Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda.
Department of General Virology, Uganda Virus Research Institute, Entebbe 256, Uganda.
Viruses. 2020 Nov 10;12(11):1283. doi: 10.3390/v12111283.
The General Population Cohort (GPC) in south-western Uganda has a low HIV-1 incidence rate (<1%). However, new infections continue to emerge. In this research, 3796 HIV-1 sequences (GPC: = 1418, non-GPC sites: = 1223, Central Uganda: = 1010 and Eastern Uganda: = 145) generated between 2003-2015 were analysed using phylogenetic methods with demographic data to understand HIV-1 transmission in this cohort and inform the epidemic response. HIV-1 subtype A1 was the most prevalent strain in the GPC area (GPC and non-GPC sites) (39.8%), central (45.9%) and eastern (52.4%) Uganda. However, in the GPC alone, subtype D was the predominant subtype (39.1%). Of the 524 transmission clusters identified by Cluster Picker, all large clusters (≥5 individuals, = 8) involved individuals from the GPC. In a multivariate analysis, clustering was strongly associated with being female (adjusted Odds Ratio, aOR = 1.28; 95% CI, 1.06-1.54), being >25 years (aOR = 1.52; 95% CI, 1.16-2.0) and being a resident in the GPC (aOR = 6.90; 95% CI, 5.22-9.21). Phylogeographic analysis showed significant viral dissemination (Bayes Factor test, BF > 3) from the GPC without significant viral introductions (BF < 3) into the GPC. The findings suggest localized HIV-1 transmission in the GPC. Intensifying geographically focused combination interventions in the GPC would contribute towards controlling HIV-1 infections.
乌干达西南部的一般人群队列（GPC）的 HIV-1 发病率较低（<1%）。然而，新的感染仍在不断出现。在这项研究中，分析了 2003 年至 2015 年间在 GPC 地区（GPC：= 1418，非 GPC 地点：= 1223，乌干达中部：= 1010，乌干达东部：= 145）生成的 3796 条 HIV-1 序列，使用系统发生方法和人口统计学数据来了解该队列中的 HIV-1 传播，并为疫情应对提供信息。HIV-1 亚型 A1 是 GPC 地区（GPC 和非 GPC 地点）（39.8%）、乌干达中部（45.9%）和东部（52.4%）最流行的毒株。然而，仅在 GPC 地区，亚型 D 是主要的亚型（39.1%）。在 Cluster Picker 识别的 524 个传播群集中，所有大群集（≥5 人，= 8）都涉及 GPC 地区的个体。在多变量分析中，聚类与女性（调整后的优势比，aOR = 1.28；95%置信区间，1.06-1.54）、年龄>25 岁（aOR = 1.52；95%置信区间，1.16-2.0）和居住在 GPC（aOR = 6.90；95%置信区间，5.22-9.21）显著相关。系统发生地理分析显示，GPC 中存在显著的病毒传播（贝叶斯因子检验，BF > 3），而没有明显的病毒传入（BF < 3）。这些发现表明 GPC 中存在局部 HIV-1 传播。加强 GPC 中以地理为重点的综合干预措施将有助于控制 HIV-1 感染。
