyPhy 2.2.4. A sensitivity analysis was performed across thresholds of 0.1%–2.1% to justify the chosen threshold of 1.5%. Molecular transmission networks were visualized in Cytoscape 3.7.0. Bayesian phylogenetic analysis was used to identify migration events. Multivariable logistic regression was used to assess factors associated with clustering and high linkage. Results Among 296 MSM with successful sequencing, CRF07_BC was the predominant subtype (57.09%). CRF01_AE (20.61%) and CRF55_01B (5.07%) were also common. A total of 2.70% were classified as unique recombinant forms (URFs). We identified 129 MSM (43.6%, 129/296) within molecular transmission clusters. Large clusters (≥10 members) contained 117/129 (90.7%) of clustered individuals.CRF07_BC was the most frequent subtype in clusters (71.3% of clustered cases), but logistic regression showed it was associated with lower odds of high-degree connectivity (AOR = 0.209). Most clustered cases were from Yinchuan (57.4%). The strongest connection intensity appeared within Yinchuan, then between Yinchuan and Wuzhong. The most robust network connections were among MSM aged 25–39. Basic reproduction number (R 0 ) analysis showed the CRF01_AE subtype remained stable. CRF07_BC showed an increasing trend since 2020, while other subtypes rose sharply after 2022. Employment as a worker (AOR = 4.019) and infection with CRF07_BC (AOR = 0.209) or CRF55_01B (AOR = 0.201) were significantly associated with high-degree linkage; age groups showed no statistically significant associations. Conclusion MSM aged 25–39 showed the highest connectivity in transmission networks. The high clustering rate (43.6%) and identified acquired drug resistance (38.2% among sequenced individuals) underscore the urgent need for targeted interventions. These findings are limited to ART-experienced MSM with viremia (VL > 200 copies/mL) and cannot be generalized to the broader MSM population or to virologically suppressed individuals.