Genomic surveillance of Rift Valley fever virus: From sequencing to lineage assignment

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cg.authorship.typesCGIAR and developing country instituteen
cg.authorship.typesCGIAR and advanced research instituteen
cg.contributor.affiliationInternational Livestock Research Instituteen
cg.contributor.affiliationSouth African National Bioinformatics Instituteen
cg.contributor.affiliationUniversity of KwaZulu-Natalen
cg.contributor.affiliationStellenbosch Universityen
cg.contributor.affiliationUniversidade Federal de Minas Geraisen
cg.contributor.affiliationKenya Medical Research Instituteen
cg.contributor.affiliationCentre for the AIDS Programme of Research in South Africaen
cg.contributor.affiliationUniversity of Washingtonen
cg.contributor.crpAgriculture for Nutrition and Health
cg.contributor.crpLivestock
cg.contributor.donorFederal Ministry for Economic Cooperation and Development, Germanyen
cg.contributor.donorRockefeller Foundationen
cg.contributor.donorAfrica Centres for Disease Control and Preventionen
cg.contributor.donorUnited States Defense Threat Reduction Agencyen
cg.coverage.countryEgypt
cg.coverage.countryKenya
cg.coverage.iso3166-alpha2EG
cg.coverage.iso3166-alpha2KE
cg.coverage.regionNorthern Africa
cg.coverage.regionEastern Africa
cg.creator.identifierJohn Juma: 0000-0002-1481-5337
cg.creator.identifierKristina Roesel: 0000-0002-2553-1129
cg.creator.identifierBernard Bett: 0000-0001-9376-2941
cg.creator.identifierSamuel O. Oyola: 0000-0002-6425-7345
cg.howPublishedFormally Publisheden
cg.identifier.doihttps://doi.org/10.1186/s12864-022-08764-6en
cg.isijournalISI Journalen
cg.issn1471-2164en
cg.issue1en
cg.journalBMC Genomicsen
cg.reviewStatusPeer Reviewen
cg.subject.ilriRVFen
cg.subject.ilriZOONOTIC DISEASESen
cg.subject.impactAreaNutrition, health and food security
cg.subject.sdgSDG 2 - Zero hungeren
cg.volume23en
dc.contributor.authorJuma, Johnen
dc.contributor.authorFonseca, V.en
dc.contributor.authorKonongoi, Samson L.en
dc.contributor.authorHeusden, P. vanen
dc.contributor.authorRoesel, Kristinaen
dc.contributor.authorSang, R.en
dc.contributor.authorBett, Bernard K.en
dc.contributor.authorChristoffels, A.en
dc.contributor.authorOliveira, T. deen
dc.contributor.authorOyola, Samuel O.en
dc.date.accessioned2022-07-21T10:13:40Zen
dc.date.available2022-07-21T10:13:40Zen
dc.identifier.urihttps://hdl.handle.net/10568/120243
dc.titleGenomic surveillance of Rift Valley fever virus: From sequencing to lineage assignmenten
dcterms.abstractGenetic evolution of Rift Valley fever virus (RVFV) in Africa has been shaped mainly by environmental changes such as abnormal rainfall patterns and climate change that has occurred over the last few decades. These gradual environmental changes are believed to have effected gene migration from macro (geographical) to micro (reassortment) levels. Presently, 15 lineages of RVFV have been identified to be circulating within the Sub-Saharan Africa. International trade in livestock and movement of mosquitoes are thought to be responsible for the outbreaks occurring outside endemic or enzootic regions. Virus spillover events contribute to outbreaks as was demonstrated by the largest epidemic of 1977 in Egypt. Genomic surveillance of the virus evolution is crucial in developing intervention strategies. Therefore, we have developed a computational tool for rapidly classifying and assigning lineages of the RVFV isolates. The computational method is presented both as a command line tool and a web application hosted at https://www.genomedetective.com/app/typingtool/rvfv/. Validation of the tool has been performed on a large dataset using glycoprotein gene (Gn) and whole genome sequences of the Large (L), Medium (M) and Small (S) segments of the RVFV retrieved from the National Center for Biotechnology Information (NCBI) GenBank database. Using the Gn nucleotide sequences, the RVFV typing tool was able to correctly classify all 234 RVFV sequences at species level with 100% specificity, sensitivity and accuracy. All the sequences in lineages A (n = 10), B (n = 1), C (n = 88), D (n = 1), E (n = 3), F (n = 2), G (n = 2), H (n = 105), I (n = 2), J (n = 1), K (n = 4), L (n = 8), M (n = 1), N (n = 5) and O (n = 1) were also correctly classified at phylogenetic level. Lineage assignment using whole RVFV genome sequences (L, M and S-segments) did not achieve 100% specificity, sensitivity and accuracy for all the sequences analyzed. We further tested our tool using genomic data that we generated by sequencing 5 samples collected following a recent RVF outbreak in Kenya. All the 5 samples were assigned lineage C by both the partial (Gn) and whole genome sequence classifiers. The tool is useful in tracing the origin of outbreaks and supporting surveillance efforts.en
dcterms.accessRightsOpen Access
dcterms.audienceAcademicsen
dcterms.audienceScientistsen
dcterms.available2022-07-18
dcterms.bibliographicCitationJuma, J., Fonseca, V., Konongoi, S.L., Heusden, P. van, Roesel, K., Sang, R., Bett, B., Christoffels, A., Oliveira, T. de and Oyola, S.O. 2022. Genomic surveillance of Rift Valley fever virus: From sequencing to lineage assignment. BMC Genomics 23: 520.en
dcterms.extent520en
dcterms.issued2022-12
dcterms.languageen
dcterms.licenseCC-BY-4.0
dcterms.publisherSpringeren
dcterms.subjectrift valley fever virusen
dcterms.subjectgenomicsen
dcterms.subjectzoonosesen
dcterms.typeJournal Article

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