Luo Yefei, Wu Hao, Liang Caiyun, Cai Yanshan, Gu Yuzhou, Li Qingmei, Liu Fanghua, Zhao Yuteng, Chen Yuncong, Li Shunming, Chen Xi, Jiang Liyun, Han Zhigang
Department of AIDS control and Prevention, Guangzhou Center for Disease Control and Prevention, Guangzhou, People's Republic of China.
Department of AIDS control and Prevention, Guangzhou Center for Disease Control and Prevention, Guangzhou, People's Republic of China; Institute of Public Health, Guangzhou Medical University & Guangzhou Center for Disease Control and Prevention, Guangzhou, People's Republic of China.
Acta Trop. 2024 Dec;260:107396. doi: 10.1016/j.actatropica.2024.107396. Epub 2024 Sep 14.
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 substitutions per site per year [95 % highest posterior density (HPD) interval: 1.39 × 10-2.49 × 10)], 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.
本研究调查了HIV-1 CRF59_01B在中国的时空动态及其传播网络。
2007年至2020年期间，共从四个地区（中国10个省份）收集了250条HIV-1 CRF59_01B的部分pol基因序列。随后进行系统发育树构建和聚类识别。分别采用贝叶斯天际线模型和出生-死亡易感-感染-移除模型对亚型和大聚类进行系统发育动力学分析。使用贝叶斯系统发育方法（beast-classic软件包）对这些序列进行系统发育分析和特征扩散分析。进行基于距离的分子网络分析以确定可能的关系。
使用1.3%的遗传距离阈值，我们识别出45个聚类，其中包含62.40%（156/250）的序列。三个聚类（6.67%，3/45）有10条或更多序列，被视为“大聚类”。六个聚类（13.33%）包含来自不同地区（中国东南部、东北部、东南部和中部）的序列。13个聚类（28.89%）仅包含男男性行为者的序列，三个聚类（6.67%）仅包含异性恋者的序列，12个聚类（26.67%）包含两组的序列。CRF59_01B的替换率为每年每个位点1.91×10⁻³替换[95%最高后验密度（HPD）区间：1.39×10⁻³-2.49×10⁻³]，CRF59_01B的最近共同祖先时间为1992.83（95%HPD：1977.97-2002.81）。贝叶斯天际线图显示，CRF59_01B的有效种群大小从2000年到2015年增加，2015年后保持稳定。大聚类在2013年至2020年期间持续增长。系统发育地理分析表明，CRF59_01B最有可能起源于中国东南部，后验概率为97.44%，然后传播到其他地区。
我们的研究揭示了HIV-1 CRF59_01B的时间和地理起源以及在中国各地区和风险群体之间的传播过程，这有助于制定有针对性的艾滋病预防策略。
