Unreported Rift Valley fever virus circulation during 2023–2024 El Niño event detected by slaughterhouse-based surveillance in southern Kenya

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.