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.

Ethiopia is the second most populous country in Africa and the sixth most affected by COVID-19 on the continent. Despite having experienced five infection waves, >499,000 cases, and ~7500 COVID-19-related deaths as of January 2023, there is still no detailed genomic epidemiological report on the introduction and spread of SARS-CoV-2 in Ethiopia. In this study, we reconstructed and elucidated the COVID-19 epidemic dynamics. Specifically, we investigated the introduction, local transmission, ongoing evolution, and spread of SARS-CoV-2 during the first four infection waves using 353 high-quality near-whole genomes sampled in Ethiopia. Our results show that whereas viral introductions seeded the first wave, subsequent waves were seeded by local transmission. The B.1.480 lineage emerged in the first wave and notably remained in circulation even after the emergence of the Alpha variant. The B.1.480 was outcompeted by the Delta variant. Notably, Ethiopia’s lack of local sequencing capacity was further limited by sporadic, uneven, and insufficient sampling that limited the incorporation of genomic epidemiology in the epidemic public health response in Ethiopia. These results highlight Ethiopia’s role in SARS-CoV-2 dissemination and the urgent need for balanced, near-real-time genomic sequencing.

Background: Biomedical wastes (BMWs) generated from medical laboratories are hazardous and can endanger both humans and the environment. Highly infectious biomedical wastes are produced at an unacceptably high rate from health laboratories in developing countries with poor management systems, such as Ethiopia. The purpose of this study was to assess the rate of biomedical waste generation, management practices, and associated factors in public healthcare medical laboratories in Addis Ababa, Ethiopia. Materials and methods: From July 13 to September 25, 2020, a health institution-based cross-sectional study was conducted in 6 hospital laboratories and 20 health centres laboratories in Addis Ababa, Ethiopia. Data on socio-demographic characteristics, knowledge and practice of biomedical waste management and generation rate were collected d in health facilities using pre tested data collection tools. SPSS version 20 was used to manage the data. To identify independent predictors of the dependent variable, descriptive statistics, Pearson correlation, linear, and logistic regression analysis were used. The strength of the association was determined using an odds ratio with a 95% confidence interval. Results: In this study, the mean ± SD daily generation rate of biomedical wastes was 4.9 ± 3.13 kg/day per medical laboratory. Nineteen medical laboratories (74.3%) had proper biomedical waste management practice, which is significantly associated with professionals’ knowledge of biomedical waste management policies and guidelines, the availability of separate financial sources for biomedical waste management, and the level of training of professionals. Conclusion: The study found that medical laboratories in Addis Ababa’s public healthcare facilities generate a significant amount of biomedical waste. Nearly two-thirds of hospitals performed proper waste segregation, collection, storage, and treatment procedures for biomedical waste generated in their laboratories. However, there was a poor transportation and disposal method. As a result, paying special attention and implementing the current national guidelines for biomedical waste management is recommended.

Purpose: Rapid severe acute respiratory syndrome coronavirus 2 test kits are crucial for bridging diagnostic gaps in health facilities and community screening mainly in resource limited settings. However, there is no objective evidence on their diagnostic performance. Thus, the study aimed to evaluate comparative diagnostic performance of three selected SARS-CoV-2 IgG/IgM rapid test kits in Ethiopia. Methods: A cross-sectional study was conducted among 200 clients between May and July 2020 in Addis Ababa, Ethiopia. The performance of three SARS-CoV-2 rapid test kits EGENE, CTK BIOTECKs Onsite, and ACON Biotech were evaluated using blood specimens against RT-PCR on respiratory swabs. Sensitivity, specificity, and agreement with each other and to RT-PCR were computed using Vassarstats, MedCalc and SPSS version 23 statistical software. Results: Test kits showed a heterogeneous comparative diagnostic performance in their sensitivity and specificity. The sensitivity was 61.18% (95% CI: 49.96– 71.37%), 74.12% (95% CI: 63.28– 82.74%) and 83.53% (95% CI: 73.57– 90.38%) for kit A, B and C, respectively. Similarly, the specificity was 96.52% (90.81– 98.88%), 94.78% (88.52– 97.86%) and 94.78% (88.52– 97.86%) for test kit A, B and C, respectively. The test kits have an agreement with RT-PCR with kappa value of 0.60 (0.48– 0.83), 0.71 (0.65– 0.93), and 0.80 (0.76– 1.04) for A, B, and C, respectively. There was a significant difference on diagnostic performance among the three test kits and PCR with a p-value < 0.001 Cochran’s Q test. Conclusion: The diagnostic performance of the test kits was promising and recommended for COVID-19 diagnostics in combination with RT-PCR to detect more infected patients. It allows determining the seroprevalence of the virus and true extent of SARS-COV-2 community spread in resource limited settings. We underline countries to evaluate rapid diagnostic test kits before diagnostic use.

Background: COVID-19 is an ongoing public health pandemic regardless of the countless efforts made by various actors. Quality diagnostic tests are important for early detection and control. Notably, several commercially available one step RT-PCR based assays have been recommended by the WHO. Yet, their analytic and diagnostic performances have not been well documented in resource-limited settings. Hence, this study aimed to evaluate the diagnostic sensitivities and specificities of three commercially available one step reverse transcriptase-polymerase chain reaction (RT-PCR) assays in Ethiopia in clinical setting. Methods: A cross-sectional study was conducted from April to June, 2021 on 279 respiratory swabs originating from community surveillance, contact cases and suspect cases. RNA was extracted using manual extraction method. Master-mix preparation, amplification and result interpretation was done as per the respective manufacturer. Agreements between RT-PCRs were analyzed using kappa values. Bayesian latent class models (BLCM) were fitted to obtain reliable estimates of diagnostic sensitivities, specificities of the three assays and prevalence in the absence of a true gold standard. Results: Among the 279 respiratory samples, 50(18%), 59(21.2%), and 69(24.7%) were tested positive by TIB, Da An, and BGI assays, respectively. Moderate to substantial level of agreement was reported among the three assays with kappa value between 0 .55 and 0.72. Based on the BLCM relatively high specificities (95% CI) of 0.991(0.973–1.000), 0.961(0.930–0.991) and 0.916(0.875–0.952) and considerably lower sensitivities with 0.813(0.658–0.938), 0.836(0.712–0.940) and 0.810(0.687–0.920) for TIB MOLBIOL, Da An and BGI respectively were found. Conclusions: While all the three RT-PCR assays displayed comparable sensitivities, the specificities of TIB MOLBIOL and Da An were considerably higher than BGI. These results help adjust the apparent prevalence determined by the three RT-PCRs and thus support public health decisions in resource limited settings and consider alternatives as per their prioritization matrix.

The SARS-CoV-2 genome occupies a unique place in infection biology – it is the most highly sequenced genome on earth (making up over 20% of public sequencing datasets) with fine scale information on sampling date and geography, and has been subject to unprecedented intense analysis. As a result, these phylogenetic data are an incredibly valuable resource for science and public health. However, the vast majority of the data was sequenced by tiling amplicons across the full genome, with amplicon schemes that changed over the pandemic as mutations in the viral genome interacted with primer binding sites. In combination with the disparate set of genome assembly workflows and lack of consistent quality control (QC) processes, the current genomes have many systematic errors that have evolved with the virus and amplicon schemes. These errors have significant impacts on the phylogeny, and therefore over the last few years, many thousands of hours of researchers time has been spent in “eyeballing” trees, looking for artefacts, and then patching the tree. Given the huge value of this dataset, we therefore set out to reprocess the complete set of public raw sequence data in a rigorous amplicon-aware manner, and build a cleaner phylogeny. Here we provide a global tree of 4,471,579 samples, built from a consistently assembled set of high quality consensus sequences from all available public data as of June 2024, viewable at https://viridian.taxonium.org . Each genome was constructed using a novel assembly tool called Viridian ( https://github.com/iqbal-lab-org/viridian ), developed specifically to process amplicon sequence data, eliminating artefactual errors and mask the genome at low quality positions. We provide simulation and empirical validation of the methodology, and quantify the improvement in the phylogeny. We hope the tree, consensus sequences and Viridian will be a valuable resource for researchers.