Abstract
Rift Valley fever (RVF) is a zoonotic arbovirus, and livestock cases are often underreported in endemic countries due to reliance on passive clinical surveillance. During the 2023–2024 El Niño event, Kenya experienced widespread flooding, but no RVF outbreaks were reported in the southern regions. We implemented slaughterhouse-based surveillance in southern Kenya from May 2023—June 2024, using five consecutive cross-sectional surveys. Cattle, sheep, and goats were tested for anti-RVFV IgG and IgM antibodies, with concurrent recording of post-mortem lesions. Using age estimates from dentition, catalytic models estimated the force of infection (FOI) over time and spatial analysis assessed the Loitokitok sub-county for hotspots. Among 955 animals, 10.2% were IgG-positive, with seroprevalence and FOI increasing after El Niño rains, reaching 22.6% by May 2024. Six animals (0.6%) were IgM-positive, indicating recent infection, with cases detected in 3/5 sampling periods, including before the rains. All recently infected IgM-positive animals were deemed fit for slaughter and none had lesions. Adult animals in endemic areas, void of clinical and pathological signs, may therefore play a role in the silent spread and maintenance of RVFV. Slaughterhouse-based surveillance offers a practical and scalable platform for improving RVF detection and monitoring livestock in endemic regions.
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Data availability
The dataset used to generate this analysis is available at https://doi.org/10.5281/zenodo.17078167. Other associated data, including the georeferenced locations, is available on reasonable request by writing to the corresponding author.
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Acknowledgements
We thank the slaughterhouse employees for accommodating our sampling within their routines. We also appreciate the owners of the livestock for allowing us to sample their animals and time providing the origin information. We are grateful to Mr Issac Nayayio, Mr. James Kayiaa, Ms. Cecelia Parsae, and Ms. Terry (Ivey) Lekanayi for their contributions to sampling and laboratory work. We also thank Ms. Elly Wallis, Programme Manager of the Liverpool-Wellcome Clinical PhD Fellowship, for her invaluable logistical support.
Funding
This study has been funded by KNG’s Liverpool—Wellcome Trust Clinical PhD fellowship [223502/Z/21/Z]. Field activities also benefited from support of the “Loitoktiok One Health Initiative”, which was part of the CGIAR Initiative on One Health, supported by contributors to the CGIAR Trust Fund (https://www.cgiar.org/funders).
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K.N.G, E.M.F, M.B, and AS conceived the study. Methodology was developed by K.N.G, V.M, M.B, E.M.F, A.S, E.A.J.C, and F.S. V.M, A.R, and R.R.O curated the data. Formal analysis, including laboratory work, was carried out by K.N.G, A.K, and R.M. K.N.G developed the software and prepared the visualizations. K.N.G wrote the original draft of the manuscript, and all authors reviewed and edited the manuscript. E.M.F, M.B, and A.S supervised the work. Funding was acquired by K.N.G. Project administration was managed by K.N.G, R.R.O, and A.R. Resources were provided by E.M.F. M.B was responsible for validation.
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Gerken, K.N., Rereu, A., Mutai, V. et al. Unreported Rift Valley fever virus circulation during 2023–2024 El Niño event detected by slaughterhouse-based surveillance in southern Kenya. Sci Rep (2026). https://doi.org/10.1038/s41598-026-44706-y
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DOI: https://doi.org/10.1038/s41598-026-44706-y
