Molecular footprints of a traveling epidemic: CRF01_AE-cluster 5 (01_C5) might spread across Northeast and South China via middle-aged MSM

HIV-1 CRF01_AE exhibits multiple distinct sub-subtypes (01_C1-C8) with different transmission dynamics across China. Understanding their geographical distribution, transmission patterns, and key affected populations is critical for optimizing targeted interventions. We conducted a comprehensive molecular epidemiological study analyzing 4,011 partial pol sequences and demographic data from newly diagnosed CRF01_AE cases (2016–2019) in Shenyang (Northeast China) and Shenzhen (South China) by constructing the CRF01_AE molecular network in China (n = 6140). Sub-subtyping was performed using an online HIV subtyping tool and phylogenetic analysis. A molecular network was constructed based on genetic distance, and viral dispersal in large clusters (size≥10) in the network was assessed using Bayesian inference. 01_C5 (46.7%), 01_C4 (37.2%), 01_C1 (8.1%), 01_C2 (2.3%), 01_C3 (0.3%), and 01_C8 (