Abstract
The emergence of variants in the wake of the COVID-19 pandemic has put a strain on healthcare systems in Africa. The Afroscreen project is strengthening national sentinel surveillance systems, combined with sequencing capabilities to identify potentially highly virulent variants of interest at an early stage. The aim of this article is to present the results of this project and discuss the related challenges. Surveillance was based on national surveillance sentinel systems, either hospital-based or peripheral, and RT-PCR diagnostic capabilities, coupled with sequencing in the event of positivity, from July 2022 to June 2024. In 11 African countries (Senegal, Guinea, Côte d’Ivoire, Togo, Benin, Niger, Cameroon, the Central African Republic (CAR), Burkina Faso, Madagascar and the Democratic Republic of the Congo), it was possible to demonstrate a decline in the circulation of SARS-CoV-2 over the surveillance period, with only the Omicron variant circulating. Setting up and coordinating a multicountry sentinel surveillance system during a pandemic period is a real challenge. This highlights the need to strengthen surveillance systems during interepidemic and pandemic periods and the question of their sustainability in line with emerging disease preparedness and response programs.
Data availability
The data are provided within the manuscript or supplementary information files.The datasets generated and analyzed during the current study are available in the Zenodo repository: [https://zenodo.org/records/15050557].Concerning SARS-CoV-2 sequencing, no new data were analyzed in this study. Data sharing about sequencing is not applicable to this article. SARS-CoV-2 genomes analyzed by Afroscreen partners (On 17th December 2025, n=10957; [https://www.afroscreen.org/en/sequence-data-management-and-sharing/]) are available on the global initiative on sharing avian influenza data (GISAID) database [https://gisaid.org/].
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Acknowledgements
We would like to thank members from the AFROSCREEN project (https://www.afroscreen.org/en/network/) for their work and support on genomic surveillance in Africa.
Funding
This work was supported by Agence Française de Développement through the AFROSCREEN project (grant agreement CZZ3209), coordinated by ANRS | Maladies infectieuses émergentes in partnership with Institut Pasteur and IRD.
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Concept, design, protocol writing: VR and MA. Epidemiological data collection: KJJOK, RHL, PH, MCT, ITi, RR, SC, JN, MAB, RK and ITr. Technical support and coordination: JP, EG, VR and MA. Epidemiological data cleaning, analysis and drafting of the manuscript: JP, VR and MA. Manuscript revision: KJJOK, RHL, PH, ITrAll the authors read and approved the final manuscript.
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All experimental protocols were approved by a named institutional and/or licensing committee. Although surveillance data were used, requests for ethics committees were made in each country: Le Comité National d’Ethique pour la Recherche en Santé (CNERS) in Benin (n°82/MS/DC/SGM/CNERS/SA), le Comité d’éthique pour la recherche en santé (CERS) in Burkina Faso (CERS-2022-04-74), le Comité national d’éthique pour la protection des personnes dans la recherche medical (CRERSHC) in Cameroon (CE n°00360/CRERSHC/2022), le Comité Scientifique de Validation des Protocoles et Résultats de la Recherche en Santé (CSVPRS) in Central African Republic (n°09/UB/FACSS/IPB/CES/2022), le Comité National d’Ethique des Sciences de la Vie et de la Santé (CNESVS) in Côte d’Ivoire (n°035 − 22/MSHPCMU/CNESVS-km), le Comité National de l’Éthique de la Santé (CE) in Democratic Republic of Congo (ESP/CE/47/2025), le comité national d’éthique pour la recherche en santé (CNERS) in Guinea (n°199/CNERS/23), the National Biomedical Research Ethics Committee (CERBM) in Madagascar (n°13/MSANP/SG/AMM/CERBM), le Comité National Ethique pour la Recherche en Santé (CNERS) in Niger (n°020/2022/CNERS), le Comité National Ethique pour la Recherche en Santé (CNERS) Senegal (032/MSAS/CNERS/SP) and le Comité de Bioéthique pour la Recherche en Santé (CBRS) Togo (018/2022/CBRS). Informed consent was obtained from all subjects and/or their legal guardian(s).
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Poublan, J., Kadio, K.JJ.O., Konu, R. et al. Challenges in strengthening sentinel surveillance network during COVID-19 pandemic in Africa. Sci Rep (2026). https://doi.org/10.1038/s41598-026-36363-y
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DOI: https://doi.org/10.1038/s41598-026-36363-y
