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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dc.creatorDomelevo Entfellner, Jean-Baka
dc.creatorOkoth, Edward A.
dc.creatorOnzere, C.K.
dc.creatorUpton, C.
dc.creatorNjau, E.P.
dc.creatorHöper, D.
dc.creatorHenson, Sonal P.
dc.creatorOyola, Samuel O.
dc.creatorBochere, Edwina
dc.creatorMachuka, Eunice M.
dc.creatorBishop, Richard P.
dc.date2024-09-14
dc.date2024-09-17T13:36:30Z
dc.date2024-09-17T13:36:30Z
dc.date.accessioned2026-06-27T17:04:44Z
dc.descriptionAfrican 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.
dc.identifierhttps://hdl.handle.net/10568/152254
dc.identifier.urihttp://hdl.handle.net/123456789/141566
dc.languageen
dc.publisherMDPI
dc.rightsOpen Access
dc.sourceDomelevo 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.
dc.subjectafrican swine fever
dc.subjectswine
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 enrichment
dc.typeJournal Article

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Instituto Internacional de Investigaciones Pecuarias (ILRI)