HIVseqDB: a portable resource for NGS and sample metadata integration for HIV-1 drug resistance analysis.

Summary: Human immunodeficiency virus (HIV) remains a public health threat, with drug resistance being a major concern in HIV treatment. Next-generation sequencing (NGS) is a powerful tool for identifying low-abundance drug resistance mutations (LA-DRMs) that conventional Sanger sequencing cannot reliably detect. To fully understand the significance of LA-DRMs, it is necessary to integrate NGS data with clinical and demographic data.

Study design approaches for future active-controlled HIV prevention trials.

Objectives: Vigorous discussions are ongoing about future efficacy trial designs of candidate human immunodeficiency virus (HIV) prevention interventions. The study design challenges of HIV prevention interventions are considerable given rapid evolution of the prevention landscape and evidence of multiple modalities of highly effective products; future trials will likely be 'active-controlled', i.e.

Finding women in fishing communities around Lake Victoria: "Feasibility and acceptability of using phones and tracking devices".

Introduction: Women in fishing communities have both high HIV prevalence and incidence, hence they are a priority population for HIV prevention and treatment interventions. However, their mobility is likely to compromise the effectiveness of interventions. We assessed the acceptability, feasibility and of using phones and global positioning system (GPS) devices for tracking mobility, to inform future health research innovations.

An Optimised Indirect ELISA Protocol for Detection and Quantification of Anti-viral Antibodies in Human Plasma or Serum: A Case Study Using SARS-CoV-2.

Advanced immunoassays are crucial in assessing antibody responses, serving immune surveillance goals, characterising immunological responses to evolving viral variants, and guiding subsequent vaccination initiatives. This protocol outlines an indirect ELISA protocol to detect and quantify virus-specific antibodies in plasma or serum after exposure to viral antigens. The assay enables the measurement of IgG, IgA, and IgM antibodies specific to the virus of interest, providing qualitative and quantitative optical densities and concentration data.

Diagnostic accuracy of two confirmatory tests for diabetes mellitus in adult Ugandans with recently diagnosed tuberculosis.

Objective: The optimal confirmatory tests for diabetes mellitus (DM) in patients with tuberculosis (TB) vary across populations. This study aimed to evaluate the performance of two confirmatory tests for DM against the oral glucose tolerance test (OGTT) as the reference test in adult Ugandans with recently diagnosed TB.

Methods: A total of 232 adult participants receiving TB treatment underwent initial screening for DM with random blood glucose (RBG) measurement.

Feasibility and acceptability of undertaking postmortem studies for tuberculosis medical research in a low income country.

Introduction: If we are to break new ground in difficult-to-treat or difficult-to-vaccinate diseases (such as HIV, malaria, or tuberculosis), we must have a better understanding of the immune system at the site of infection in humans. For tuberculosis (TB), the initial site of infection is the lungs, but obtaining lung tissues from subjects suffering from TB has been limited to bronchoalveolar lavage (BAL) or sputum sampling, or surgical resection of diseased lung tissue.

Methods: We examined the feasibility of undertaking a postmortem study for human tuberculosis research at Mulago National Referral Hospital in Kampala, Uganda.

Evaluating pooled testing for asymptomatic screening of healthcare workers in hospitals.

Background: There is evidence that during the COVID pandemic, a number of patient and HCW infections were nosocomial. Various measures were put in place to try to reduce these infections including developing asymptomatic PCR (polymerase chain reaction) testing schemes for healthcare workers. Regularly testing all healthcare workers requires many tests while reducing this number by only testing some healthcare workers can result in undetected cases.

Recently activated CD4 T cells in tuberculosis express OX40 as a target for host-directed immunotherapy.

After Mycobacterium tuberculosis (Mtb) infection, many effector T cells traffic to the lungs, but few become activated. Here we use an antigen receptor reporter mouse (Nur77-GFP) to identify recently activated CD4 T cells in the lungs. These Nur77-GFP cells contain expanded TCR clonotypes, have elevated expression of co-stimulatory genes such as Tnfrsf4/OX40, and are functionally more protective than Nur77-GFP cells.

Sustained spike-specific IgG antibodies following CoronaVac (Sinovac) vaccination in sub-Saharan Africa, but increased breakthrough infections in baseline spike-naive individuals.

Introduction: This study investigated the antibody responses to the inactivated COVID-19 vaccine, CoronaVac (Sinovac Biotech) in the African population to provide valuable insights into long-term immunity and breakthrough infections against SARS-CoV-2 in individuals with varying prior IgG seropositivity.

Methods: Real-life cohorts were used to longitudinally track antibody levels against the SARS-CoV-2 spike and nucleoprotein in 60 participants over 12 months to examine the levels of multiple antibody isotypes (S-IgG, S-IgM, S-IgA, N-IgG, and N-IgM).

Results: Throughout the 12 months, we observed consistently high and stable seropositivity rates for spike-IgG antibodies, spike-IgM antibodies showed a decline in frequencies over time, and spike-IgA levels remained moderate and stable.

Using electronic medical records to understand the impact of SARS-CoV-2 lockdown measures on maternal and neonatal outcomes in Kampala, Uganda.

Kawempe National Referral Hospital (KNRH) is a tertiary facility with over 21,000 pregnant or postpartum women admitted annually. The hospital, located in Kampala, Uganda, uses an Electronic Medical Records (EMR) system to capture patient data. Used since 2017, this readily available electronic health record (EHR) has the benefit of informing real-time clinical care, especially during pandemics such as COVID-19.

Molecular epidemiology of in non-pregnant populations: a systematic review.

(group B , GBS) has recently emerged as an important pathogen among adults. However, it is overlooked in this population, with all global efforts being directed towards its containment among pregnant women and neonates. This systematic review assessed the molecular epidemiology and compared how the lineages circulating among non-pregnant populations relate to those of pregnant and neonatal populations worldwide.

Prevalence and Factors Associated with Illicit Drug and High-Risk Alcohol Use among Adolescents Living in Urban Slums of Kampala, Uganda.

Background; Illicit drug and high risk alcohol use among adolescents leads to poor health outcomes. We enrolled adolescents from urban slums in Kampala, Uganda, to assess baseline prevalence, and factors associated with illicit drug and high-risk alcohol consumption. Methods; We conducted a cross-sectional study using data collected in a cohort that enrolled 14-19-year-old male and female participants from 25-March-2019 to 30-March 2020.

Longitudinal data resource from the Wellbeing of Older People cohort of people aged >50 years in Uganda and South Africa from 2009 to 2019.

Background: The population of people aged ≥60 years continues to increase globally, and has been projected by the United Nations Population Division to increase to 21% of the total population by 2050. In addition, the number of older people living with HIV has continued to increase owing to the introduction of antiretroviral therapy as a treatment for HIV-infected people. Most of the older people living with HIV are in sub-Saharan Africa, an area that faces the biggest burden of HIV globally.

Type 2 diabetes progression in an adult Ugandan population with new-onset diabetes: an observational prospective study.

Background: The rate of progression of type 2 diabetes following diagnosis varies across individuals and populations. Studies investigating the progression of type 2 diabetes in adult African populations with newly diagnosed diabetes are limited. We aimed to investigate the prevalence and predictors of short-term (one year) diabetes progression in an adult Ugandan population with new-onset type 2 diabetes (type 2 diabetes diagnosed in < 3 months) initiated on oral hypoglycaemic agents (OHA).

Adjunctive Dexamethasone for Tuberculous Meningitis in HIV-Positive Adults.

Background: Adjunctive glucocorticoids are widely used to treat human immunodeficiency virus (HIV)-associated tuberculous meningitis despite limited data supporting their safety and efficacy.

Methods: We conducted a double-blind, randomized, placebo-controlled trial involving HIV-positive adults (≥18 years of age) with tuberculous meningitis in Vietnam and Indonesia. Participants were randomly assigned to receive a 6-to-8-week tapering course of either dexamethasone or placebo in addition to 12 months of antituberculosis chemotherapy.

Burden and predictors of diabetic kidney disease in an adult Ugandan population with new-onset diabetes.

Background: Despite the growing evidence of diabetic kidney disease (DKD) in adult patients with long-standing diabetes in sub-Saharan Africa, data on its burden and correlates in adult African patients with new-onset diabetes are limited. We, therefore, undertook this study to determine the burden and predictors of DKD in an adult population with new-onset diabetes in Uganda.

Methods: We collected data on the relevant sociodemographic, clinical, anthropometric, and metabolic characteristics in 519 participants with newly diagnosed diabetes recruited from seven tertiary hospitals.

Immunological factors linked to geographical variation in vaccine responses.

Vaccination is one of medicine's greatest achievements; however, its full potential is hampered by considerable variation in efficacy across populations and geographical regions. For example, attenuated malaria vaccines in high-income countries confer almost 100% protection, whereas in low-income regions these same vaccines achieve only 20-50% protection. This trend is also observed for other vaccines, such as bacillus Calmette-Guérin (BCG), rotavirus and yellow fever vaccines, in terms of either immunogenicity or efficacy.

Recommendations on data sharing in HIV drug resistance research.

 • Human immunodeficiency virus (HIV) drug resistance has implications for antiretroviral treatment strategies and for containing the HIV pandemic because the development of HIV drug resistance leads to the requirement for antiretroviral drugs that may be less effective, less well-tolerated, and more expensive than those used in first-line regimens.  • HIV drug resistance studies are designed to determine which HIV mutations are selected by antiretroviral drugs and, in turn, how these mutations affect antiretroviral drug susceptibility and response to future antiretroviral treatment regimens.  • Such studies collectively form a vital knowledge base essential for monitoring global HIV drug resistance trends, interpreting HIV genotypic tests, and updating HIV treatment guidelines.

Perceptions of the Intervention Utility and Effectiveness in Supporting and Reintegrating Youths Born of Genocidal Rape in Rwanda.

Background: Birth through genocidal rape has a detrimental impact on the health of the offspring; however, there is scarce literature that focuses on efforts to support and reintegrate people born of this crime due to the lack of needs assessments that can inform policies and interventions.

Objective: This study sought to explore perceptions of the intervention utility and effectiveness in supporting and reintegrating offspring born of the 1994 genocidal rape against the Tutsi in Rwanda.

Methods: A purposive sample of 16 dyads of non-partnered mothers raped in the 1994 genocide against the Tutsi and their offspring participated in semi-structured qualitative interviews.

Whole-genome sequencing across 449 samples spanning 47 ethnolinguistic groups provides insights into genetic diversity in Nigeria.

African populations have been drastically underrepresented in genomics research, and failure to capture the genetic diversity across the numerous ethnolinguistic groups (ELGs) found on the continent has hindered the equity of precision medicine initiatives globally. Here, we describe the whole-genome sequencing of 449 Nigerian individuals across 47 unique self-reported ELGs. Population structure analysis reveals genetic differentiation among our ELGs, consistent with previous findings.

Understanding the drivers of preferential migration of people living with HIV to fishing communities of Lake Victoria in Uganda.

Fishing communities around Lake Victoria have among the highest burdens of HIV globally. Growing evidence suggests that high HIV prevalence is partially due to selective migration of people living with HIV to fishing communities. However, the reasons for this preferential migration are unclear.

Spike protein is a key target for stronger and more persistent T-cell responses-a study of mild and asymptomatic SARS-CoV-2 infection.

Objectives: Understanding the immune response in very mild and asymptomatic COVID-19 is crucial for developing effective vaccines and immunotherapies, yet remains poorly characterized. This longitudinal study examined the evolution of interferon (IFN)-γ responses to SARS-CoV-2 peptides in 109 asymptomatic or mildly symptomatic Ugandan COVID-19 patients across 365 days and explored their association with antibody generation.

Methods: T-cell responses to spike-containing clusters of differentiation (CD4)-S and CD8 nCoV-A (CD8-A) megapools, and the non-spike CD4-R and CD8 nCoV-B (CD8-B) megapools, were assessed and correlated with demographic and temporal variables.

The bacterial profile and antibiotic susceptibility pattern in respiratory tract samples from art-experienced HIV-positive adults in Uganda.

Introduction: Microbial infections are a major cause of morbidity and mortality among people living with HIV (PLWH). Respiratory tract infections (RTIs) are responsible for approximately 70% of illnesses among PLWH. Drug resistant bacteria are highly prevalent among PLWH and this is a public health concern.