Reassortment and distinct evolutionary dynamics of Rift Valley Fever virus genomic segments

Abstract

Rift Valley Fever virus (RVFV) is a member of Bunyaviridae family that causes a febrile disease affecting mainly ruminants and occasionally humans in Africa, with symptoms that range from mid to severe. RVFV has a tri-segmented ssRNA genome that permits reassortment and could generate more virulent strains. In this study, we reveal the importance of reassortment for RVFV evolution using viral gene genealogy inference and phylodynamics. We uncovered seven events of reassortment that originated RVFV lineages with discordant origins among segments. Moreover, we also found that despite similar selection regimens, the three segments have distinct evolutionary dynamics; the longer segment L evolves at a significant lower rate. Episodes of discordance between population size estimates per segment also coincided with reassortment dating. Our results show that RVFV segments are decoupled enough to have distinct demographic histories and to evolve under different molecular rates.

Phylogeography of Rift Valley Fever Virus in Africa and the Arabian Peninsula

“…Interestingly, Freire et al . [33] found a lower evolutionary rate in the large minigenomic segment, suggesting a distinct evolutionary history in the three segments; our results corroborated this finding [33]. …”

“…The substitution rate estimates in our study were similar to those in previous studies [33,43]. Other studies have reported higher rates [32,44]: for example, estimates from Aradaib et al .…”

“…Sequences for the three segments of the RVFV genome were available for strains sampled over a span of 66 years (1944–2010). RVFV minigenomic segments showed differences in amounts of genetic change and time scale [33]. These minigenomic segments have previously been used to derive phylogenetic and ecological insights regarding RVFV circulation in Africa and the Arabian Peninsula [32,33].…”

“…RVFV minigenomic segments showed differences in amounts of genetic change and time scale [33]. These minigenomic segments have previously been used to derive phylogenetic and ecological insights regarding RVFV circulation in Africa and the Arabian Peninsula [32,33]. These analyses used phylogenetic approaches similar to ours; however, our analysis takes advantage of a discrete-traits phylogenetic analysis using Markov Jumps to infer the history of between-country and between-host movements.…”

“…A molecular clock-based phylogenetic analysis was performed for each segment separately in BEAST [29], using the best-fitting nucleotide substitution model for each segment, an uncorrelated lognormal relaxed molecular clock [30], and a GMRF Bayesian skyride tree prior [31]. Because variation among virus sampling dates (i.e., 1944–2010) is of meaningful magnitude relative to the time to most recent common ancestor of the clade in question [32,33], the temporal information associated with sampling each isolate had to be taken into consideration [30,34]. Sampling dates were used as prior information to calibrate the tree, estimate ages of different RVFV lineages, and infer evolutionary history of the strains [29].…”