National HIV and Retrovirology Laboratories, National Microbiology Laboratory at the JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
Department of Community Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada.
PLoS One. 2020 Aug 28;15(8):e0237560. doi: 10.1371/journal.pone.0237560. eCollection 2020.
Pakistan is considered by the World Health Organization to currently have a "concentrated" HIV-1 epidemic due to a rapid rise in infections among people who inject drugs (PWID). Prevalence among the country's nearly 105,000 PWID is estimated to be 37.8% but has been shown to be higher in several large urban centers. A lack of public health resources, the common use of professional injectors and unsafe injection practices are believed to have fueled the outbreak. Here we evaluate the molecular characteristics of HIV-1 sequences (n = 290) from PWID in several Pakistani cities to examine transmission dynamics and the association between rates of HIV-1 transmission with regards to regional trends in opioid trafficking. Tip-to-tip (patristic) distance based phylogenetic cluster inferences and BEAST2 Bayesian phylodynamic analyses of time-stamped data were performed on HIV-1 pol sequences generated from dried blood spots collected from 1,453 PWID as part of a cross-sectional survey conducted in Pakistan during 2014/2015. Overall, subtype A1 strains were dominant (75.2%) followed by CRF02_AG (14.1%), recombinants/unassigned (7.2%), CRF35_AD (2.1%), G (1.0%) and C (0.3%). Nearly three quarters of the PWID HIV-1 sequences belonged to one of five distinct phylogenetic clusters. Just below half (44.4%) of individuals in the largest cluster (n = 118) did seek help injecting from professional injectors which was previously identified as a strong correlate of HIV-1 infection. Spikes in estimated HIV-1 effective population sizes coincided with increases in opium poppy cultivation in Afghanistan, Pakistan's western neighbor. Structured coalescent analysis was undertaken in order to investigate the spatial relationship of HIV-1 transmission among the various cities under study. In general terms, our analysis placed the city of Larkana at the center of the PWID HIV-1 epidemic in Pakistan which is consistent with previous epidemiological data.
世界卫生组织认为，由于注射吸毒者（PWID）感染率迅速上升，巴基斯坦目前正面临“集中”的 HIV-1 流行。据估计，该国近 105,000 名 PWID 中的流行率为 37.8%，但在几个大城市中心的流行率更高。缺乏公共卫生资源、专业注射者的普遍使用以及不安全的注射行为被认为是疫情爆发的原因。在这里，我们评估了来自巴基斯坦几个城市的 PWID 的 HIV-1 序列（n=290）的分子特征，以研究传播动态以及 HIV-1 传播率与阿片剂贩运地区趋势之间的关联。对从 1453 名 PWID 采集的干血斑中提取的 HIV-1 pol 序列进行基于 tip-to-tip（亲缘）距离的系统发育聚类推断和基于时间戳数据的 BEAST2 贝叶斯系统发育分析。这些序列是在 2014/2015 年期间在巴基斯坦进行的横断面调查中生成的。总体而言，A1 亚型毒株占主导地位（75.2%），其次是 CRF02_AG（14.1%）、重组/未分类（7.2%）、CRF35_AD（2.1%）、G（1.0%）和 C（0.3%）。将近四分之三的 PWID HIV-1 序列属于五个不同的系统发育簇之一。最大簇（n=118）中的近一半（44.4%）个体确实寻求专业注射者的帮助注射，这被先前确定为 HIV-1 感染的一个强相关因素。估计的 HIV-1 有效种群数量的增加与巴基斯坦西部邻国阿富汗罂粟种植的增加相吻合。进行了结构化合并分析，以调查研究中各个城市之间 HIV-1 传播的空间关系。总体而言，我们的分析将巴基斯坦的拉卡纳市置于 PWID HIV-1 流行的中心，这与之前的流行病学数据一致。
