Complete genome sequencing and comparative phylogenomics of nine African swine fever virus (ASFV) isolates of the virulent East African p72 genotype IX without viral sequence enrichment

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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.affiliationWashington State Universityen
cg.contributor.affiliationUniversity of Victoriaen
cg.contributor.affiliationSokoine University of Agricultureen
cg.contributor.affiliationFriedrich Loeffler Instituten
cg.contributor.donorUnited States Defense Threat Reduction Agencyen
cg.coverage.regionAfrica
cg.coverage.regionEastern Africa
cg.creator.identifierJean-Baka Domelevo Entfellner: 0000-0002-8282-1325en
cg.creator.identifierAbworo: 0000-0003-0689-823Xen
cg.creator.identifierSonal P Henson: 0000-0002-2002-5462en
cg.creator.identifierSamuel O. Oyola: 0000-0002-6425-7345en
cg.creator.identifierEunice Machuka: 0000-0002-1142-3442en
cg.creator.identifierRichard Bishop: 0000-0002-3720-9970en
cg.howPublishedFormally Publisheden
cg.identifier.doihttps://doi.org/10.3390/v16091466en
cg.isijournalISI Journalen
cg.issn1999-4915en
cg.issue9en
cg.journalVirusesen
cg.reviewStatusPeer Reviewen
cg.subject.actionAreaResilient Agrifood Systems
cg.subject.ilriASFen
cg.subject.ilriPIGSen
cg.subject.impactAreaNutrition, health and food security
cg.subject.impactPlatformNutrition, Health and Food Security
cg.subject.sdgSDG 2 - Zero hungeren
cg.volume16en
dc.contributor.authorDomelevo Entfellner, Jean-Bakaen
dc.contributor.authorOkoth, Edward A.en
dc.contributor.authorOnzere, C.K.en
dc.contributor.authorUpton, C.en
dc.contributor.authorNjau, E.P.en
dc.contributor.authorHöper, D.en
dc.contributor.authorHenson, Sonal P.en
dc.contributor.authorOyola, Samuel O.en
dc.contributor.authorBochere, Edwinaen
dc.contributor.authorMachuka, Eunice M.en
dc.contributor.authorBishop, Richard P.en
dc.date.accessioned2024-09-17T13:36:30Zen
dc.date.available2024-09-17T13:36:30Zen
dc.identifier.urihttps://hdl.handle.net/10568/152254
dc.titleComplete genome sequencing and comparative phylogenomics of nine African swine fever virus (ASFV) isolates of the virulent East African p72 genotype IX without viral sequence enrichmenten
dcterms.abstractAfrican swine fever virus (ASFV) is endemic to African wild pigs (<i>Phacochoerus</i> and <i>Potamochoerus</i>), in which viral infection is asymptomatic, and <i>Ornithodoros</i> soft ticks. However, ASFV causes a lethal disease in Eurasian domestic pigs (<i>Sus scrofa</i>). While Sub-Saharan Africa is believed to be the original home of ASFV, publicly available whole-genome ASFV sequences show a strong bias towards p72 Genotypes I and II, which are responsible for domestic pig pandemics outside Africa. To reduce this bias, we hereby describe nine novel East African complete genomes in p72 Genotype IX and present the phylogenetic analysis of all 16 available Genotype IX genomes compared with other ASFV p72 clades. We also document genome-level differences between one specific novel Genotype IX genome sequence (KE/2013/Busia.3) and a wild boar cell-passaged derivative. The Genotype IX genomes clustered with the five available Genotype X genomes. By contrast, Genotype IX and X genomes were strongly phylogenetically differentiated from all other ASFV genomes. The p72 gene region, on which the p72-based virus detection primers are derived, contains consistent SNPs in Genotype IX, potentially resulting in reduced sensitivity of detection. In addition to the abovementioned cell-adapted variant, eight novel ASFV Genotype IX genomes were determined: five from viruses passaged once in primary porcine peripheral blood monocytes and three generated from DNA isolated directly from field-sampled kidney tissues. Based on this methodological simplification, genome sequencing of ASFV field isolates should become increasingly routine and result in a rapid expansion of knowledge pertaining to the diversity of African ASFV at the whole-genome level.en
dcterms.accessRightsOpen Access
dcterms.audienceAcademicsen
dcterms.audienceScientistsen
dcterms.available2024-09-14en
dcterms.bibliographicCitationDomelevo Entfellner, J.-B., Okoth, E.A., Onzere, C.K., Upton, C., Njau, E.P., Höper, D., Henson, S.P., Oyola, S.O., Bochere, E., Machuka, E.M. and Bishop, R.P. 2024. Complete genome sequencing and comparative phylogenomics of nine African swine fever virus (ASFV) isolates of the virulent East African p72 genotype IX without viral sequence enrichment. Viruses 16(9): 1466.en
dcterms.extent1466en
dcterms.issued2024-09-14en
dcterms.languageen
dcterms.licenseCC-BY-4.0
dcterms.publisherMDPIen
dcterms.subjectafrican swine feveren
dcterms.subjectswineen
dcterms.typeJournal Article

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