Submission ID 131905
| Issue/Objective | Rift Valley fever virus (RVFV) is a priority zoonotic pathogen with epidemic potential in Africa. Rwanda has experienced repeated RVF outbreaks since 2012, including major events in 2022, 2024, and 2025. Whether these outbreaks reflect repeated introductions or sustained endemic circulation remains unclear, limiting effective preparedness. |
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| Methodology/Approach | We performed genomic surveillance of RVFV from livestock in Rwanda between 2022 and 2025. PCR-positive samples from cattle, sheep, and goats were sequenced using Oxford Nanopore Technologies through metagenomic and amplicon-based approaches. We generated 55 RVFV genome segments (≥80% coverage), including nine near-complete genomes, and conducted time-resolved phylogenetic analyses of all three genome segments using the Nextstrain pipeline. |
| Results | All sequences clustered within RVFV lineage C and formed a well-supported clade with viruses from the 2022 outbreak, with a most recent common ancestor dated to 2021-2022. Viruses from the 2024 outbreak clustered closely with 2022 sequences, indicating sustained local transmission following a single introduction. Sequences from 2025 formed multiple sub-clusters, consistent with sporadic spillover events or low-level persistence rather than emergence of a novel lineage. No clustering with vaccine strains or recent West African outbreaks was observed. |
| Discussion/Conclusion | Our findings provide genomic evidence of persistent RVFV circulation in Rwanda despite large-scale vaccination campaigns, highlighting the critical role of real-time genomic surveillance for epidemic preparedness and control. |
| Presenters and Affiliations | Pacifique Ndishimye Stansile Jean Claude Udahemuka Stansile & University of Rwanda Audace Mukiza Stansile & Gihundwe District Hospital Evodie Uwibambe Rwanda Agriculture and Animal Resources Development Board Leandre Murhula Masirika Congo Outbreaks, Research for Development Fabrice Ndayisenga Rwanda Agriculture and Animal Resources Development Board Marion Koopmans Erasmus University Medical Center |
