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bioRxiv · 10.64898/2026.06.04.730228

Persistent circulation of Rift Valley fever virus lineage C in Rwanda, 2022-2025

Udahemuka, J. C.·Cassidy, H.·Schuele, L.·Uwibambe, E.·Ngabo, M. G.·Masirika, L. M.·Otani, S.·Gashegu, M.·Twizere, J. C.·Aarestrup, F.·Ndayisenga, F.·Munnink, B. B. O.·Koopmans, M. P. G.·Ndishimye, P.
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Abstract

Rwanda has experienced recurrent Rift Valley fever virus outbreaks in the last decade. In this study, we investigated whether these outbreaks resulted from repeated introductions or sustained local circulation. We generated RVFV whole-genome sequences from livestock samples collected between 2022 and 2025 using Nanopore sequencing. Genomic analyses indicated the outbreaks resulted from sustained local circulation of lineage C rather than repeated introductions, suggesting ongoing transmission likely driven by sporadic spillover. This study underscores the importance of continuous genomic surveillance in endemic settings.

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Udahemuka, J. C., Cassidy, H., Schuele, L., Uwibambe, E., Ngabo, M. G., Masirika, L. M., Otani, S., Gashegu, M., Twizere, J. C., Aarestrup, F., Ndayisenga, F., Munnink, B. B. O., Koopmans, M. P. G., Ndishimye, P.. 2026-06-05. Persistent circulation of Rift Valley fever virus lineage C in Rwanda, 2022-2025. https://doi.org/10.64898/2026.06.04.730228

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