Genomic epidemiology of Rift Valley fever in East Africa

dc.contributor.advisorChristoffels, Alan
dc.contributor.authorJuma, John
dc.date.accessioned2023-11-20T07:57:24Z
dc.date.accessioned2024-05-17T07:57:47Z
dc.date.available2023-11-20T07:57:24Z
dc.date.available2024-05-17T07:57:47Z
dc.date.issued2023
dc.descriptionDoctor Scientiae - DScen_US
dc.description.abstractRift Valley fever (RVF) is a climate-driven zoonotic disease of significant importance to public and livestock health given its epidemic potential. The disease was first identified in 1930 in the great rift valley region of Kenya following massive abortion among pregnant ewes in a sheep farm. RVF is caused by the Rift Valley fever virus (RVFV) belonging to the genus Phlebovirus, family Phenuiviridae and order Bunyavirales. RVF primarily affects domestic ruminants, wild animals and humans with varying degrees of fatalities. In this PhD research, tools and methods that will be of immense importance in conducting genomic surveillance of RVFV were developed. Furthermore, we have applied phylodynamic and phylogeographic approaches to understand the transmission dynamics of the virus in East Africa. In the second chapter, we utilized publicly available genetic sequence data of the virus to build a tool that rapidly detects circulating lineages. A general observation made in this work is the paucity of RVFV genetic data globally. Only a handful of sequence data is available from countries that have previously experienced RVF outbreaks such as South Africa, Kenya and Madagascar. The genetic information in the sequence data is crucial in identifying lineage defining single nucleotide polymorphisms (SNPs) or mutations. Using these mutations, we developed a command line tool that rapidly characterizes RVFV isolates using the 15 alphabet (A to O) nomenclature.en_US
dc.identifier.urihttps://hdl.handle.net/10566/15272
dc.language.isoenen_US
dc.publisherUniversity of the Western Capeen_US
dc.rights.holderUniversity of the Western Capeen_US
dc.subjectSouth Africaen_US
dc.subjectKenyaen_US
dc.subjectAmpliconen_US
dc.subjectBayesianen_US
dc.subjectRift valley feveren_US
dc.subjectEast Africaen_US
dc.subjectGenomicen_US
dc.titleGenomic epidemiology of Rift Valley fever in East Africaen_US

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