The Molecular Epidemiology and Transmission Dynamics of HIV Type 1 in a General Population Cohort in Uganda

• Main Authors: Deogratius Ssemwanga, Nicholas Bbosa, Rebecca N. Nsubuga, Alfred Ssekagiri, Anne Kapaata, Maria Nannyonjo, Faridah Nassolo, Alex Karabarinde, Joseph Mugisha, Janet Seeley, Gonzalo Yebra, Andrew Leigh Brown, Pontiano Kaleebu
• Format: Article
• Language: English
• Published: MDPI AG 2020-11-01
• Series: Viruses
• Subjects: molecular epidemiology; HIV-1; transmission networks; phylogenetic; demographic; general population
• Online Access: https://www.mdpi.com/1999-4915/12/11/1283

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 <i>pol</i> sequences (GPC: <i>n</i> = 1418, non-GPC sites: <i>n</i> = 1223, Central Uganda: <i>n</i> = 1010 and Eastern Uganda: <i>n</i> = 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, <i>n</i> = 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.