The origin and spread of HIV‐1 CRF59_01B epidemic in China: A molecular network and phylogeographic analysis

• Published in: Journal of medical virology 2024-07, Vol.96 (7), p.e29799-n/a
• Main Authors: Yan, Huanchang, Wu, Hao, Li, Shunming, Wang, Jiahang, Luo, Yefei, Luo, Rui, Gu, Yuzhou, Cai, Yanshan, Tang, Shixing, Hao, Yuantao, Gu, Jing, Han, Zhigang, Liu, Yu
• Format: Article
• Language: English
• Subjects: Bayesian analysis; Bayesian phylogeographic analysis; China - epidemiology; Clustering; Conditional probability; CRF59_01B; Epidemics; Female; Gene sequencing; Genotype; HIV; HIV Infections - epidemiology; HIV Infections - transmission; HIV Infections - virology; HIV-1 - classification; HIV-1 - genetics; HIV‐1; Human immunodeficiency virus; Humans; Male; Molecular Epidemiology; molecular network; Network analysis; Phylogeny; Phylogeography; Pol gene; pol Gene Products, Human Immunodeficiency Virus - genetics
• ISSN: 0146-6615; 1096-9071; 1096-9071
• DOI: 10.1002/jmv.29799

Human immunodeficiency virus type 1 CRF59_01B, identified in China in 2013, has been detected nationwide, exhibiting notably high prevalence in Guangzhou and its vicinity. This study aimed to unravel its origin and migration. A data set was established, incorporating all available CRF59_01B pol gene sequences and their metadata from Guangzhou and the public database. Bayesian phylogeographic analysis demonstrated that CRF59_01B originated in Shenzhen, the neighboring city of Guangzhou, around 1998 with posterior probability of 0.937. Molecular network analysis detected 1131 transmission links and showed a remarkably high clustering rate (78.9%). Substantial inter‐city transmissions (26.5%, 300/1131) were observed between Shenzhen and Guangzhou while inter‐region transmissions linked Guangzhou with South (46) and Southwest (64) China. The centre of Guangzhou was the hub of CRF59_01B transmission, including the inflow from Shenzhen (3.57 events/year) and outflow to the outskirts of Guangzhou (>2 events/year). The large‐scale analysis revealed significant migration from Shenzhen to Guangzhou (5.08 events/year) and North China (0.59 events/year), and spread from Guangzhou to Central (0.47 events/year), East (0.42 events/year), South (0.76 events/year), Southwest China (0.76 events/year) and Shenzhen (1.89 events/year). Shenzhen and Guangzhou served as the origin and the hub of CRF59_01B circulation, emphasizing inter‐city cooperation and data sharing to confine its nationwide diffusion.