{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T18:17:53Z","timestamp":1790619473098,"version":"4.1.0"},"reference-count":82,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2024,7,17]],"date-time":"2024-07-17T00:00:00Z","timestamp":1721174400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"German Federal Ministry of Economic Cooperation and Development","award":["101103171"],"award-info":[{"award-number":["101103171"]}]},{"name":"Regional Scholarship and Innovation Fund of the African Partnership for Skills in Applied Sciences, Engineering, and Technology (PASET-RSIF)","award":["101103171"],"award-info":[{"award-number":["101103171"]}]},{"name":"Global Health EDCTP3 Joint Undertaking","award":["101103171"],"award-info":[{"award-number":["101103171"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Rift Valley fever (RVF), a mosquito-borne transboundary zoonosis, was first confirmed in Rwanda\u2019s 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.<\/jats:p>","DOI":"10.3390\/v16071148","type":"journal-article","created":{"date-parts":[[2024,7,17]],"date-time":"2024-07-17T08:48:29Z","timestamp":1721206109000},"page":"1148","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":20,"title":["Genomic Epidemiology of Rift Valley Fever Virus Involved in the 2018 and 2022 Outbreaks in Livestock in Rwanda"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0009-0005-0586-3029","authenticated-orcid":false,"given":"Isidore","family":"Nsengimana","sequence":"first","affiliation":[{"name":"Department of Veterinary Microbiology, Parasitology and Biotechnology, Sokoine University of Agriculture, Morogoro P.O. Box 3000, Tanzania"},{"name":"SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture, Morogoro P.O. Box 3297, Tanzania"},{"name":"Rwanda Inspectorate, Competition and Consumer Protection Authority, Kigali P.O. Box 375, Rwanda"},{"name":"Department of Entomology, and Center for Emerging Zoonotic & Arthropod-Borne Pathogens (CeZAP), Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1481-5337","authenticated-orcid":false,"given":"John","family":"Juma","sequence":"additional","affiliation":[{"name":"International Livestock Research Institute (ILRI), Nairobi P.O. Box 30709, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2553-1129","authenticated-orcid":false,"given":"Kristina","family":"Roesel","sequence":"additional","affiliation":[{"name":"International Livestock Research Institute (ILRI), Nairobi P.O. Box 30709, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Methode N.","family":"Gasana","sequence":"additional","affiliation":[{"name":"Department of Animal Resource Research and Technology Transfer, Rwanda Agriculture and Animal Resources Development Board (RAB), Huye P.O. Box 5016, Rwanda"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fabrice","family":"Ndayisenga","sequence":"additional","affiliation":[{"name":"Department of Animal Resource Research and Technology Transfer, Rwanda Agriculture and Animal Resources Development Board (RAB), Huye P.O. Box 5016, Rwanda"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claude M.","family":"Muvunyi","sequence":"additional","affiliation":[{"name":"Rwanda Biomedical Center (RBC), Kigali P.O. Box 7162, Rwanda"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9386-9850","authenticated-orcid":false,"given":"Emmanuel","family":"Hakizimana","sequence":"additional","affiliation":[{"name":"Rwanda Biomedical Center (RBC), Kigali P.O. Box 7162, Rwanda"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5911-5115","authenticated-orcid":false,"given":"Jean N.","family":"Hakizimana","sequence":"additional","affiliation":[{"name":"SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture, Morogoro P.O. Box 3297, Tanzania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9683-0353","authenticated-orcid":false,"given":"Gillian","family":"Eastwood","sequence":"additional","affiliation":[{"name":"Department of Entomology, and Center for Emerging Zoonotic & Arthropod-Borne Pathogens (CeZAP), Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Augustino A.","family":"Chengula","sequence":"additional","affiliation":[{"name":"Department of Veterinary Microbiology, Parasitology and Biotechnology, Sokoine University of Agriculture, Morogoro P.O. Box 3000, Tanzania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bernard","family":"Bett","sequence":"additional","affiliation":[{"name":"International Livestock Research Institute (ILRI), Nairobi P.O. Box 30709, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher J.","family":"Kasanga","sequence":"additional","affiliation":[{"name":"Department of Veterinary Microbiology, Parasitology and Biotechnology, Sokoine University of Agriculture, Morogoro P.O. Box 3000, Tanzania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6425-7345","authenticated-orcid":false,"given":"Samuel O.","family":"Oyola","sequence":"additional","affiliation":[{"name":"International Livestock Research Institute (ILRI), Nairobi P.O. Box 30709, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,7,17]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"2295","DOI":"10.1007\/s00705-018-3843-5","article-title":"Taxonomy of the family Arenaviridae and the order Bunyavirales: Update 2018","volume":"163","author":"Maes","year":"2018","journal-title":"Arch. Virol."},{"key":"ref_2","unstructured":"British Colonial Office (1913). East Africa Protectorate (Kenya) Annual Report 1912\u20131913, Colon Reports\u2014Annual; British Colonial Office."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1002\/path.1700340418","article-title":"Virus Disease of Sheep","volume":"XXXIV","author":"Daubney","year":"1931","journal-title":"J. Path."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Sindato, C., Karimuribo, E.D., Pfeiffer, D.U., Mboera, L.E., Kivaria, F., Dautu, G., Bernard, B., and Paweska, J.T. (2014). Spatial and temporal pattern of rift valley fever outbreaks in Tanzania; 1930 to 2007. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0088897"},{"key":"ref_5","unstructured":"OIE (2019). Rift Valley Fever Aetiology, Epidemiology, Diagnosis, Prevention and Control References. OIE Tech. Dis. Cards., Available online: https:\/\/www.woah.org\/fileadmin\/Home\/eng\/Animal_Health_in_the_World\/docs\/pdf\/Disease_cards\/RIFT_VALLEY_FEVER.pdf."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Makoschey, B., van Kilsdonk, E., Hubers, W.R., Vrijenhoek, M.P., Smit, M., Wichgers Schreur, P.J., Kortekaas, J., and Moulin, V. (2016). Rift Valley Fever Vaccine Virus Clone 13 Is Able to Cross the Ovine Placental Barrier Associated with Foetal Infections, Malformations, and Stillbirths. PLoS Negl. Trop. Dis., 10.","DOI":"10.1371\/journal.pntd.0004550"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"2008","DOI":"10.3201\/eid1912.121527","article-title":"Epidemiologic Investigations into Outbreaks of Rift Valley Fever in Humans, South Africa, 2008\u20132011","volume":"19","author":"Archer","year":"2013","journal-title":"Emerg. Infect. Dis."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Himeidan, Y.E., Kweka, E.J., Mahgoub, M.M., El Rayah, E.A., and Ouma, J.O. (2014). Recent outbreaks of Rift Valley fever in East Africa and the Middle East. Front. Public Health, 2.","DOI":"10.3389\/fpubh.2014.00169"},{"key":"ref_9","unstructured":"WHO (2020, December 15). Rift Valley Fever Key Facts. Available online: https:\/\/www.who.int\/news-room\/fact-sheets\/detail\/rift-valley-fever."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1084","DOI":"10.1086\/378747","article-title":"Rift Valley Fever Epidemic in Saudi Arabia: Epidemiological, Clinical, and Laboratory Characteristics","volume":"37","author":"Madani","year":"2003","journal-title":"Clin. Infect. Dis."},{"key":"ref_11","unstructured":"Mariner, J. (2018). Rift Valley Fever Surveillance, Food and Agriculture Organization of the United Nations (FAO)."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"22","DOI":"10.4269\/ajtmh.2010.09-0318","article-title":"Epidemiologic and Clinical Aspects of a Rift Valley Fever Outbreak in Humans in Tanzania, 2007","volume":"83","author":"Mohamed","year":"2010","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1146\/annurev-ento-010715-023819","article-title":"Rift Valley Fever: An Emerging Mosquito-Borne Disease","volume":"61","author":"Linthicum","year":"2016","journal-title":"Annu. Rev. Entomol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"246","DOI":"10.3201\/eid1902.120834","article-title":"Rift valley fever, Sudan, 2007 and 2010","volume":"19","author":"Aradaib","year":"2013","journal-title":"Emerg. Infect. Dis."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"6162","DOI":"10.1128\/JVI.00335-11","article-title":"Genetic Evidence for Rift Valley Fever Outbreaks in Madagascar Resulting from Virus Introductions from the East African Mainland rather than Enzootic Maintenance","volume":"85","author":"Carroll","year":"2011","journal-title":"J. Virol."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Metras, R., Porphyre, T., Pfeiffer, D.U., Kemp, A., Thompson, P.N., Collins, L.M., and White, R.G. (2012). Exploratory Space-Time Analyses of Rift Valley Fever in South Africa in 2008\u20132011. PLoS Negl. Trop. Dis., 6.","DOI":"10.1371\/journal.pntd.0001808"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"338","DOI":"10.3201\/eid2502.181289","article-title":"Rift valley fever reemergence after 7 years of quiescence, South Africa, May 2018","volume":"25","author":"Kgaladi","year":"2019","journal-title":"Emerg. Infect. Dis."},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Cosseddu, G.M., Magwedere, K., Molini, U., Pinoni, C., Khaiseb, S., Scacchia, M., Marcacci, M., Capobianco Dondona, A., Valleriani, F., and Polci, A. (2020). Genetic diversity of rift valley fever strains circulating in namibia in 2010 and 2011. Viruses, 12.","DOI":"10.3390\/v12121453"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"300","DOI":"10.3201\/eid2002.130996","article-title":"Reemergence of rift valley fever, Mauritania, 2010","volume":"20","author":"Faye","year":"2014","journal-title":"Emerg. Infect. Dis."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"183","DOI":"10.4269\/ajtmh.19-0596","article-title":"Identi fi cation of Bunyamwera and Possible Other Orthobunyavirus Infections and Disease in Cattle during a Rift Valley Fever Outbreak in Rwanda in 2018","volume":"103","author":"Dutuze","year":"2020","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Griffith, E.F., Schurer, J.M., Mawindo, B., Kwibuka, R., Turibyarive, T., and Amuguni, J.H. (2023). The Use of Drones to Deliver Rift Valley Fever Vaccines in Rwanda: Perceptions and Recommendations. Vaccines, 11.","DOI":"10.20944\/preprints202302.0381.v1"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"995","DOI":"10.4269\/ajtmh.22-0410","article-title":"Detection of Sporadic Outbreaks of Rift Valley Fever in Uganda through the National Viral Hemorrhagic Fever Surveillance System, 2017\u20132020","volume":"108","author":"Nyakarahuka","year":"2023","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1376","DOI":"10.1016\/j.jiph.2022.10.024","article-title":"Multiple Rift Valley Fever outbreaks in Uganda: Should there be global concern?","volume":"15","author":"Sah","year":"2022","journal-title":"J. Infect. Public Health"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"659","DOI":"10.4269\/ajtmh.18-0732","article-title":"First laboratory-confirmed outbreak of human and animal rift valley fever virus in Uganda in 48 years","volume":"100","author":"Shoemaker","year":"2019","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1590\/S0102-311X2001000700022","article-title":"Climate-disease connections: Rift Valley Fever in Kenya","volume":"17","author":"Anyamba","year":"2001","journal-title":"Cad. Sa\u00fade P\u00fablica Minist. Sa\u00fade Funda\u00e7\u00e3o Oswaldo Cruz Esc. Nac. Sa\u00fade P\u00fablica"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1126\/science.285.5426.397","article-title":"Climate and satellite indicators to forecast Rift Valley fever epidemics in Kenya","volume":"285","author":"Linthicum","year":"1999","journal-title":"Science"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1051\/vetres\/2010033","article-title":"Rift Valley fever virus (Bunyaviridae: Phlebovirus): An update on pathogenesis, molecular epidemiology, vectors, diagnostics and prevention","volume":"41","author":"Pepin","year":"2010","journal-title":"Vet. Res."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1186\/1297-9716-44-78","article-title":"Towards a better understanding of Rift Valley fever epidemiology in the south-west of the Indian Ocean","volume":"44","author":"Balenghien","year":"2013","journal-title":"Vet. Res."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"14","DOI":"10.4269\/ajtmh.2010.09-0293","article-title":"Risk factors for severe rift valley fever infection in Kenya, 2007","volume":"83","author":"Anyangu","year":"2010","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"ref_30","unstructured":"WHO (2024, April 01). Rift Valley Fever. Available online: https:\/\/www.who.int\/health-topics\/rift-valley-fever#tab=tab_1."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"372","DOI":"10.1017\/S0950268810001020","article-title":"Rift Valley fever in Kenya: History of epizootics and identification of vulnerable districts","volume":"139","author":"Murithi","year":"2011","journal-title":"Epidemiol. Infect."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1017\/S0022172400062434","article-title":"Rift Valley fever virus (family Bunyaviridae, genus Phlebovirus). Isolations from Diptera collected during an inter-epizootic period in Kenya","volume":"95","author":"Linthicum","year":"1985","journal-title":"J. Hyg."},{"key":"ref_33","first-page":"121","article-title":"Rift Valley fever virus-infected mosquito ova and associated pathology: Possible implications for endemic maintenance","volume":"2","author":"Oviedo","year":"2011","journal-title":"Res. Rep. Trop. Med."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"1187","DOI":"10.1099\/jgv.0.001296","article-title":"Rift valley fever: Biology and epidemiology","volume":"100","author":"Wright","year":"2019","journal-title":"J. Gen. Virol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"104692","DOI":"10.1016\/j.antiviral.2019.104692","article-title":"Mechanisms of inter-epidemic maintenance of Rift Valley fever phlebovirus","volume":"174","author":"Rissmann","year":"2020","journal-title":"Antivir. Res."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"875","DOI":"10.1099\/jgv.0.000765","article-title":"Rift valley fever virus: Strategies for maintenance, survival and vertical transmission in mosquitoes","volume":"98","author":"Lumley","year":"2017","journal-title":"J. Gen. Virol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1007\/s40588-018-0110-1","article-title":"Rift Valley Fever Virus\u2014How and Where Virus Is Maintained During Inter-epidemic Periods","volume":"6","author":"Bett","year":"2019","journal-title":"Curr. Clin. Microbiol. Rep."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"274","DOI":"10.1016\/j.antiviral.2016.07.005","article-title":"Rift Valley fever virus: Unanswered questions","volume":"132","author":"Bird","year":"2016","journal-title":"Antivir. Res."},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Clark, M.H.A., Warimwe, G.M., Di Nardo, A., Lyons, N.A., and Gubbins, S. (2018). Systematic literature review of Rift Valley fever virus seroprevalence in livestock, wildlife and humans in Africa from 1968 to 2016. PLoS Negl. Trop. Dis., 12.","DOI":"10.1371\/journal.pntd.0006627"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1261","DOI":"10.1017\/S0950268807009806","article-title":"Prevalence of antibodies against Rift Valley fever virus in Kenyan wildlife","volume":"136","author":"Evans","year":"2008","journal-title":"Epidemiol. Infect."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s11262-018-1611-y","article-title":"Molecular aspects of Rift Valley fever virus and the emergence of reassortants","volume":"55","author":"Gaudreault","year":"2018","journal-title":"Virus Genes"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1016\/j.antiviral.2012.06.001","article-title":"Molecular biology and genetic diversity of Rift Valley fever virus","volume":"95","author":"Ikegami","year":"2012","journal-title":"Antivir. Res."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"2805","DOI":"10.1128\/JVI.02095-06","article-title":"Complete Genome Analysis of 33 Ecologically and Biologically Diverse Rift Valley Fever Virus Strains Reveals Widespread Virus Movement and Low Genetic Diversity due to Recent Common Ancestry","volume":"81","author":"Bird","year":"2007","journal-title":"J. Virol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"11152","DOI":"10.1128\/JVI.01519-08","article-title":"Multiple Virus Lineages Sharing Recent Common Ancestry Were Associated with a Large Rift Valley Fever Outbreak among Livestock in Kenya during 2006\u20132007","volume":"82","author":"Bird","year":"2008","journal-title":"J. Virol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"8196","DOI":"10.1128\/JVI.73.10.8196-8200.1999","article-title":"Genetic Reassortment of Rift Valley Fever Virus in Nature","volume":"73","author":"Sall","year":"1999","journal-title":"J. Virol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"618","DOI":"10.1016\/0035-9203(79)90004-X","article-title":"The Rift Valley fever epizootic in Egypt 1977\u20131978 1. Description of the epizootic and virological studies","volume":"73","author":"Meegan","year":"1979","journal-title":"Trans. R. Soc. Trop. Med. Hyg."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1016\/S0923-2516(89)80081-0","article-title":"General aspects of the 1987 Rift Valley fever epidemic in Mauritania","volume":"140","author":"Digoutte","year":"1989","journal-title":"Res. Virol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"2270","DOI":"10.3201\/eid1712.111035","article-title":"Molecular epidemiology of rift valley fever virus","volume":"17","author":"Grobbelaar","year":"2011","journal-title":"Emerg. Infect. Dis."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"2569","DOI":"10.1056\/NEJMsr1813907","article-title":"Pathogen Genomics in Public Health, Special Report","volume":"381","author":"Armstrong","year":"2019","journal-title":"N. Engl. J. Med."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"1038","DOI":"10.1016\/j.pt.2021.08.007","article-title":"Progress and challenges in virus genomic epidemiology","volume":"37","author":"Hill","year":"2021","journal-title":"Trends Parasitol."},{"key":"ref_51","doi-asserted-by":"crossref","unstructured":"Juma, J., Konongoi, S.L., Nsengimana, I., Mwangi, R., Akoko, J., Nyamota, R., Muli, C., Dobi, P.O., Kiritu, E., and Osiany, S. (2023). Using Multiplex Amplicon PCR Technology to Efficiently and Timely Generate Rift Valley Fever Virus Sequence Data for Genomic Surveillance. Viruses, 15.","DOI":"10.3390\/v15020477"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1002\/vms3.135","article-title":"First occurrence of Rift Valley fever outbreak in Niger, 2016","volume":"5","author":"Lagare","year":"2019","journal-title":"Vet. Med. Sci."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"e06041","DOI":"10.2903\/j.efsa.2020.6041","article-title":"Rift Valley Fever\u2014Epidemiological update and risk of introduction into Europe","volume":"18","author":"Nielsen","year":"2020","journal-title":"EFSA J."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1093\/infdis\/jiq004","article-title":"Sequential rift valley fever outbreaks in Eastern Africa caused by multiple lineages of the virus","volume":"203","author":"Nderitu","year":"2011","journal-title":"J. Infect. Dis."},{"key":"ref_55","unstructured":"Rwanda Agriculture and Animal Resources Development Board (RAB) (2023, July 14). Annual Report 2012\u20132013, Available online: https:\/\/www.rab.gov.rw\/index.php?eID=dumpFile&t=f&f=67225&token=a888ab974e8fc10e70b622866a1fe15f21562166."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"e1","DOI":"10.4102\/jsava.v88i0.1379","article-title":"Seroprevalence of rift valley fever in cattle along the Akagera-Nyabarongo rivers, Rwanda","volume":"88","author":"Umuhoza","year":"2017","journal-title":"J. S. Afr. Vet. Assoc."},{"key":"ref_57","unstructured":"WOAH (2024, April 01). WAHIS Dashboard. Available online: https:\/\/wahis.woah.org\/#\/dashboards\/qd-dashboard."},{"key":"ref_58","first-page":"124","article-title":"Does the global warming modify the local Rwandan climate?","volume":"5","author":"Henninger","year":"2013","journal-title":"Nat. Sci."},{"key":"ref_59","unstructured":"National Institute of Statistics of Rwanda (NISR) (2021). The Republic of Rwanda Agricultural Household Survey 2020 Report, NISR."},{"key":"ref_60","unstructured":"Ministry of Agriculture and Animal Resources (MINAGRI) (2022). Annual Report 2021\u20132022, Ministry of Agriculture and Animal Resources."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"3506","DOI":"10.1128\/JCM.00936-07","article-title":"Highly sensitive and broadly reactive quantitative reverse transcription-PCR assay for high-throughput detection of Rift Valley fever virus","volume":"45","author":"Bird","year":"2007","journal-title":"J. Clin. Microbiol."},{"key":"ref_62","doi-asserted-by":"crossref","unstructured":"Juma, J. (2022). Rvfvampliconseq: A Nextflow Pipeline for Analyzing Rift Valley Fever Virus Amplicon Sequencing Data from Illumina Instrument. BMC Genom., 23.","DOI":"10.1186\/s12864-022-08764-6"},{"key":"ref_63","unstructured":"Andrews, S. (2023, July 18). Babraham Bioinformatics\u2014FastQC a Quality Control Tool for High Throughput Sequence Data. Available online: https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"Fastp: An Ultra-Fast All-in-One FASTQ Preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows\u2013Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_66","doi-asserted-by":"crossref","unstructured":"Grubaugh, N.D., Gangavarapu, K., Quick, J., Matteson, N.L., De Jesus, J.G., Main, B.J., Tan, A.L., Paul, L.M., Brackney, D.E., and Grewal, S. (2019). An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar. Genome Biol., 20.","DOI":"10.1186\/s13059-018-1618-7"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"3022","DOI":"10.1093\/molbev\/msab120","article-title":"MEGA11: Molecular Evolutionary Genetics Analysis Version 11","volume":"38","author":"Tamura","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"ref_68","doi-asserted-by":"crossref","unstructured":"Drummond, A.J., and Rambaut, A. (2007). BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol., 7.","DOI":"10.1186\/1471-2148-7-214"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"vew007","DOI":"10.1093\/ve\/vew007","article-title":"Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)","volume":"2","author":"Rambaut","year":"2016","journal-title":"Virus Evol."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"1307","DOI":"10.1093\/genetics\/161.3.1307","article-title":"Estimating Mutation Parameters, Population History and Genealogy Simultaneously from Temporally Spaced Sequence Data","volume":"161","author":"Drummond","year":"2002","journal-title":"Genetics"},{"key":"ref_71","unstructured":"Rambaut, A. (2024, May 27). Figtree ver 1.4.4. Institute of Evolutionary Biology, University of Edinburgh, Edinburgh. Molecular Evolution, Phylogenetics and Epidemiology., Available online: http:\/\/tree.bio.ed.ac.uk\/software\/figtree\/."},{"key":"ref_72","doi-asserted-by":"crossref","unstructured":"Juma, J., Fonseca, V., Konongoi, S.L., van Heusden, P., Roesel, K., Sang, R., Bett, B., Christoffels, A., de Oliveira, T., and Oyola, S.O. (2022). Genomic surveillance of Rift Valley fever virus: From sequencing to lineage assignment. BMC Genom., 23.","DOI":"10.1186\/s12864-022-08764-6"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"405","DOI":"10.4269\/ajtmh.1995.53.405","article-title":"Characterization of clone 13, a naturally attenuated avirulent isolate of Rift Valley fever virus which is altered in the small segment","volume":"53","author":"Muller","year":"1995","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"ref_74","doi-asserted-by":"crossref","unstructured":"Smith, L.J., Schurer, J.M., Ntakiyisumba, E., Shyaka, A., and Amuguni, J.H. (2021). Rift valley fever knowledge, mitigation strategies and communication preferences among male and female livestock farmers in eastern province, Rwanda. PLoS Negl. Trop. Dis., 15.","DOI":"10.1371\/journal.pntd.0009705"},{"key":"ref_75","doi-asserted-by":"crossref","unstructured":"Ndumu, D.B., Bakamutumaho, B., Miller, E., Nakayima, J., Downing, R., Balinandi, S., Monje, F., Tumusiime, D., Nanfuka, M., and Meunier, N. (2021). Serological evidence of Rift Valley fever virus infection among domestic ruminant herds in Uganda. BMC Vet. Res., 17.","DOI":"10.1186\/s12917-021-02867-0"},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"955","DOI":"10.1073\/pnas.0806490106","article-title":"Prediction of a Rift Valley fever outbreak","volume":"106","author":"Anyamba","year":"2009","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_77","unstructured":"FAO (2024, April 02). FAOSTAT. Available online: https:\/\/www.fao.org\/faostat\/en\/#data\/TCL)."},{"key":"ref_78","unstructured":"Ministry of Agriculture and Animal Resources (MINAGRI) (2018). Annual Report 2017\/2018, Ministry of Agriculture and Animal Resources."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1111\/j.1865-1682.2007.01013.x","article-title":"Epidemiological patterns of foot-and-mouth disease worldwide","volume":"55","author":"Rweyemamu","year":"2008","journal-title":"Transbound. Emerg. Dis."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"100060","DOI":"10.1016\/j.jvacx.2020.100060","article-title":"Theoretical risk of genetic reassortment should not impede development of live, attenuated Rift Valley fever (RVF) vaccines commentary on the draft WHO RVF Target Product Profile","volume":"5","author":"Monath","year":"2020","journal-title":"Vaccine X"},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"1649","DOI":"10.4269\/ajtmh.20-0387","article-title":"Epidemiological investigation of a rift valley fever outbreak in humans and livestock in Kenya, 2018","volume":"103","author":"Hassan","year":"2020","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"11353","DOI":"10.1038\/srep11353","article-title":"Reassortment and distinct evolutionary dynamics of Rift Valley Fever virus genomic segments","volume":"5","author":"Freire","year":"2015","journal-title":"Sci. Rep."}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/16\/7\/1148\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T15:18:07Z","timestamp":1760109487000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/16\/7\/1148"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,7,17]]},"references-count":82,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2024,7]]}},"alternative-id":["v16071148"],"URL":"https:\/\/doi.org\/10.3390\/v16071148","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,7,17]]}}}