{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,24]],"date-time":"2026-10-24T01:59:11Z","timestamp":1792807151369,"version":"4.5.0"},"reference-count":54,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2023,2,9]],"date-time":"2023-02-09T00:00:00Z","timestamp":1675900800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"German government","award":["BMZ001201"],"award-info":[{"award-number":["BMZ001201"]}]},{"name":"German government","award":["HDTRA11910031"],"award-info":[{"award-number":["HDTRA11910031"]}]},{"name":"Rockefeller Foundation and the Africa CDC","award":["BMZ001201"],"award-info":[{"award-number":["BMZ001201"]}],"id":[{"id":"https:\/\/ror.org\/03sfkwk85","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Rockefeller Foundation and the Africa CDC","award":["HDTRA11910031"],"award-info":[{"award-number":["HDTRA11910031"]}],"id":[{"id":"https:\/\/ror.org\/03sfkwk85","id-type":"ROR","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000774","name":"Department of Defense\u2019s Defense Threat Reduction Agency","doi-asserted-by":"publisher","award":["BMZ001201"],"award-info":[{"award-number":["BMZ001201"]}],"id":[{"id":"10.13039\/100000774","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000774","name":"Department of Defense\u2019s Defense Threat Reduction Agency","doi-asserted-by":"publisher","award":["HDTRA11910031"],"award-info":[{"award-number":["HDTRA11910031"]}],"id":[{"id":"10.13039\/100000774","id-type":"DOI","asserted-by":"publisher"}]},{"name":"CGIAR Fund Donors","award":["BMZ001201"],"award-info":[{"award-number":["BMZ001201"]}]},{"name":"CGIAR Fund Donors","award":["HDTRA11910031"],"award-info":[{"award-number":["HDTRA11910031"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Rift Valley fever (RVF) is a febrile vector-borne disease endemic in Africa and continues to spread in new territories. It is a climate-sensitive disease mostly triggered by abnormal rainfall patterns. The disease is associated with high mortality and morbidity in both humans and livestock. RVF is caused by the Rift Valley fever virus (RVFV) of the genus Phlebovirus in the family Phenuiviridae. It is a tripartite RNA virus with three genomic segments: small (S), medium (M) and large (L). Pathogen genomic sequencing is becoming a routine procedure and a powerful tool for understanding the evolutionary dynamics of infectious organisms, including viruses. Inspired by the utility of amplicon-based sequencing demonstrated in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and Ebola, Zika and West Nile viruses, we report an RVFV sample preparation based on amplicon multiplex polymerase chain reaction (amPCR) for template enrichment and reduction of background host contamination. The technology can be implemented rapidly to characterize and genotype RVFV during outbreaks in a near-real-time manner. To achieve this, we designed 74 multiplex primer sets covering the entire RVFV genome to specifically amplify the nucleic acid of RVFV in clinical samples from an animal tissue. Using this approach, we demonstrate achieving complete RVFV genome coverage even from samples containing a relatively low viral load. We report the first primer scheme approach of generating multiplex primer sets for a tripartite virus which can be replicated for other segmented viruses.<\/jats:p>","DOI":"10.3390\/v15020477","type":"journal-article","created":{"date-parts":[[2023,2,9]],"date-time":"2023-02-09T02:32:07Z","timestamp":1675909927000},"page":"477","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["Using Multiplex Amplicon PCR Technology to Efficiently and Timely Generate Rift Valley Fever Virus Sequence Data for Genomic Surveillance"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1481-5337","authenticated-orcid":false,"given":"John","family":"Juma","sequence":"first","affiliation":[{"name":"International Livestock Research Institute (ILRI), Nairobi P.O. Box 30709, Kenya"},{"name":"South African National Bioinformatics Institute (SANBI), University of the Western Cape, Cape Town 7535, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samson L.","family":"Konongoi","sequence":"additional","affiliation":[{"name":"International Livestock Research Institute (ILRI), Nairobi P.O. Box 30709, Kenya"},{"name":"Centre for Virus Research, Kenya Medical Research Institute (KEMRI), Nairobi P.O. Box 54840, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isidore","family":"Nsengimana","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Parasitology and Biotechnology, Sokoine University of Agriculture, Morogoro 3019, Tanzania"},{"name":"Rwanda Inspectorate, Competition and Consumer Protection Authority, Kigali P.O. Box 375, Rwanda"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Reuben","family":"Mwangi","sequence":"additional","affiliation":[{"name":"International Livestock Research Institute (ILRI), Nairobi P.O. Box 30709, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James","family":"Akoko","sequence":"additional","affiliation":[{"name":"International Livestock Research Institute (ILRI), Nairobi P.O. Box 30709, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9569-1953","authenticated-orcid":false,"given":"Richard","family":"Nyamota","sequence":"additional","affiliation":[{"name":"International Livestock Research Institute (ILRI), Nairobi P.O. Box 30709, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Collins","family":"Muli","sequence":"additional","affiliation":[{"name":"International Livestock Research Institute (ILRI), Nairobi P.O. Box 30709, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul O.","family":"Dobi","sequence":"additional","affiliation":[{"name":"International Livestock Research Institute (ILRI), Nairobi P.O. Box 30709, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0513-8300","authenticated-orcid":false,"given":"Edward","family":"Kiritu","sequence":"additional","affiliation":[{"name":"International Livestock Research Institute (ILRI), Nairobi P.O. Box 30709, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shebbar","family":"Osiany","sequence":"additional","affiliation":[{"name":"International Livestock Research Institute (ILRI), Nairobi P.O. Box 30709, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amos A.","family":"Onwong\u2019a","sequence":"additional","affiliation":[{"name":"Department of Veterinary Services, Ministry of Agriculture, Livestock and Fisheries, Nairobi P.O. Box 30028, Kenya"},{"name":"Department of Medical Laboratory Sciences, Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi 00200, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rachael W.","family":"Gachogo","sequence":"additional","affiliation":[{"name":"Division of Immunology, Department of Human Pathology, University of Cape Town, Cape Town 7925, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4875-8385","authenticated-orcid":false,"given":"Rosemary","family":"Sang","sequence":"additional","affiliation":[{"name":"Centre for Virus Research, Kenya Medical Research Institute (KEMRI), Nairobi P.O. Box 54840, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0420-2916","authenticated-orcid":false,"given":"Alan","family":"Christoffels","sequence":"additional","affiliation":[{"name":"South African National Bioinformatics Institute (SANBI), University of the Western Cape, Cape Town 7535, South Africa"}],"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":"Bernard","family":"Bett","sequence":"additional","affiliation":[{"name":"International Livestock Research Institute (ILRI), Nairobi P.O. Box 30709, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6425-7345","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":[[2023,2,9]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"2505","DOI":"10.1007\/s00705-017-3358-5","article-title":"Changes to Taxonomy and the International Code of Virus Classification and Nomenclature Ratified by the International Committee on Taxonomy of Viruses (2017)","volume":"162","author":"Adams","year":"2017","journal-title":"Arch. Virol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1002\/path.1700340418","article-title":"Enzootic Hepatitis or Rift Valley Fever. 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