Investigating the impact of Rift Valley fever virus inter-isolate genome variability on viral transmission and emergence

Rift Valley fever (RVF) is a vector-transmitted disease with a widespread pattern of endemism across Africa and the Arabian Peninsula. Despite the significant threat posed to humans and ruminant animals, the impact of genomic sequence variation among Rift Valley fever virus (RVFV) isolates remains poorly understood. In this thesis, putative increases in RVFV virulence and transmissibility were explored by comparing virulence associated genomic regions of two Kenyan RVFV isolates; one taken from a widespread outbreak in 2006 and a second ancestral isolate taken from a mosquito during an inter-epidemic period in 1983. Reverse genetics approaches were used to generate recombinant viruses by cloning the medium (M) segment proteins or the non-structural protein of S (NSs) of the desired isolates into a plasmid-based rescue system for the recovery of RVFV strain ZH-548. Infectious cell culture assays performed using the recombinant viruses found the NSs proteins to be functionally analogous, where the NSs recombinant viruses were found to comparably modulate the IFN-β response and exhibited similar replication kinetics in human, bovine and mosquito cells. By contrast, the 2006 M recombinant virus was found to produce larger plaques and replicate to higher titres than the 1983 virus during the log phase of replication in human and bovine cells. The corresponding 20% disparity in viral replication rate was not found to significantly impact transmission, as indicated by the computed results of a mathematical model developed to examine the effect of within-host viral replication on the R0 of RVFV. However, peak titre disparities reported in lambs and calves challenged with comparable viruses were found to elicit large changes in viral transmission, indicating non-equivalence of in vitro and in vivo data. The modelling results identified increases in peak in titre, particularly in lambs, as a high risk for RVFV transmission and identified the need for further animal experiments.