Most African countries have recorded relatively lower COVID-19 burdens than Western countries. This has been attributed to early and strong political commitment and robust implementation of public health measures, such as nationwide lockdowns, travel restrictions, face mask wearing, testing, contact tracing, and isolation, along with community education and engagement. Other factors include the younger population age strata and hypothesized but yet-to-be confirmed partially protective cross-immunity from parasitic diseases and/or other circulating coronaviruses. However, the true burden may also be underestimated due to operational and resource issues for COVID-19 case identification and reporting. In this perspective article, we discuss selected best practices and challenges with COVID-19 contact tracing in Nigeria, Rwanda, South Africa, and Uganda. Best practices from these country case studies include sustained, multi-platform public communications; leveraging of technology innovations; applied public health expertise; deployment of community health workers; and robust community engagement. Challenges include an overwhelming workload of contact tracing and case detection for healthcare workers, misinformation and stigma, and poorly sustained adherence to isolation and quarantine. Important lessons learned include the need for decentralization of contact tracing to the lowest geographic levels of surveillance, rigorous use of data and technology to improve decision-making, and sustainment of both community sensitization and political commitment. Further research is needed to understand the role and importance of contact tracing in controlling community transmission dynamics in African countries, including among children. Also, implementation science will be critically needed to evaluate innovative, accessible, and cost-effective digital solutions to accommodate the contact tracing workload.

Background: Traditional infectious disease surveillance systems face significant limitations, including delayed detection, underreporting of asymptomatic cases, and inequitable health care access. Wastewater-based epidemiology (WBE), enhanced with genomic analysis, offers a noninvasive and cost-effective alternative for early pathogen detection and variant characterization, particularly valuable for monitoring international disease transmission. Objective: This study aimed to implement and evaluate a genomics-enhanced WBE surveillance system for detecting and characterizing SARS-CoV-2 variants among international travelers at the Kigali International Airport, Rwanda, and to assess its potential as an early warning system for pandemic preparedness. Methods: Between May and December 2023, we collected wastewater samples from international flights arriving at the Kigali International Airport under Rwanda’s National One Health strategy. Molecular detection was performed using polymerase chain reaction (PCR) assays, followed by whole-genome sequencing of positive samples. Bioinformatics analysis included quality assessment with Nanoplot (version 1.41.6), genome mapping using minimap2 (version 2.26), and lineage identification using the Freyja tool (version 1.4.5). Spatial and temporal analyses were used to identify transmission patterns and variant origins. Results: Of 630 wastewater samples collected from flights originating from 9 countries, 603 were successfully processed, with 21% (132/617) testing positive for SARS-CoV-2. Whole-genome sequencing was conducted on 33 samples, yielding an average viral sequence depth of 1250 reads with 92% genome coverage (range 78%‐97%). Genomic analysis identified 7 SARS-CoV-2 variants, including Omicron subvariants XBB.1.5, XBB.1.16.6 (eg, 5.1), GE.1, and FE.1.1.1. Notably, 70% (23/33) of sequenced samples could not be assigned to existing lineages, suggesting potential novel variants. Most samples came from Qatar (21.4%, 135/1630), the United Arab Emirates (19.5%, 123/1630), and the United Kingdom (19.4%, 122/1630). Positive samples were detected from 11 countries, with variants frequently found in flights from the United Kingdom, France, Belgium, Kenya, Tanzania, and South Africa. Sample collection capacity increased from 6 in week 1 to 33 by week 27. SARS-CoV-2 positivity rates showed seasonal variation, with a marked decline in June-July 2023. Conclusions: Genomics-enhanced WBE demonstrated a high sensitivity for the early detection of SARS-CoV-2 variants among international travelers, including potential novel variants undetectable through traditional surveillance. Its noninvasive and cost-effective nature, combined with the ability to generate population-level epidemiological insights, makes it particularly suitable for resource-limited settings. This approach supports Rwanda’s National One Health strategy and offers a scalable model for advancing global health security in Sub-Saharan Africa through innovative surveillance tools.

Background: Ebola Virus Disease (EVD) is a severe and often fatal illness that affects humans and has significant public health implications, including high mortality rates, strain on healthcare systems, and social and economic disruption. On 20 September 2022, Uganda declared an Ebola disease outbreak caused by the Sudan ebolavirus species. The neighboring countries of Uganda were classified by World Health Organization (WHO) as being at high risk of Sudan Ebola Virus Disease (SUDV) importation. The country of Rwanda implemented different sustainable strategies and activities to prepare and ensure a timely and effective response to SUDV outbreaks once it has arrived in the country. We aimed to highlight the sustainable strategies and activities implemented for SUDV preparedness and the subsequent lessons learnt in Rwanda. Methods: This paper reviewed the documentation on activities implemented for SUDV preparedness, with a focus on lessons learned from different countries. The paper analyzed the common themes and highlighted the key components of EVD preparedness in Rwanda after declaration of SUDV outbreak in Uganda. Results: The key components of SUDV preparedness include its readiness assessment in Rwanda, effective coordination, collaboration and leadership mechanisms, enhancing the early detection and surveillance system, effective risk communication and community engagement, capacity building of healthcare providers on case management and infection prevention and control (IPC), and continual preparedness. These components were essential to ensure timely and effective preparation and response to SUDV related outbreaks. Conclusion: A multi-sectoral approach involving all stakeholders was necessary to ensure timely and effective preparation and response. Continuous investment in preparedness, strengthening of health systems, and the review of preparedness components provided insights into the best practices for SUDV preparedness, which were essential to prevent future outbreaks and minimize their impact. This will inform other countries about the role of timely development of preparedness plans.

The burden of bacterial bloodstream infections (BSIs) is rapidly increasing in Africa including Rwanda. This is a retrospective study investigates the diversity, distribution, and antimicrobial susceptibility profiles of BSIs bacteria in three tertiary referral hospitals in Rwanda between 2020 and 2022. A total of 1,532 blood culture tests were performed for visiting patients. Overall, the proportions of Gram-negative and Gram-positive bacteria were 48.2% and 51.8, respectively. Staphylococcus aureus was the predominant species accounting for 25% of all Gram-positive BSIs species and Klebsiella species representing 41% of all Gram-negative BSIs species. Antimicrobial susceptibility testing revealed that Amikacin exhibited the highest activity against Enterobacter spp., Serratia spp. and Escherichia coli in >92% of cases and Klebsiella spp. in 75.7%. Meropenem and Imipenem were highly efficacious to Salmonella spp. (100% susceptibility), Enterobacter spp. (96.2% and 91.7%, respectively), and Escherichia coli (94.7% and 95.5%, respectively). The susceptibility of Enterococcus spp., S. aureus, and Streptococcus spp. to Vancomycin was 100%, 99.5% and 97.1%, respectively. Klebsiella spp. was highly sensitive to Colistin (98.7%), Polymyxin B (85.6%), Imipenem (84.9%), and Meropenem (78.5%). We recommend strengthening the implementation of integrated transdisciplinary and multisectoral One Health including AMR-stewardship for the surveillance, prevention, and control of AMR in Rwanda.

Rwanda’s health security can only be strengthened through integrated One Health approaches that link human, animal, and environmental health. Emergin