Objective Partner-level sexually transmitted infection (STI) data from eastern Africa are rare, despite high STI burden. To address this gap, we examined STI prevalence and clustering among cohabiting couples in two high HIV-burden Ugandan communities, representing the largest population-based, couple-level STI study in the region.Methods We analysed data from the Sexually Transmitted Infection Prevalence Study (STIPS), a cross-sectional, population-based study in southern Uganda which tested participants for chlamydia, gonorrhoea, trichomonas, syphilis, high-titre syphilis and herpes simplex virus-2 (HSV-2). We restricted the present analysis to STIPS participants in a cohabiting sexual relationship. Poisson regression with robust standard errors was used to estimate prevalence ratios (PRs) and corresponding 95% confidence intervals (CIs) of all STIs by partner's infection status.Results Among 423 cohabiting heterosexual couples, at least one partner tested positive for a curable STI (chlamydia, gonorrhoea, trichomonas or high-titre syphilis) in 37% of couples. STIs were strongly clustered within partner dyads. For example, female participants with male partners with gonorrhoea had increased prevalence of not only gonorrhoea (PR 10.4, 95% CI 6.4 to 16.8) but also HIV (PR 2.2, 95% CI 1.5 to 3.2), chlamydia (PR 2.5, 95% CI 1.1 to 5.7), trichomonas (PR 2.4, 95% CI 1.2 to 4.7) and HSV-2 (PR 1.3, 95% CI 1.1 to 1.7).Conclusion Partners of individuals with an STI are more likely to have a curable STI, which may be the same or may be a different pathogen; broad screening of partners could be essential to curbing transmission and preventing reinfection. Comprehensive couple-based approaches, including partner notification, treatment and counselling strategies, are critical for reducing STI disease burden.

As healthcare becomes increasingly globalized, postgraduate medical education must evolve to prepare clinicians for an increasingly interconnected, diverse, and intercultural healthcare landscape. This article offers nine practical tips for designing and sustaining global learning networks-virtual, collaborative frameworks that connect trainees, educators, and institutions across borders. The recommendations are organized under four themes: (1) designing equitable curricula, (2) facilitating global collaboration, (3) developing culturally competent educators and learners, and (4) sustaining and evaluating learning networks. These recommendations are grounded in the theoretical frameworks of systems thinking and communities of practice. We emphasize co-created curricula, digital platforms for international engagement, culturally responsive pedagogy, inclusive assessment strategies, and decentralized leadership models. Each tip is grounded in peer-reviewed literature, international case studies, and lessons from our collaborative experiences. We address barriers such as time zones, resource inequities, and quality assurance. By embedding global perspectives into postgraduate programmes, global learning networks strengthen intercultural competence, enhance professional identity formation, expand access to medical education in low-resource settings, and foster mutual learning across diverse health systems. This guide supports postgraduate medical educators in cultivating culturally competent clinicians and advancing a more equitable, collaborative, and resilient global healthcare workforce.

HIV-1 Nef mediates immune evasion and viral pathogenesis in part through the downregulation of cell surface cluster of differentiation 4 (CD4) and major histocompatibility complex class I (MHC-I) on infected cells. While the Nef function of circulating viral populations found early in infection has been associated with reservoir size in early-treated cohorts, there is limited research on how its activity impacts reservoir size in people initiating treatment during chronic infection. In addition, there is little research on its role in the persistence of viral variants during long-term antiretroviral therapy (ART). Phylogenetically distinct nef genes (n = 82) with varying estimated times of reservoir entry were selected from viral outgrowth variants stimulated from the reservoir of South African women living with HIV who initiated ART during chronic infection (n = 16). These nef genes were synthesized and used in a pseudovirus infection assay that measures CD4 and MHC-I downregulation via flow cytometry. Downregulation measures were compared to the size of the replication-competent viral reservoir (RC-VR), estimated by quantitative viral outgrowth assay at 5 years after treatment initiation, as well as proviral survival time. Maximum Nef-mediated MHC-I downregulation was significantly associated with RC-VR size (P = 0.034), but this association was not observed for CD4 downregulation. Conversely, we did not find a consistent association between intraparticipant MHC-I or CD4 downregulation and the variant timing of entry into the reservoir. These data support a role for Nef-mediated MHC-I downregulation in determining RC-VR size, but more work is needed to determine Nef's role in the survival of individual viral variants over time.IMPORTANCERational design of HIV cure interventions requires an understanding of the viral determinants of reservoir dynamics. For an equitable cure, it needs to be broadly applicable. While African women bear the greatest burden of HIV globally, most cure research has focused on men in the global North. Our study aims to elucidate viral determinants of HIV persistence in South African women on antiretroviral therapy. We hypothesized that the HIV protein Nef subverts immune clearance of infected cells by downregulating surface levels of two cellular proteins, CD4 and MHC-I. We compared this downregulation capacity with reservoir size and variant survival in the reservoir. We found a positive association between an individual's reservoir size and MHC-I downregulation, but there was little evidence for a survival benefit with stronger MHC-I reduction. These data support earlier work and suggest that Nef's interaction with MHC-I may be a target to restrict the latent reservoir in cure strategies.

BACKGROUND:Although 30-day hospital readmission is a widely followed quality measure, there are limited US nationwide data to evaluate its trends among people with HIV (PWH) and the sex disparity over time. We describe the 30-day all-cause unplanned readmission trends among PWH and people without HIV (PWoH) in the United States. SETTING:Adult participants in the 2010-2020 Nationwide Readmissions Database, which weighted represents all US hospitalizations each year. METHODS:We defined index admission and unplanned readmission using the US Centers for Medicare & Medicaid Services criteria. Overall and sex-specific readmission risks were tabulated among the index admissions from adult PWH and PWoH each year in the 2010-2020 Nationwide Readmissions Database. Random effect linear and Poisson regressions were used to estimate risk difference and annual percentage change of the trend. We added a spline in 2015 and additionally stratified the analysis by age and patient's zip code median household income. All analyses were weighted to generate national estimates. RESULTS:Approximately 140,000 index admissions from PWH and 25 million from PWoH were included each year. For PWoH between 2010 and 2020, annual readmission risk was stable at ∼12%. For PWH, readmission risk was stable at ∼22% during 2010-2015 and decreased from 22.0% in 2016 to 20.1% in 2020 (RD= -1.60 [95% CI: -2.24,-0.95]). Nonpregnant female PWH continued to have higher readmission risk than male PWH for all subgroups and all years. Nonpregnant female PWH <40 years had no reduction in readmission risk between 2016 and 2020 (RD= -0.45 [95% CI: -2.43, 1.53]). CONCLUSIONS:There remains strong need for readmission reduction interventions focusing on PWH, especially for young female PWH.

IntroductionLymphogranuloma venereum (LGV) caused by L-serovars of Chlamydia trachomatis (CT) is a sexually transmitted infection (STI) causing asymptomatic infection, and anogenital disease. Epidemiologically, LGV has been strongly associated with human immunodeficiency virus (HIV) infection.MethodsUsing a retrospective longitudinal study design, we first described unadjusted and adjusted associations between demographic and sociobehavioral characteristics and rectal (r) CT (rCT) and rLGV in sexual health clinic attendees in Baltimore, MD, between 2009 and 2016 at baseline visits. Rectal samples that tested positive for CT with the Aptima AC2 assay underwent DNA extraction and in-house L-serovar PCR analysis. Then, patients were followed over 24 months and incident STIs were described using multivariable Cox-proportional hazard regression models.ResultsIn 292/391 (73.4%) patients who were male-assigned at birth (MAB), LGV prevalence was 20/292 (6.8% (95% confidence interval, 4.2%-10.4%)). In the final multivariable regression model, LGV was significantly associated with age greater than 25 years, transgender identity, and a history of syphilis. Baseline LGV was not associated with incident HIV or gonorrhea, but after adjusting for age, race, HIV status, and history of syphilis, LGV was marginally associated with a new syphilis diagnosis (hazard ratio 2.35 (95% confidence interval, 0.96-5.73), P = 0.06) over 24 months follow-up.ConclusionLymphogranuloma venereum accounted for almost 7% of rCT in patients MAB attending sexual health clinics in Baltimore between 2009 and 2016. Lymphogranuloma venereum was not associated with prevalent or incident HIV as in other studies. FDA-cleared tests and better surveillance measures are required to understand changes in the epidemiology of LGV in the United States.

Background Oral human papillomavirus (HPV) infection and the oral microbiome are associated with oropharyngeal cancer. However, population-based data on the association of oral microbiome with oral HPV infection are limited.Method A cross-sectional analysis of 5496 20-59-year-old participants in the 2009-2012 National Health and Nutrition Examination Survey was performed. Associations with oral HPV infection were assessed using multivariable logistic regression for oral microbiome alpha-diversity (within-sample diversity), and using principal coordinate analysis and permutational multivariate analysis of variance for beta-diversity (between-sample heterogeneity).Results Overall, for alpha-diversity, a lower number of observed amplicon sequence variants (adjusted odds ratio [aOR] = 0.996; 95% confidence interval [CI] = .992-.999) and reduced Faith's phylogenetic diversity (aOR = 0.95; 95% CI = .90-.99) were associated with high-risk oral HPV infection. beta-diversity showed differentiation of oral microbiome community by high-risk oral HPV infection as measured by Bray-Curtis dissimilarity (R2 = 0.054%; P = .029) and unweighted UniFrac distance (R2 = 0.046%; P = .045). There were differential associations when stratified by sex.Conclusions Both oral microbiome alpha-diversity and beta-diversity were marginally associated with oral HPV infection. Longitudinal studies are needed to characterize the role of the microbiome in the natural history of oral HPV infection. Oral microbiome alpha-diversity (within-sample richness and phylogenetic diversity) and beta-diversity (Bray-Curtis dissimilarity and unweighted UniFrac distance) are associated with high-risk oral HPV infection, and the associations are driven by males.

Background. A substantial proportion of persons on antiretroviral therapy (ART) considered lost to follow-up have actually transferred their human immunodeficiency virus (HIV) care to other facilities. However, the relationship between facility switching and virologic outcomes, including viral rebound, is poorly understood. Methods. We used data from 40 communities (2015-2020) in the Rakai Community Cohort Study to estimate incidence of facility switching and viral rebound. Persons aged 15-49 years living with serologically confirmed HIV who self-reported ART use and contributed >= 1 follow-up visit were included. Facility switching and virologic outcomes were assessed between 2 consecutive study visits (ie, index and follow-up visits, interval of approximately 18 months). Those who reported different HIV treatment facilities between index and follow-up study visits were classified as having switched facilities. Virologic outcomes included viral rebound among individuals initially suppressed (<200 copies/mL). Multivariable Poisson regression was used to estimate associations between facility switching and viral rebound. Results. Overall, 2257 persons who self-reported ART use (median age, 35 years; 65% female, 92% initially suppressed) contributed 3335 visit-pairs and 5959 person-years to the analysis. Facility switching was common (4.8 per 100 person-years; 95% confidence interval [CI], 4.2-5.5) and most pronounced in persons aged <30 years and fishing community residents. Among persons suppressed at their index visit (n = 2076), incidence of viral rebound was more than twice as high in persons who switched facilities (adjusted incidence rate ratio = 2.27; 95% CI, 1.16-4.45). Conclusions. Facility switching was common and associated with viral rebound among persons initially suppressed. Investments in more agile, person-centered models for mobile clients are needed to address system inefficiencies and bottlenecks that can disrupt HIV care continuity.

Background Thirty-day hospital readmission measures quality of care, but there are limited data among people with HIV (PWH) and people without HIV (PWoH) in the era of universal recommendation for antiretroviral therapy. We descriptively compared 30-day all-cause, unplanned readmission risk between PWH and PWoH. Methods A retrospective cohort study was conducted using the 2019 Nationwide Readmissions Database (2019/01/ 01-2019/12/31), - 2019/12/31), an all-payer database that represents all US hospitalizations. Index (initial) admissions and readmissions were determined using US Centers for Medicare & Medicaid Services definitions. fi nitions. Crude and age- adjusted risk ratios (aRR) comparing the 30-day all-cause, unplanned readmission risk between PWH to PWoH were estimated using random effect logistic regressions and predicted marginal estimates. Survey weights were applied to all analyses. Findings We included 24,338,782 index admissions from 18,240,176 individuals. The median age was 52(IQR = 40-60) - 60) years for PWH and 61(IQR = 38-74) - 74) years for PWoH. The readmission risk was 20.9% for PWH and 12.2% for PWoH (age-adjusted-RR:1.88 [95%CI = 1.84-1.92]). - 1.92]). Stratified fi ed by age and sex, young female (age 18-29 - 29 and 30-39 - 39 years) PWH had a higher readmission risk than young female PWoH (aRR = 3.50 [95%CI = 3.11-3.88] - 3.88] and aRR = 4.00 [95%CI = 3.67-4.32], - 4.32], respectively). While the readmission risk increased with age among PWoH, the readmission risk was persistently high across all age groups among PWH. The readmission risk exceeded 30% for PWH admitted for hypertensive heart disease, heart failure, and chronic kidney disease. Interpretation PWH have a disproportionately higher risk of readmission than PWoH, which is concerning given the aging profile fi le of PWH. More efforts are needed to address readmissions among PWH.

Background Syphilis diagnosis in the emergency department (ED) setting is often missed due to the lack of ED-specific testing strategies. We characterized ED patients with high-titer syphilis infections (HTSIs) with the goal of defining a screening strategy that most parsimoniously identifies undiagnosed, untreated syphilis infections.Methods Unlinked, de-identified remnant serum samples from patients attending an urban ED, between 10 January and 9 February 2022, were tested using a three-tier testing algorithm, and sociodemographic variables were extracted from ED administrative database prior to testing. Patients who tested positive for treponemal antibodies in the first tier and positive at high titer (>= 1:8) for nontreponemal antibodies in the second tier were classified as HTSI. Human immunodeficiency virus (HIV) status was determined with Bio-Rad enzyme-linked immunosorbent assay and confirmatory assays. Exact logistic regression and classification and regression tree (CART) analyses were performed to determine factors associated with HTSI and derive screening strategies.Results Among 1951 unique patients tested, 23 (1.2% [95% confidence interval, .8%-1.8%]) had HTSI. Of those, 18 (78%) lacked a primary care physician, 5 (22%) were HIV positive, and 8 (35%) were women of reproductive age (18-49 years). CART analysis (area under the curve of 0.67) showed that using a screening strategy that measured syphilis antibodies in patients with HIV, without a primary care physician, and women of reproductive age would have identified most patients with HTSI (21/23 [91%]).Conclusions We show a high prevalence of HTSI in an urban ED and propose a feasible, novel screening strategy to curtail community transmission and prevent long-term complications. Approximately 1% of patients attending an urban emergency department had a high-titer syphilis infection (rapid plasma reagin >= 1:8). Lack of primary care physician, having HIV, and being a woman of reproductive age are suggested risk factors to include in a screening strategy.

To date, an affordable, effective treatment for an HIV-1 cure remains only a concept with most "latency reversal" agents (LRAs) lacking specificity for the latent HIV-1 reservoir and failing in early clinical trials. We assessed HIV-1 latency reversal using a multivalent HIV-1-derived virus-like particle (HLP) to treat samples from 32 people living with HIV-1 (PLWH) in Uganda, US and Canada who initiated combined antiretroviral therapy (cART) during chronic infection. Even after 5-20 years on stable cART, HLP could target CD4(+) T cells harbouring latent HIV-1 reservoir resulting in 100-fold more HIV-1 release into culture supernatant than by common recall antigens, and 1000-fold more than by chemotherapeutic LRAs. HLP induced release of a divergent and replication-competent HIV-1 population from PLWH on cART. These findings suggest HLP provides a targeted approach to reactivate the majority of latent HIV-1 proviruses among individuals infected with HIV-1.

Background:Empirical data on transportation access and HIV treatment outcomes in sub-Saharan Africa are rare. We assessed the association between household transport ownership and HIV viral suppression in rural Uganda. Methods:The study was conducted among people living with HIV aged 15-49 years using cross-sectional data from the Rakai Community Cohort Study (RCCS), collected from June 14, 2018, to November 6, 2020. Transport ownership was defined as household possession of a car, motorcycle, or bicycle. HIV viral suppression was defined as < 1000 HIV RNA copies/ml. Poisson regression with robust variance estimation identified unadjusted and adjusted prevalence ratios and 95% confidence intervals (CI) of HIV viral suppression by transport ownership. Results:The study included 3,060 persons aged 15-49 living with HIV. Overall HIV viral suppression was 86.5% and was higher among women compared to men (89.3% versus 81.6%; adjusted prevalence ratio: 1.14, 95% CI: 1.10, 1.18). A total of 874 participants (28.6%) resided in households that owned at least one means of transport. HIV viral suppression was 79.8% among men and 88.2% among women from households without any means of transport, compared to 85.4% among men and 92.4% among women from households with at least one means of transport. Adjusted prevalence ratios of HIV viral suppression were 1.11 (95% CI: 1.04, 1.18) for males and 1.06 (95% CI: 1.03, 1.10) for females from households owning at least one means of transport compared with those from households with none. Conclusion:There was increased HIV viral suppression among people living with HIV from households with transport means compared to those from households without transport means, suggesting transport may facilitate access to, and continued engagement with, HIV treatment services.

OBJECTIVES:Migration is associated with increased risk of HIV infection in Africa, but evidence about non-HIV sexually transmitted infection (STI) burden among African migrants is limited. METHODS:We used data from the Sexually Transmitted Infection Prevalence Study, a cross-sectional population-based study of chlamydia, gonorrhoea, trichomoniasis, syphilis and herpes simplex virus type 2 prevalence in southern Uganda, to compare STI prevalence between adults aged 18 and 49 years with and without a recent history of migration. Migration status was determined using household census data, with a recent migration history defined as having moved into one's community of current residence within the last ~18 months. Unadjusted and adjusted modified Poisson regression models were used to compare individual STI prevalence risk by recent migration status with associations reported as adjusted prevalence risk ratios (adjPRRs) with 95% CIs. Adjusted models included participants' sex, age, community type, education, occupation and marital status. RESULTS:Among 1825 participants, 358 (19.6%) had a recent migration history. Overall, migrants exhibited a significantly higher combined prevalence of curable STIs (gonorrhoea, chlamydia, high-titre syphilis (rapid plasma regain ≥1:8) and trichomoniasis) as compared with long-term residents (34.4% vs 24.2%; adjPRR=1.23; 95% CI 1.03 to 1.47). Significant differences in curable STI prevalence by migration status were concentrated among persons living with HIV (49.4% prevalence in migrants vs 32.6% in long-term residents; adjPRR=1.42; 95% CI 1.10 to 1.85) and among women (38.8% in migrants vs 27.8% in long-term residents; adjPRR=1.26; 95% CI 1.01 to 1.58). High-titre syphilis prevalence was especially elevated among male migrants (11.2% in migrants vs 4.9% in long-term residents; adjPRR=1.82; 95% CI 1.06 to 3.13). CONCLUSIONS:The prevalence of non-HIV STIs is higher among migrants. Tailored outreach and service delivery approaches that address the needs of mobile populations are crucial for integrated HIV and STI epidemic control in Uganda to optimise resources and reduce transmission risks.

BACKGROUND:HIV treatment programs in Africa have implemented centralized testing for routine viral load monitoring (VLM), which may result in specimen processing delays inhibiting timely return of viral load results. Decentralized, point-of-care (PoC) VLM is a promising tool for expediting HIV clinical decision-making but remains unavailable in most African settings. We qualitatively explored the perceived feasibility and appropriateness of PoC VLM to address gaps along the viral load monitoring continuum in rural Uganda. METHODS:Between May and September 2022, we conducted 15 in-depth interviews with HIV clinicians (facility in-charges, clinical officers, nurses, counselors) and six focus group discussions with 47 peer health workers from three south-central Ugandan districts. Topics explored centralized VLM implementation and opportunities/challenges to optimizing routine VLM implementation with PoC testing platforms. We explored perspectives on PoC VLM suitability and feasibility using iterative thematic analysis. Applying the Framework Method, we then mapped salient constraints and enablers of PoC VLM to constructs from the Consolidated Framework for Implementation Research. RESULTS:Clinicians and peers alike emphasized centralized viral load monitoring's resource-intensiveness and susceptibility to procedural/infrastructural bottlenecks (e.g., supply stockouts, testing backlogs, community tracing of clients with delayed VLM results), inhibiting timely clinical decision-making. Participants reacted enthusiastically to the prospect of PoC VLM, anticipating accelerated turnarounds in specimen processing, shorter and/or fewer client encounters with treatment services, and streamlined efficiencies in HIV care provision (including expedited VLM-driven clinical decision-making). Anticipated constraints to PoC VLM implementation included human resource requirements for processing large quantities of specimens (especially when machinery require repair), procurement and maintenance costs, training needs in the existing health workforce for operating point-of-care technology, and insufficient space in lower-tier health facilities to accommodate installation of new laboratory equipment. CONCLUSIONS:Anticipated implementation challenges, primarily clustering around resource requirements, did not diminish enthusiasm for PoC VLM monitoring among rural Ugandan clinicians and peer health workers, who perceived PoC platforms as potential solutions to existing inefficiencies within the centralized VLM ecosystem. Prioritizing PoC VLM rollout in facilities with available resources for optimal implementation (e.g., adequate physical and fiscal infrastructure, capacity to manage high specimen volumes) could help overcome anticipated barriers to decentralizing viral load monitoring.

Objectives:Public sharing of de-identified biomedical data promotes collaboration between researchers and accelerates the development of disease prevention and treatment strategies. However, open-access data sharing presents challenges to researchers who need to protect the privacy of study participants, ensure that data are used appropriately, and acknowledge the inputs of all involved researchers. This article presents an approach to data sharing which addresses the above challenges by using a publicly available dashboard with de-identified, aggregated participant data from a large HIV surveillance cohort. Materials and Methods:Data in this study originated from the Rakai Community Cohort Study (RCCS), which was integrated into a centralized data mart as part of a larger data management strategy for the Rakai Health Sciences Program in Uganda. These data were used to build a publicly available, protected health information (PHI)-secured visualization dashboard for general research use. Results:Using two unique case studies, we demonstrate the capability of the dashboard to generate the following hypotheses: firstly, that HIV prevention strategies ART and circumcision have differing levels of impact depending on the marital status of investigated communities; secondly, that ART is very successful in comparison to circumcision as an interventional strategy in certain communities. Discussion:The democratization of large-scale anonymized epidemiological data using public-facing dashboards has multiple benefits, including facilitated exploration of research data and increased reproducibility of research findings. Conclusion:By allowing the public to explore data in depth and form new hypotheses, public-facing dashboard platforms have significant potential to generate new relationships and collaborations and further scientific discovery and reproducibility.

Objective Voluntary medical male circumcision (MC) is a critical tool in combination HIV prevention programmes in Africa. Self-reported MC (SrMC) status is used in HIV epidemiological surveys to assess MC coverage but is subject to response bias with limited validation. This study evaluated the utility of SrMC status as a marker of MC as well as self-reported genital lesions for genital ulcer disease (GUD) among Ugandan men. Methods Male participants aged 18–49 years in the cross-sectional Sexually Transmitted Infection Prevalence study, conducted between May and October 2019, responded to a questionnaire capturing SrMC status and current genital ulcer symptoms followed by clinical assessment to verify MC and presence of GUD. Sensitivity, specificity, positive predictive value, negative predictive value and corresponding CIs (95% CI) for SrMC status and GUD were estimated. Results There were 853 male participants, of whom 470 (55.1%) self-reported being circumcised and 23 (2.7%) self-reported GUD (SrGUD). MC was clinically confirmed in 50.2% (n=428) of participants with sensitivity of SrMC status at 99% (95% CI: 98% to 100%) and specificity 89% (95% CI: 86% to 92%). Specificity of SrMC was lowest among persons living with HIV and viremic (>1000 copies/mL) at 72% (95% CI: 46% to 90%). 18 participants had clinically confirmed GUD, but only 12 SrGUD symptoms, corresponding to a sensitivity and specificity of 67% (95% CI: 41% to 87%) and 99% (95% CI: 98% to 99%), respectively. Conclusions SrMC status is a robust proxy for clinically confirmed MC status and may reliably be used to assess MC coverage in this setting. Conversely, GUD symptoms were under-reported, which may impact effective syndromic management of sexually transmitted infections and warrants further examination.

AbstractPeople living with HIV can be simultaneously infected with genetically distinct variants. This can occur either at the time of initial infection (“coinfection”) or at a later time-point (“superinfection”). Multiple infection provides the necessary conditions for the generation of novel recombinant forms of HIV and may worsen clinical outcomes and increase the rate of transmission to HIV seronegative sexual partners. To date, studies of HIV multiple infection have relied on insensitive bulk-sequencing, labor intensive single genome amplification protocols, or deep-sequencing of short genome regions. Here, we identified multiple infections in whole-genome or near whole-genome HIV RNA deep-sequence data generated from plasma samples of 2,029 people living with viremic HIV who participated in the population-based Rakai Community Cohort Study. We estimated individual- and population-level probabilities of being multiply infected and assessed epidemiological risk factors using the novel Bayesian deep-phylogenetic multiple infection model (deep-phyloMI) which accounts for bias due to partial sequencing success and false-negative and false-positive detection rates. We estimated that between 2010 and 2020, 5.79% (95% highest posterior density interval (HPD) 4.56% - 7.07%) of sequenced participants with viremic HIV had a multiple infection at time of sampling. Participants living in high-HIV prevalence communities along Lake Victoria were 2.22-fold (95% HPD 1.28 - 3.43) more likely to harbor a multiple infection compared to individuals in lower prevalence neighboring communities. This work introduces a high-throughput surveillance framework for identifying people with multiple HIV infections and quantifying population-level prevalence and risk factors of multiple infection for clinical and epidemiological investigations.Author summaryHIV exists as a population of genetically distinct viral variants among people living with HIV. People living with HIV can be infected with genetically distinct variants. Identification of these mixed infections requires generating viral genomic data from people living with HIV. In the past, the approaches used to identify multiple infections from viral genomic data have had poor sensitivity or required labor intensive protocols that are prohibitive in application to large data sets. Prior work has also only utilized data generated from only small portions of the viral genome and the statistical procedures used to generate population-level estimates from sequencing data generated from individual infections has not accounted for incomplete sampling of the within-host viral population or sources of sequencing error, which may confound multiple infection estimates. Here, we develop a statistical model that addresses these limitations and allows for the identification of multiple infections and the estimation of population-level risk of multiple infection from deep-sequence data. We fit this model to population-based HIV genomic data from people living with HIV in southern Uganda and estimate that approximately 6% of viremic participants harbor a multiple infection at a given point in time. We show that the prevalence of multiple infections is higher in key populations with high HIV prevalence. These findings inform our understanding of the sexual risk networks that give rise to multiple infections and aid in efforts to model HIV epidemiological dynamics and evolution during a period of incidence declines and shifting transmission dynamics across Eastern and Southern Africa.

Timing of human immunodeficiency virus-1 (HIV-1) reservoir formation is important for informing HIV cure efforts. It is unclear how much of the variability seen in dating reservoir formation is due to sampling and gene-specific differences. We used a Bayesian extension of root to tip regression (bayroot) to reestimate formation date distributions in participants from Swedish and South African cohorts, and assessed the impact of variable timing, frequency, and depth of sampling on these estimates. Significant shifts in formation date distributions were only observed with use of faster-evolving genes, while timing, frequency, and depth of sampling had minor or no significant effect on estimates. We explored methodological sources of variability in the dating of HIV-1 reservoir formation, and show that faster-evolving genes can cause significant shifts in formation date distributions, while timing, frequency, and depth of sampling had little effect on estimates.

There is limited data on human immunodeficiency virus (HIV) evolutionary trends in African populations. We evaluated changes in HIV viral diversity and genetic divergence in southern Uganda over a 24-year period spanning the introduction and scale-up of HIV prevention and treatment programs using HIV sequence and survey data from the Rakai Community Cohort Study, an open longitudinal population-based HIV surveillance cohort. Gag (p24) and env (gp41) HIV data were generated from people living with HIV (PLHIV) in 31 inland semi-urban trading and agrarian communities (1994-2018) and four hyperendemic Lake Victoria fishing communities (2011-2018) under continuous surveillance. HIV subtype was assigned using the Recombination Identification Program with phylogenetic confirmation. Inter-subtype diversity was evaluated using the Shannon diversity index, and intra-subtype diversity with the nucleotide diversity and pairwise TN93 genetic distance. Genetic divergence was measured using root-to-tip distance and pairwise TN93 genetic distance analyses. Demographic history of HIV was inferred using a coalescent-based Bayesian Skygrid model. Evolutionary dynamics were assessed among demographic and behavioral population subgroups, including by migration status. 9931 HIV sequences were available from 4999 PLHIV, including 3060 and 1939 persons residing in inland and fishing communities, respectively. In inland communities, subtype A1 viruses proportionately increased from 14.3% in 1995 to 25.9% in 2017 (P < .001), while those of subtype D declined from 73.2% in 1995 to 28.2% in 2017 (P < .001). The proportion of viruses classified as recombinants significantly increased by nearly four-fold from 12.2% in 1995 to 44.8% in 2017. Inter-subtype HIV diversity has generally increased. While intra-subtype p24 genetic diversity and divergence leveled off after 2014, intra-subtype gp41 diversity, effective population size, and divergence increased through 2017. Intra- and inter-subtype viral diversity increased across all demographic and behavioral population subgroups, including among individuals with no recent migration history or extra-community sexual partners. This study provides insights into population-level HIV evolutionary dynamics following the scale-up of HIV prevention and treatment programs. Continued molecular surveillance may provide a better understanding of the dynamics driving population HIV evolution and yield important insights for epidemic control and vaccine development.

The principal barrier to an HIV cure is the presence of a latent viral reservoir (LVR) made up primarily of latently infected resting CD4+ (rCD4) T-cells. Studies in the United States have shown that the LVR decays slowly (half-life=3.8 years), but this rate in African populations has been understudied. This study examined longitudinal changes in the inducible replication competent LVR (RC-LVR) of ART-suppressed Ugandans living with HIV (n=88) from 2015-2020 using the quantitative viral outgrowth assay, which measures infectious units per million (IUPM) rCD4 T-cells. In addition, outgrowth viruses were examined with site-directed next-generation sequencing to assess for possible ongoing viral evolution. During the study period (2018-19), Uganda instituted a nationwide rollout of first-line ART consisting of Dolutegravir (DTG) with two NRTI, which replaced the previous regimen that consisted of one NNRTI and the same two NRTI. Changes in the RC-LVR were analyzed using two versions of a novel Bayesian model that estimated the decay rate over time on ART as a single, linear rate (model A) or allowing for an inflection at time of DTG initiation (model B). Model A estimated the population-level slope of RC-LVR change as a non-significant positive increase. This positive slope was due to a temporary increase in the RC-LVR that occurred 0-12 months post-DTG initiation (p<0.0001). This was confirmed with model B, which estimated a significant decay pre-DTG initiation with a half-life of 7.7 years, but a significant positive slope post-DTG initiation leading to a transient estimated doubling-time of 8.1 years. There was no evidence of viral failure in the cohort, or consistent evolution in the outgrowth sequences associated with DTG initiation. These data suggest that either the initiation of DTG, or cessation of NNRTI use, is associated with a significant temporary increase in the circulating RC-LVR.