Godfrey Kigozi

COVID-19 pandemic restrictions disrupted HIV services globally, but few studies have explored experiences from rural Africa or experiences of virologically unsuppressed individuals who may experience heightened barriers to care. We sought to explore COVID-19–related disruptions and adaptations to HIV service delivery in rural Rakai, Uganda. We conducted qualitative, in-depth interviews with 38 people living with HIV, all with high-level viremia (≥1,000 copies/ml), and 15 HIV clinicians. We also conducted six focus group discussions with peer health workers. Findings were analyzed thematically using a team-based inductive and deductive approach. Participants described the disruptive impact of COVID-19, precipitating transportation barriers and constraints to facility access, human resource gaps, and anticipated and enacted stigma. HIV services adapted, however, through approaches such as multimonth antiretroviral treatment dispensing, intensified community-based antiretroviral treatment delivery, flexibility in working hours, and changes in service access locations. Findings can inform HIV service delivery responses to future public health emergencies.

Summary: Background: As HIV incidence declines in African settings with high treatment coverage, it remains unclear how transmission is structured within populations and whether new infections arise from external introductions or local transmission. We characterized the molecular epidemiology of ongoing transmission in a mature multi-subtype epidemic in Uganda. Methods: We analyzed HIV genome sequences and survey data from the Rakai Community Cohort Study collected between 1994 and 2019. We identified phylogenetic clusters at 5·3% and 2·5% genetic distance thresholds and inferred long-horizon transmission chains with phylogeographic models. Newly diagnosed infections identified between 2016 and 2019 were mapped onto subtype- specific phylogenies to assess their origins and transmission context. A Bayesian negative binomial branching process model estimated undersampled chain sizes and case reproduction numbers. Findings: Among 4215 participants living with HIV between December 2016 and May 2019, 474 were newly diagnosed, of whom 269 had at least one pure-subtype sequence available. We identified 649 phylogenetic clusters at 5·3% genetic distance and 673 phylogeographic chains including ≥2 individuals. Most clusters and chains were small (median sizes 2 [IQR 2–3] and 3 [2–4], respectively), with new diagnoses rarely clustered together. Only 46/269 (17·1%) new diagnoses had phylogeographic external origins, while the remaining 82·9% were partially or fully linked to local chains. Mixed-subtypes/recombinant chains were larger and had higher case reproduction numbers (A1/D: 0.84 [95% CrI: 0.79-0.93]; mixed: 0.84 [0.73-0.97]) than single- subtype chains (A1: 0.56 [0.51-0.60]; D: 0.63 [0.59-0.66]; C: 0.55 [0.41-0.71]), yet all estimates were less than one. Interpretation: HIV transmission was fragmented across numerous, slowly propagating lineages, maintained by local clusters with occasional introduction. Continued transmission across many chains suggests that further reductions in HIV incidence will require maintaining high levels of population-wide treatment and prevention coverage. Funding: The National Institute of Allergy and Infectious Diseases, the Gates Foundation, and the HIV Prevention Trials Network Laboratory Center

Accurate interpretation of survey questions about sensitive matters such as sexual practices is crucial for obtaining reliable data to inform effective public health interventions. Describing sexual practices involves reflecting on acts and contextually attributing meanings. However, participants in sexual behaviour studies may struggle to understand questions, affecting the validity of the data. We investigated factors that shape the understanding of survey questions on sexual practices in South Central Uganda using a survey instrument and a semi-structured cognitive interview guide. Participants (n = 24), stratified by age, sex, and community type, and including persons with disabilities, were recruited. Interviews were conducted in person, and data were analysed using thematic analysis and an analytic matrix. A complex interaction between awareness or knowledge of the practice, memory retrieval, denial, sexual involvement, and cultural beliefs influenced participants' understanding of survey questions on sexual activities. Specifically, awareness and knowledge of the practice facilitated spontaneous and accurate responses, while a lack of familiarity led to hesitation and confusion. Memory retrieval was easier for recent experiences, and denial slowed down the process. This study highlights the importance of considering individual, interpersonal, and community-level factors to improve the accuracy and reliability of survey research on sexual practices for effective public health interventions.

SUMMARY: Background: Novel HIV prevention interventions such as long-acting pre-exposure prophylaxis (PrEP) could substantially reduce HIV transmission in Africa. However, efficient implementation in high-prevalence settings where incidence has declined requires an understanding of the contemporary dynamics driving new infections. Methods: We identified incident HIV cases from a longitudinal, population-based cohort in Uganda. We individually matched cases to HIV-negative controls; traced and enrolled reported sexual partners; and enrolled female sex workers (FSWs) from reported venues. Conditional logistic regression, transmission modeling, and phylogenetics were used to characterize transmission networks. Findings: From 2021-2024, 38,899 HIV tests among 22,255 people identified 187 people with incident infections (47.6% male); 164 (88%) were enrolled and matched to 164 HIV-negative controls. Overall, 593 non-sex-worker partners (371 enrolled,62.6%), 146 FSW partners (21 enrolled,14.4%), and 28 venues (208 FSWs enrolled) were reported. Incident infection was most strongly predicted by partnership with a FSW (odds ratio:15.5; 95%CI:3.7-64.8), identified in 43.0% of male cases versus 6.3% of controls. Men with FSW partners had larger sexual networks than men without (median:6 vs 2 partners), and 91.2% of men with FSW partners also had non-sex-worker partners. Transmission modeling attributed 34.4% (95%CI:31.5-36.8%) of all male infections and 80.0% (95%CI:73.2-84.4%) of infections among male clients to sex with FSWs. Oral PrEP use among HIV-negative partners of incident cases was low (8.9% in women; 2.1% in men). Interpretation: Men with FSW partners accounted for a substantial share of incident HIV infections and had markedly higher odds of infection than men without such partnerships. Together with the high potential for onward transmission within male client networks, these findings suggest that inclusion of male clients in long-acting HIV prevention strategies could be highly efficient and impactful. Funding: National Institutes of Health, United States; Gates Foundation; National Health and Medical Research Council, Australia

We analyzed perinatal transmission in a pre–antiretroviral therapy Ugandan cohort by maternal human immunodeficiency virus type 1 subtype and infant sex in 131 mother-child pairs. Among all children, if the mother was infected with subtype A there was a nearly 3-fold increased risk of perinatal transmission compared with subtype D (risk ratio [RR], 2.96 [95% confidence interval (CI), 1.46–6.01]; P = .008). When stratifying infants by both sex and maternal subtype, significantly more female (56.3% [9 of 16]) than male (9.1% [1 of 11]) infants born to mothers with subtype A were infected (RR, 6.19 [95% CI, .91–42.12]; P = .02). In contrast, among infants born to mothers with subtype D, transmission rates were comparable across sex (RR, 1.59 [95% CI, .57–4.41]; P = .39).