Identification of Anthrax as the Cause of a Cluster of Unexplained Deaths, Uganda, 2023: The Role of Metagenomic Next-Generation Sequencing and Postmortem Specimens.

Between April and November 2023, 27 unexplained human deaths that presented with swelling of the arms, skin sores with black centers, difficulty in breathing, obstructed swallowing, headaches, and other body aches were reported in Kyotera District, Uganda by the Public Health Emergency Operations Center. Subsequently, the death of cattle on farms and the consumption of carcass meat by some residents were also reported. Field response teams collected clinical/epidemiological data and autopsy samples to determine the cause of deaths.

Emerging SARS-CoV-2 Variants in Uganda in the Era of COVID-19 Vaccination.

The emergence of SARS-CoV-2 variants has heightened concerns about vaccine efficacy, posing challenges in controlling the spread of COVID-19. As part of the COVID-19 Vaccine Effectiveness and Variants (COVVAR) study in Uganda, this study aimed to genotype and characterize SARS-CoV-2 variants in patients with COVID-19-like symptoms who tested positive on a real-time PCR. Amplicon deep sequencing was performed on 163 oropharyngeal/nasopharyngeal swabs collected from symptomatic patients.

Case Reports of Human Monkeypox Virus Infections, Uganda, 2024.

Mpox is a zoonotic disease caused by the monkeypox virus. We report on human mpox cases in Uganda identified by PCR and confirmed by deep sequencing. Phylogenetic analysis revealed clustering with other clade Ib sequences associated with recent outbreaks in the Democratic Republic of the Congo.

COVID-19 vaccine uptake and associated factors among individuals living in a peri-urban area in Uganda: A cross-sectional study.

Introduction: The Corona virus disease (COVID-19) is a respiratory illness that is caused by SARS-CoV-2 virus. This virus was first reported in China in December 2019. It then spread to all countries and from March 11, 2020, the World Health Organization declared the COVID-19 outbreak a pandemic.

Intra- and inter-subtype HIV diversity between 1994 and 2018 in southern Uganda: a longitudinal population-based study.

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. (p24) and (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.

Next-Generation Sequencing Reveals a High Frequency of HIV-1 Minority Variants and an Expanded Drug Resistance Profile among Individuals on First-Line ART.

We assessed the performance and clinical relevance of Illumina MiSeq next-generation sequencing (NGS) for HIV-1 genotyping compared with Sanger sequencing (SS). We analyzed 167 participants, 45 with virologic failure (VL ≥ 1000 copies/mL), i.e.

The 2023 South Sudanese outbreak of Hepatitis E emphasizes ongoing circulation of genotype 1 in North, Central, and East Africa.

In April 2023, an outbreak of acute hepatitis was reported amongst internally displaced persons in the Nazareth community of South Sudan. IgM serology-based screening suggested the likely etiologic agent to be Hepatitis E virus (HEV). In this study, plasma specimens collected from anti-HEV IgM-positive cases were subjected to additional RT-qPCR testing and sequencing of extracted nucleic acids, resulting in the recovery of five full and eight partial HEV genomes.

Sequence Notes: Near Full-Length Genome Analysis of the First-Reported HIV-1 Circulating Recombinant Form (CRF)_10CD in Uganda.

HIV-1 is characterized by remarkable genetic diversity resulting from its high replication rate, error-prone reverse transcriptase enzyme and recombination events. In Uganda, HIV-1 subtype diversity is mostly dominated by subtypes A, D, and A1/D Unique Recombinant Forms (URFs). In this study, deep sequences of HIV from patients with known antiretroviral therapy (ART) status were analyzed to determine the subtypes and to identify drug-resistance mutations circulating in the study population.

Increasing intra- and inter-subtype HIV diversity despite declining HIV incidence in Uganda.

HIV incidence has been declining in Africa with scale-up of HIV interventions. However, there is limited data on HIV evolutionary trends in African populations with waning epidemics. We evaluated changes in HIV viral diversity and genetic divergence in southern Uganda over a twenty-five-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.

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.

Geographic and Population Distributions of Human Immunodeficiency Virus (HIV)-1 and HIV-2 Circulating Subtypes: A Systematic Literature Review and Meta-analysis (2010-2021).

Background: HIV poses significant challenges for vaccine development due to its high genetic mutation and recombination rates. Understanding the distribution of HIV subtypes (clades) across regions and populations is crucial. In this study, a systematic review of the past decade was conducted to characterize HIV-1/HIV-2 subtypes.

QuasiFlow: a Nextflow pipeline for analysis of NGS-based HIV-1 drug resistance data.

Summary: Next-generation sequencing (NGS) enables reliable detection of resistance mutations in minority variants of human immunodeficiency virus type 1 (HIV-1). There is paucity of evidence for the association of minority resistance to treatment failure, and this requires evaluation. However, the tools for analyzing HIV-1 drug resistance (HIVDR) testing data are mostly web-based which requires uploading data to webservers.

A large population sample of African HIV genomes from the 1980s reveals a reduction in subtype D over time associated with propensity for CXCR4 tropism.

We present 109 near full-length HIV genomes amplified from blood serum samples obtained during early 1986 from across Uganda, which to our knowledge is the earliest and largest population sample from the initial phase of the HIV epidemic in Africa. Consensus sequences were made from paired-end Illumina reads with a target-capture approach to amplify HIV material following poor success with standard approaches. In comparisons with a smaller 'intermediate' genome dataset from 1998 to 1999 and a 'modern' genome dataset from 2007 to 2016, the proportion of subtype D was significantly higher initially, dropping from 67% (73/109), to 57% (26/46) to 17% (82/465) respectively (p < 0.

Detection of HIV-1 Transmission Clusters from Dried Blood Spots within a Universal Test-and-Treat Trial in East Africa.

The Sustainable East Africa Research in Community Health (SEARCH) trial was a universal test-and-treat (UTT) trial in rural Uganda and Kenya, aiming to lower regional HIV-1 incidence. Here, we quantify breakthrough HIV-1 transmissions occurring during the trial from population-based, dried blood spot samples. Between 2013 and 2017, we obtained 549 and 488 HIV-1 consensus sequences from 745 participants: 469 participants infected prior to trial commencement and 276 SEARCH-incident infections.

HIV-1 drug resistance genotyping success rates and correlates of Dried-blood spots and plasma specimen genotyping failure in a resource-limited setting.

Background: HIV-1 drug resistance genotyping is critical to the monitoring of antiretroviral treatment. Data on HIV-1 genotyping success rates of different laboratory specimen types from multiple sources is still scarce.

Methods: In this cross-sectional study, we determined the laboratory genotyping success rates (GSR) and assessed the correlates of genotyping failure of 6837 unpaired dried blood spot (DBS) and plasma specimens.

Rapid Replacement of SARS-CoV-2 Variants by Delta and Subsequent Arrival of Omicron, Uganda, 2021.

Genomic surveillance in Uganda showed rapid replacement of severe acute respiratory syndrome coronavirus 2 over time by variants, dominated by Delta. However, detection of the more transmissible Omicron variant among travelers and increasing community transmission highlight the need for near-real-time genomic surveillance and adherence to infection control measures to prevent future pandemic waves.

Employing phylogenetic tree shape statistics to resolve the underlying host population structure.

Background: Host population structure is a key determinant of pathogen and infectious disease transmission patterns. Pathogen phylogenetic trees are useful tools to reveal the population structure underlying an epidemic. Determining whether a population is structured or not is useful in informing the type of phylogenetic methods to be used in a given study.

Evaluation of the performance of 25 SARS-CoV-2 serological rapid diagnostic tests using a reference panel of plasma specimens at the Uganda Virus Research Institute.

Introduction: Serological testing is needed to better understand the epidemiology of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. Rapid diagnostic tests (RDTs) have been developed to detect specific antibodies, IgM and IgG, to the virus. The performance of 25 of these RDTs was evaluated.

Phylogenetic Networks and Parameters Inferred from HIV Nucleotide Sequences of High-Risk and General Population Groups in Uganda: Implications for Epidemic Control.

Phylogenetic inference is useful in characterising HIV transmission networks and assessing where prevention is likely to have the greatest impact. However, estimating parameters that influence the network structure is still scarce, but important in evaluating determinants of HIV spread. We analyzed 2017 HIV sequences (728 Lake Victoria fisherfolk communities (FFCs), 592 female sex workers (FSWs) and 697 general population (GP)) to identify transmission networks on Maximum Likelihood (ML) phylogenetic trees and refined them using time-resolved phylogenies.

HIV drug resistance among adults initiating antiretroviral therapy in Uganda.

Background: WHO revised their HIV drug resistance (HIVDR) monitoring strategy in 2014, enabling countries to generate nationally representative HIVDR prevalence estimates from surveys conducted using this methodology. In 2016, we adopted this strategy in Uganda and conducted an HIVDR survey among adults initiating or reinitiating ART.

Methods: A cross-sectional survey of adults aged ≥18 years initiating or reinitiating ART was conducted at 23 sites using a two-stage cluster design sampling method.

Impact of mhealth messages and environmental cues on hand hygiene practice among healthcare workers in the greater Kampala metropolitan area, Uganda: study protocol for a cluster randomized trial.

Background: Hand hygiene (HH) among healthcare workers (HCWs) is critical for infection prevention and control (IPC) in healthcare facilities (HCFs). Nonetheless, it remains a challenge in HCFs, largely due to lack of high-impact and efficacious interventions. Environmental cues and mobile phone health messaging (mhealth) have the potential to improve HH compliance among HCWs, however, these remain under-studied.

Short Communication: Validation of the Asante HIV-1 Rapid Recency Assay for Detection of Recent HIV-1 Infections in Uganda.

Point of care rapid recency testing for HIV-1 may be a cost-effective tool to identify recently infected individuals for incidence estimation, and focused HIV prevention through intensified contact tracing. We validated the Asante™ HIV-1 rapid recency assay for use in Uganda. Archived specimens (serum/plasma), collected from longitudinally observed HIV-1 recently and long-term infected participants, were tested with the Asante HIV-1 rapid recency assay per manufacturer's instructions.

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

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