Molecular cluster, transmission characteristics, origin and dynamics analysis of HIV-1 CRF59_01B in China: A molecular epidemiology study

•The first time to perform evolutionary and molecular network analyses on HIV-1 CRF59_01B.•HIV-1 CRF59_01B most likely originated in Southeast China, with a stable growth of population.•MSM and heterosexual formed most of the clusters.•Large clusters and risk groups in molecular network analyses call for targeted interventions. This study investigated for the HIV-1 CRF59_01B epidemic's spatiotemporal dynamics and its transmission networks in China. Between 2007 and 2020, a total of 250 partial pol gene sequences of HIV-1 CRF59_01B were collected from four regions (10 Chinese provinces). Phylogenetic tree construction and cluster identification were then performed. The Bayesian skyline and birth–death susceptible–infected–removed models were employed for the phylodynamic analyses of subtypes and large clusters, respectively. Phylogenetic analyses and trait diffusion of these sequences were performed using Bayesian phylogenetic methods (beast-classic package). Distance-based molecular network analyses were performed to identify putative relationships. Using a genetic distance threshold of 1.3 %, We identified 45 clusters that included 62.40 % (156/250) of the sequences. Three clusters (6.67 %, 3/45) had 10 or more sequences, and were considered "large clusters". Six clusters (13.33 %) included sequences from different regions (Southeast, Northeast, Southeast, and Central China). Thirteen clusters (28.89 %) included sequences of men who had sex with men only, three clusters (6.67 %) included sequences of heterosexuals only, and 12 clusters (26.67 %) included sequences of both groups. The substitution rate of CRF59_01B was 1.91 × 10–3 substitutions per site per year [95 % highest posterior density (HPD) interval: 1.39 × 10−3–2.49 × 10−3)], the time to the most recent common ancestor of CRF59_01B was to be 1992.83 (95 % HPD: 1977.97–2002.81). A Bayesian skyline plot revealed that the effective population size of CRF59_01B increased from 2000 to 2015 and remained stable after 2015. The large clusters showed continuous growth from 2013 to 2020. Phylogeographic analysis showed that CRF59_01B B most likely originated in Southeast China, with a posterior probability of 97.44 %, and then spread to other regions. Our study revealed the temporal and geographical origins of HIV-1 CRF59_01B as well as the process of transmission among various regions and risk groups in China, which can help develop targeted HIV prevention strategies.