Congregate settings are high-risk places for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission, making strategies that rely solely on hospital-based testing ineffective in curbing transmissions. We therefore evaluated the feasibility, utility, and acceptability of testing with SARS-CoV-2 antigen rapid diagnostic tests (Ag-RDTs) in markets and trade hubs in Kampala, Uganda. Between June and September 2022, we conducted a prospective operational research study in five divisions of Kampala. Four rounds of monthly cross-sectional surveys were conducted at one market and one trading hub per division, resulting in a total of 13,086 volunteers tested. Females were more likely than males to be tested (54% versus 46%), which aligns with sex-based differences in health-seeking behavior. More tests were conducted in markets (68%) compared with trade centers (32%). Several interventions increased overall demand for testing, including 1) awareness campaigns and mobilization activities; 2) the movement of teams across congregate settings; 3) the optimization of workflow; and 4) testing traders at their workstations. The overall positivity rate during the 4 months was 0.6% (78/13,086). There was a steady decline in positivity rates by month, aligning with the trend observed at the national level. Of the 78 positive index cases identified, 105 contacts were traced; 71% of these could be reached. None of the positive patients successfully self-isolated for the 14 days specified in national guidelines. Nevertheless, this study demonstrates that testing market dwellers with Ag-RDTs is not only acceptable and feasible in Uganda but also an important public health tool for the timely detection of SARS-CoV-2. This approach may be replicated in similar settings.

Congregate settings are high-risk places for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission, making strategies that rely solely on hospital-based testing ineffective in curbing transmissions. We therefore evaluated the feasibility, utility, and acceptability of testing with SARS-CoV-2 antigen rapid diagnostic tests (Ag-RDTs) in markets and trade hubs in Kampala, Uganda. Between June and September 2022, we conducted a prospective operational research study in five divisions of Kampala. Four rounds of monthly cross-sectional surveys were conducted at one market and one trading hub per division, resulting in a total of 13,086 volunteers tested. Females were more likely than males to be tested (54% versus 46%), which aligns with sex-based differences in health-seeking behavior. More tests were conducted in markets (68%) compared with trade centers (32%). Several interventions increased overall demand for testing, including 1) awareness campaigns and mobilization activities; 2) the movement of teams across congregate settings; 3) the optimization of workflow; and 4) testing traders at their workstations. The overall positivity rate during the 4 months was 0.6% (78/13,086). There was a steady decline in positivity rates by month, aligning with the trend observed at the national level. Of the 78 positive index cases identified, 105 contacts were traced; 71% of these could be reached. None of the positive patients successfully self-isolated for the 14 days specified in national guidelines. Nevertheless, this study demonstrates that testing market dwellers with Ag-RDTs is not only acceptable and feasible in Uganda but also an important public health tool for the timely detection of SARS-CoV-2. This approach may be replicated in similar settings.

Background Although persistent low-level viremia (PLLV) has been associated with treatment failure, there is limited data about HIV drug resistance (HIVDR) during PLLV among Ugandans living with HIV. This study assessed HIVDR prevalence, patterns and associated factors among individuals on HIV-1 first-line ART who were experiencing PLLV. Methods A cross-sectional study among individuals with PLLV defined by two consecutive detectable viral load results < 1000 copies/mL and whose adherence scores were ≥ 95% over a twelve-month period. At 12 months, plasma samples of 444 eligible individuals on first-line ART were retrieved. HIVDR genotyping was performed on the protease, reverse transcriptase, and integrase regions of the HIV genome, and factors associated with HIVDR were assessed by logistic regression. Results Of the 444 individuals analyzed, only 67 (15.1%) were successfully genotyped. HIVDR prevalence was detected in 62.1% of those genotyped. Based on antiretroviral therapy (ART) drug classes, 56.1% of individuals in this study had HIVDR to NNRTIs, 42.2% to NRTIs, and 1.5% to both INSTIs and PIs. The most prevalent NRTI drug resistance mutations (DRMs) were M184V/I (40.3%) and K65R (14.9%). The NNRTI K103E/N/S and G190A mutations existed among 30% and 19.4% of individuals, respectively. The INSTI mutations N155H and R263K, together with the PI mutation M46I, were detected in < 2% of the population. Having an elevated viral load (VL between 500 and 999 copies/mL) (aOR: 6.4; 95% CI: (1.49–27.89); p = 0.01) and being below 25 years of age (aOR: 0.13; 95% CI (0.02–0.73); p = 0.02) were factors significantly associated with HIVDR during PLLV. Conclusion We report emerging HIVDR among individuals on first-line ART despite persistent low-level viremia and good drug adherence. HIVDR was associated with elevated PLLV (viral load ranges between 500 and 999 copies/mL) and young age. HIVDR genotyping for individuals on first-line ART experiencing elevated PLLV is highly recommended. Low genotyping success rates present a major impediment to HIVDR studies among individuals with PLLV, suggesting a need to adopt robust next-generation platforms for deep sequencing. Also, HIV intervention programs targeted toward the youth may positively impact HIV control.

Abstract Background Sub-Saharan African countries have a high burden of viral hepatitis and poor access to screening and care. The aim of this study was to evaluate the feasibility and acceptability of using the plasma separation card (PSC) for viral hepatitis B and C screening among people living with HIV (PLHIV) in Cameroon and Uganda. Methods This is a cross-sectional study carried out between 05/2021 and 03/2023 including 192 PLHIV in Cameroon (n = 104) and Uganda (n = 88). Basic sociodemographic variables and whole blood samples were collected. Adequate filling with blood of PSCs was used to determine feasibility together with participant responses to questions on acceptability. A logistic regression model was carried out to assess the relationship between PSC acceptability and factors of interest. Results 70% of participants reported PSC as an acceptable viral hepatitis screening tool, and it was significantly more accepted in Uganda than Cameroon (100% vs. 43.2%, p < 0.001). Similarly, 75% of PSCs had at least one spot sample filled and were viable for analysis, 99% were correctly filled in Uganda and 53.4% in Cameroon. Reported ease of method performance (aOR: 24.77 95% CI 2.97-206.42, p = 0.003) and reduced collection time (aOR: 3.73 95% CI 1.26–11.04, p = 0.017) were associated with greater odds of PSC acceptance. HBsAg + and anti-HCV + prevalence were 11.1% and 1.0%, respectively. Conclusions In spite of country differences, overall, the PSC was reported as a feasible and acceptable viral hepatitis testing method. Acceptability and feasibility of the method must be explored in heterogeneous target communities and qualitative research to better understand country-specific barriers and facilitators should be carried out.

BackgroundEffective management of the COVID-19 pandemic required rapid expansion of diagnosis. The introduction of antigen tests presented an opportunity to decentralize testing, but raised challenges with ensuring accurate and timely reporting of testing data, which is essential to guide the response. Digital solutions can help address this challenge and provide more efficient means of monitoring and quality assurance. MethodsUganda's existing laboratory investigation form was digitized in the form of an Android-based application, eLIF, which was developed by the Central Public Health Laboratory and implemented in 11 high-volume facilities between December 2021 and May 2022. The app enabled healthcare workers to report testing data via mobile phone or tablet. Uptake of the tool was monitored through a dashboard that enabled real-time visibility into data being transmitted from sites, as well as qualitative insights from site visits and online questionnaires. Results and discussionA total of 15,351 tests were conducted at the 11 health facilities during the study period. Of these, 65% were reported through eLIF, while 12% were reported through preexisting Excel-based tools. However, 23% of tests were only captured in paper registers and not transmitted to the national database, illustrating the need for increased uptake of digital tools to ensure real-time data reporting. While data captured through eLIF were transmitted to the national database within 0-3 days (min, max), data transmitted through Excel were transmitted in within 0-37 days (min, max), and data for paper-based reporting took up to 3 months. The majority of healthcare workers interviewed in an endpoint questionnaire responded that eLIF improved timeliness of patient management, and reduced reporting time. However, some functions of the app were not successfully implemented, such as providing random selections of samples for external quality assurance and enabling seamless linkage of these data. Challenges arose from broader operational complexities, such as staff workload, frequent task-shifting and unexpected changes to facility workflows, which limited adherence to the envisioned study procedures. Ongoing improvements are needed to adjust to these realities, to strengthen the technology and support to healthcare workers using it, to optimize the impact of this digital intervention.

Background: Implementation of appropriate informed consent has become a cornerstone for the use of biological materials and data from clinical care to use in research. During 2017-2018, the Ugandan National Biorepository has since sought prior informed consent for long-term storage and use of remnant clinical human biological materials, where a shortened informed consent form (ICF) was incorporated on the laboratory investigation form. This project aimed at determining the acceptability rate of broad consent from health care users (HCUs) for storage of biological materials and data for research purposes in Uganda. Methods: A cross-sectional study was conducted at three Primary Health Care Facilities. 500 HCUs above 18 years of age seeking health care at outpatient departments between March to December 2020 were invited to enrol. A shortened experimental ICF for this study was developed and attached to the Laboratory investigation form. Results: Overall the acceptability of broad consent for storage of biological materials and data was 86.2% [95% CI: 82.9%-88.9%]. Compared to participants who perceived that the informed consent information is understandable (OR=0.10, CI [0.03-0.32], participants who either partly or totally disagreed were significantly less likely to perceive information as understandable (OR=0.27, CI [0.15-0.46]. 226 out of 431 respondents that accepted storage of biological materials and data, majority (61.7%) preferred to receive feedback on results of relevance to their health. Conclusion: Acceptance of broad consent for storage of biological materials and data for future research purposes was high among HCUs. A shortened and simplified ICF may trigger discussions between participants and health care workers hence increase research participant understanding of study related materials in biobanking. This in turn could enrich ethically collected biobank resources for future research of public health relevance.

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.

AbstractInvestment in Africa over the past year with regards to SARS-CoV-2 genotyping has led to a massive increase in the number of sequences, exceeding 100,000 genomes generated to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence within their own borders, coupled with a decrease in sequencing turnaround time. Findings from this genomic surveillance underscores the heterogeneous nature of the pandemic but we observe repeated dissemination of SARS-CoV-2 variants within the continent. Sustained investment for genomic surveillance in Africa is needed as the virus continues to evolve, particularly in the low vaccination landscape. These investments are very crucial for preparedness and response for future pathogen outbreaks.One-Sentence SummaryExpanding Africa SARS-CoV-2 sequencing capacity in a fast evolving pandemic.

Here, we report SARS-CoV-2 genomic surveillance from March 2020 until January 2021 in Uganda, a landlocked East African country with a population of approximately 40 million people. We report 322 full SARS-CoV-2 genomes from 39,424 reported SARS-CoV-2 infections, thus representing 0.8% of the reported cases. Phylogenetic analyses of these sequences revealed the emergence of lineage A.23.1 from lineage A.23. Lineage A.23.1 represented 88% of the genomes observed in December 2020, then 100% of the genomes observed in January 2021. The A.23.1 lineage was also reported in 26 other countries. Although the precise changes in A.23.1 differ from those reported in the first three SARS-CoV-2 variants of concern (VOCs), the A.23.1 spike-protein-coding region has changes similar to VOCs including a change at position 613, a change in the furin cleavage site that extends the basic amino acid motif and multiple changes in the immunogenic N-terminal domain. In addition, the A.23.1 lineage has changes in non-spike proteins including nsp6, ORF8 and ORF9 that are also altered in other VOCs. The clinical impact of the A.23.1 variant is not yet clear and it has not been designated as a VOC. However, our findings of emergence and spread of this variant indicate that careful monitoring of this variant, together with assessment of the consequences of the spike protein changes for COVID-19 vaccine performance, are advisable.

Introductory paragraph SARS-CoV-2 genomic surveillance in Uganda provides an opportunity to provide a focused description of the virus evolution in a small landlocked East African country. Here we show a recent shift in the local epidemic with a newly emerging lineage A.23 evolving into A.23.1 which is now dominating the Uganda cases and has spread to 26 other countries. Although the precise changes in A.23.1 as it has adapted are different from the changes in the variants of concern (VOC), the evolution shows convergence on a similar set of proteins. The A.23.1 spike protein coding region has accumulated changes that resemble many of the changes seen in VOC including a change at position 613, a change in the furin cleavage site that extends the basic amino acid motif, and multiple changes in the immunogenic N-terminal domain. In addition, the A.23.1lineage encodes changes in non-spike proteins that other VOC show (nsp6, ORF8 and ORF9). The clinical impact of the A.23.1 variant is not yet clear, however it is essential to continue careful monitoring of this variant, as well as rapid assessment of the consequences of the spike protein changes for vaccine efficacy.

The progression of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in Africa has so far been heterogeneous, and the full impact is not yet well understood. In this study, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations predominantly from Europe, which diminished after the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1, and C.1.1. Although distorted by low sampling numbers and blind spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a source for new variants.

AbstractBackgroundGlobally response to the SARS-CoV-2 pandemic is highly limited by diagnostic methods. Currently, World Health Organization (WHO) recommends the use of molecular assays for confirmation of SARS-CoV-2 infection which are highly expensive and require specialized laboratory equipment. This is a limitation in mass testing and in low resource settings. SARS CoV-2 IgG/IgM antibody tests have had poor diagnostic performance that do not guarantee their use in diagnostics. In this study we demonstrate a concept of using a combination of RDTs in an algorithm to improve their performance for diagnostics.MethodEighty six (86) EDTA whole blood samples were collected from SARS-CoV-2 positive cases admitted at Masaka and Mbarara Regional Referral Hospitals in Uganda. These were categorized from day when confirmed positive as follows; category A (0-3 days, 10 samples), category B (4-7 days, 20 samples), Category C (8-17 days, 11 samples) and Category D (18-28 days, 20 samples). Plasma was prepared, transported to the testing laboratory and stored at −200C prior to testing. A total of 13 RDTS were tested following manufacturer’s instructions. Data was entered in Microsoft Excel exported to STATA for computation of sensitivity and specificity. We computed for all possible combinations of 2 of the 13 RDTS (13C2) that were evaluated in parallel algorithm.ResultsThe individual sensitives of the RDTs ranged between 74% and 18% and there was a general increasing trend across the categories with days since PCR confirmation. A total of 78 possible combinations of the RDTs to be used in parallel was computated. The combinations of the 2 RDTS improved the sensitivities to 90%.DiscussionWe demonstrate that use of RDTs in combinations can improve their overall sensitivity. This approach when used on a wider range of combination of RDTs may yield combinations that can give sensitivities that are of diagnostics relevance in mass testing and low resource setting.

Background: In the last decade, Low- and Middle-Income Countries (LMICs) have set up Biobanks to collect human biological materials and associated data for genomic research and public health purposes. Biobanking gives rise to ethical challenges, such as informed consent, benefit sharing, confidentiality, ownership, commercialization and public participation which are harder to navigate in LMIC settings due to disparities in research infrastructure and capacity. This paper summarizes presentations on Biobank related case studies from two countries, with a focus on challenges in the regulatory and governance framework and suggestions on how to mitigate them. Methods: Two case studies of Biobanks from LMICs have been used. The case studies were presented at the 2018 Global Forum on Bioethics in Research (GFBR) meeting on the “Ethics of data sharing and Biobanking in health research”. Results: The case studies show that an integrated, well-regulated platform for human biological materials and data ensures good quality of human biological materials, saves resources and promotes mutual collaboration of work among researchers. National regulatory bodies are required to generate Biobanking guidelines and policies to facilitate guidance to the rapidly changing landscape of science. Discussion: In general, LMICs have weaker research regulatory infrastructure and governance mechanisms for Biobanks than high-income countries. This has increased the fear of exploitation i.e. unfair distribution of risks and benefits. Establishment of Biobanks and producing effective scientific outcomes based on the Biobanking resources is difficult without a proper legislative, regulatory and governance framework. Conclusion: These two case studies from different LMICs settings show that although in both settings there is strong awareness of the scientific and population health value of Biobanks and strong commitment to their establishment, regulatory and ethical guidance show gaps that need to be addressed.