Genomic Epidemiology of Rift Valley Fever Virus Involved in the 2018 and 2022 Outbreaks in Livestock in Rwanda
Author:
Nsengimana Isidore1234ORCID, Juma John5ORCID, Roesel Kristina5ORCID, Gasana Methode N.6, Ndayisenga Fabrice6, Muvunyi Claude M.7, Hakizimana Emmanuel7ORCID, Hakizimana Jean N.2ORCID, Eastwood Gillian4ORCID, Chengula Augustino A.1, Bett Bernard5, Kasanga Christopher J.1, Oyola Samuel O.5ORCID
Affiliation:
1. Department of Veterinary Microbiology, Parasitology and Biotechnology, Sokoine University of Agriculture, Morogoro P.O. Box 3000, Tanzania 2. SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture, Morogoro P.O. Box 3297, Tanzania 3. Rwanda Inspectorate, Competition and Consumer Protection Authority, Kigali P.O. Box 375, Rwanda 4. Department of Entomology, and Center for Emerging Zoonotic & Arthropod-Borne Pathogens (CeZAP), Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA 5. International Livestock Research Institute (ILRI), Nairobi P.O. Box 30709, Kenya 6. Department of Animal Resource Research and Technology Transfer, Rwanda Agriculture and Animal Resources Development Board (RAB), Huye P.O. Box 5016, Rwanda 7. Rwanda Biomedical Center (RBC), Kigali P.O. Box 7162, Rwanda
Abstract
Rift Valley fever (RVF), a mosquito-borne transboundary zoonosis, was first confirmed in Rwanda’s livestock in 2012 and since then sporadic cases have been reported almost every year. In 2018, the country experienced its first large outbreak, which was followed by a second one in 2022. To determine the circulating virus lineages and their ancestral origin, two genome sequences from the 2018 outbreak, and thirty-six, forty-one, and thirty-eight sequences of small (S), medium (M), and large (L) genome segments, respectively, from the 2022 outbreak were generated. All of the samples from the 2022 outbreak were collected from slaughterhouses. Both maximum likelihood and Bayesian-based phylogenetic analyses were performed. The findings showed that RVF viruses belonging to a single lineage, C, were circulating during the two outbreaks, and shared a recent common ancestor with RVF viruses isolated in Uganda between 2016 and 2019, and were also linked to the 2006/2007 largest East Africa RVF outbreak reported in Kenya, Tanzania, and Somalia. Alongside the wild-type viruses, genetic evidence of the RVFV Clone 13 vaccine strain was found in slaughterhouse animals, demonstrating a possible occupational risk of exposure with unknown outcome for people working in meat-related industry. These results provide additional evidence of the ongoing wide spread of RVFV lineage C in Africa and emphasize the need for an effective national and international One Health-based collaborative approach in responding to RVF emergencies.
Funder
German Federal Ministry of Economic Cooperation and Development Regional Scholarship and Innovation Fund of the African Partnership for Skills in Applied Sciences, Engineering, and Technology Global Health EDCTP3 Joint Undertaking
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