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

IF 2.1 3区 医学 Q2 PARASITOLOGY Acta tropica Pub Date : 2024-09-14 DOI:10.1016/j.actatropica.2024.107396
Yefei Luo , Hao Wu , Caiyun Liang , Yanshan Cai , Yuzhou Gu , Qingmei Li , Fanghua Liu , Yuteng Zhao , Yuncong Chen , Shunming Li , Xi Chen , Liyun Jiang , Zhigang Han
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Abstract

Purpose

This study investigated for the HIV-1 CRF59_01B epidemic's spatiotemporal dynamics and its transmission networks in China.

Methods

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.

Results

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.

Conclusions

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.

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中国HIV-1 CRF59_01B的分子聚类、传播特征、来源和动态分析:分子流行病学研究
目的 本研究探讨了中国HIV-1 CRF59_01B疫情的时空动态及其传播网络。方法 在2007年至2020年间,从中国的4个地区(10个省)共收集到250条HIV-1 CRF59_01B的部分pol基因序列。然后进行系统发生树构建和聚类鉴定。在亚型和大聚类的系统动力学分析中,分别采用了贝叶斯天际线模型和出生-死亡易感-感染-移除模型。使用贝叶斯系统发育方法(beast-classic软件包)对这些序列进行了系统发育分析和性状扩散分析。结果使用 1.3 % 的遗传距离阈值,我们确定了 45 个聚类,其中包括 62.40 % 的序列(156/250)。有三个聚类(6.67%,3/45)拥有 10 个或更多序列,被认为是 "大聚类"。有 6 个聚类(13.33%)包含来自不同地区(东南、东北、东南和华中)的序列。有 13 个聚类(28.89%)只包含了男男性行为者的序列,有 3 个聚类(6.67%)只包含了异性恋者的序列,有 12 个聚类(26.67%)包含了两类人群的序列。CRF59_01B 的替换率为每年每个位点 1.91 × 10-3 次替换[95 % 最高后验密度(HPD)区间:1.39 × 10-3-2.49 × 10-3],CRF59_01B最近共同祖先的时间为 1992.83(95 % HPD:1977.97-2002.81)。贝叶斯天际线图显示,CRF59_01B 的有效种群规模在 2000 年至 2015 年期间不断增加,并在 2015 年之后保持稳定。从 2013 年到 2020 年,大集群持续增长。我们的研究揭示了 HIV-1 CRF59_01B 的时间和地理起源,以及在中国不同地区和高危人群中的传播过程,有助于制定有针对性的艾滋病预防策略。
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来源期刊
Acta tropica
Acta tropica 医学-寄生虫学
CiteScore
5.40
自引率
11.10%
发文量
383
审稿时长
37 days
期刊介绍: Acta Tropica, is an international journal on infectious diseases that covers public health sciences and biomedical research with particular emphasis on topics relevant to human and animal health in the tropics and the subtropics.
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