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

Deogratius Ssemwanga,Gonzalo Yebra,Joseph Mugisha,Andrew Leigh Brown,Faridah Nassolo,Maria Nannyonjo,Alex Karabarinde,Rebecca N Nsubuga,Pontiano Kaleebu,Alfred Ssekagiri,Anne Kapaata,Janet Seeley,Nicholas Bbosa

doi:10.3390/v12111283

Abstract

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

Highlights

Since the beginning of the HIV epidemic in the early 1980s, several African countries includingUganda have registered significant progress in controlling the epidemic [1]
In 1990, a random selection of one-third of seropositive adults identified in the initial General Population Cohort (GPC) serosurvey round were invited to enrol into a natural history cohort (NHC) to study the disease progression of HIV-1-infected participants within the GPC [19]
Participants were from GPC, 1223 (32.2%) from the non-GPC, 1010 (26.6%) from the Central region and

Summary

Introduction

Since the beginning of the HIV epidemic in the early 1980s, several African countries includingUganda have registered significant progress in controlling the epidemic [1]. In Uganda, HIV-1 incidence was shown to reduce in the 1990s [2]. This success was mainly due to the Government’s early acknowledgement of the impact of the epidemic and commitment to scale down the epidemic through a multifaceted approach to prevention and care [3]. Survey (UAIS) showed an overall HIV-1 prevalence of 7.3% among adults aged 15–49 years with a higher prevalence among women (8.3%) than among men (6.1%) [4]. This survey further showed a higher prevalence of HIV among women in urban areas (10.7%) compared to rural areas (7.7%); HIV prevalence was the same for men in urban and rural areas (6.1%).

Methods

Results

Discussion

Conclusion