Recent host-shifts in ranaviruses: signatures of positive selection in the viral genome

Abstract

Ranaviruses have been implicated in recent declines in global amphibian populations. Compared with the family Iridoviridae, to which the genus Ranavirus belongs, ranaviruses have a wide host range in that species/strains are known to infect fish, amphibians and reptiles, presumably due to recent host-switching events. We used eight sequenced ranavirus genomes and two selectiondetection methods (site based and branch based) to identify genes that exhibited signatures of positive selection, potentially due to the selective pressures at play during host switching. We found evidence of positive selection acting on four genes via the site-based method, three of which were newly acquired genes unique to ranavirus genomes. Using the branch-based method, we identified eight additional candidate genes that exhibited signatures of d N /d S (non-synonymous/synonymous substitution rate) .1 in the clade where intense host switching had occurred. We found that these branch-specific patterns of elevated d N /d S were enriched in a small group of viral genes that have been acquired most recently in the ranavirus genome, compared with core genes that are shared among all members of the family Iridoviridae. Our results suggest that the group of newly acquired genes in the ranavirus genome may have undergone recent adaptive changes that have facilitated interspecies and interclass host switching.

Characterization of the VP39 envelope protein from Singapore grouper iridovirus

“…Sequencing demonstrated that several ranaviruses (FV3, STIV) carry only a truncated version of the vIF-2α gene that lacks the amino-terminal binding domain for the protein kinase R and the central helical domains. All ranaviruses with truncated vIF-2α genes branched very closely to one another in the FV3-like group, which supports previous findings on sequence gain and loss during ranaviral evolution (Abrams et al 2013;Anke et al 2015). Thus, it is reasonable to infer that, based on the phylogenetic analysis, SGIV is more distantly related to an ISKNV-like megalocytivirus, which may be the result of an ISKNV-like megalocytivirus gaining and losing VP39 orthologs during its evolution.…”

Inflammation-Induced Reactivation of the Ranavirus Frog Virus 3 in Asymptomatic Xenopus laevis

“…Notably, the remarkable ability of RVs to cross species barriers of numerous ectothermic vertebrates, suggests that these pathogens possess potent immune evasion mechanisms [3]. Furthermore, although some ectothermic vertebrate species are highly susceptible to RVs, others are more resistant and may serve as asymptomatic carriers that disseminate infectious virus.…”

Virus genomes and virus-host interactions in aquaculture animals

“…Extensive comparisons of these important core genes has provided evidence for cross-species transmission in these iridoviruses, especially for the ranaviruses [68,69]. Moreover, some important genes encoding enzymes, structural proteins and immune-related proteins, such as the RGV 3β-hydroxysteroid dehydrogenase gene (RGV 3β-HSD) [70] and the RGV deoxyuridine triphosphatase gene (RGV dUTPase) [71], have been characterized and functionally analyzed.…”