Genomic epidemiology of Rift Valley fever in East Africa
Rift 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.