Genomic Epidemiology of Rift Valley Fever Virus Involved in the 2018 and 2022 Outbreaks in Livestock in Rwanda
Isidore Nsengimana,
John Juma,
Kristina Roesel,
Methode N. Gasana,
Fabrice Ndayisenga,
Claude M. Muvunyi,
Emmanuel Hakizimana,
Jean N. Hakizimana,
Gillian Eastwood,
Augustino A. Chengula,
Bernard Bett,
Christopher J. Kasanga,
Samuel O. Oyola
Affiliations
Isidore Nsengimana
Department of Veterinary Microbiology, Parasitology and Biotechnology, Sokoine University of Agriculture, Morogoro P.O. Box 3000, Tanzania
John Juma
International Livestock Research Institute (ILRI), Nairobi P.O. Box 30709, Kenya
Kristina Roesel
International Livestock Research Institute (ILRI), Nairobi P.O. Box 30709, Kenya
Methode N. Gasana
Department of Animal Resource Research and Technology Transfer, Rwanda Agriculture and Animal Resources Development Board (RAB), Huye P.O. Box 5016, Rwanda
Fabrice Ndayisenga
Department of Animal Resource Research and Technology Transfer, Rwanda Agriculture and Animal Resources Development Board (RAB), Huye P.O. Box 5016, Rwanda
Claude M. Muvunyi
Rwanda Biomedical Center (RBC), Kigali P.O. Box 7162, Rwanda
Emmanuel Hakizimana
Rwanda Biomedical Center (RBC), Kigali P.O. Box 7162, Rwanda
Jean N. Hakizimana
SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture, Morogoro P.O. Box 3297, Tanzania
Gillian Eastwood
Department of Entomology, and Center for Emerging Zoonotic & Arthropod-Borne Pathogens (CeZAP), Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
Augustino A. Chengula
Department of Veterinary Microbiology, Parasitology and Biotechnology, Sokoine University of Agriculture, Morogoro P.O. Box 3000, Tanzania
Bernard Bett
International Livestock Research Institute (ILRI), Nairobi P.O. Box 30709, Kenya
Christopher J. Kasanga
Department of Veterinary Microbiology, Parasitology and Biotechnology, Sokoine University of Agriculture, Morogoro P.O. Box 3000, Tanzania
Samuel O. Oyola
International Livestock Research Institute (ILRI), Nairobi P.O. Box 30709, Kenya
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.
