Comparative genomics of an emerging amphibian virus

Brendan Epstein, Andrew Storfer

Research output: Contribution to journalArticlepeer-review

14 Scopus citations

Abstract

Ranaviruses, a genus of the Iridoviridae, are large double-stranded DNA viruses that infect cold-blooded vertebrates worldwide. Ranaviruses have caused severe epizootics in commercial frog and fish populations, and are currently classified as notifiable pathogens in international trade. Previous work shows that a ranavirus that infects tiger salamanders throughout Western North America (Ambystoma tigrinum virus, or ATV) is in high prevalence among salamanders in the fishing bait trade. Bait ATV strains have elevated virulence and are transported long distances by humans, providing widespread opportunities for pathogen pollution. We sequenced the genomes of 15 strains of ATV collected from tiger salamanders across western North America and performed phylogenetic and population genomic analyses and tests for recombination. We find that ATV forms a monophyletic clade within the rest of the Ranaviruses and that it likely emerged within the last several thousand years, before human activities influenced its spread. We also identify several genes under strong positive selection, some of which appear to be involved in viral virulence and/or host immune evasion. In addition, we provide support for the pathogen pollution hypothesis with evidence of recombination among ATV strains, and potential bait-endemic strain recombination.

Original languageEnglish (US)
Pages (from-to)15-27
Number of pages13
JournalG3: Genes, Genomes, Genetics
Volume6
Issue number1
DOIs
StatePublished - 2016

Bibliographical note

Funding Information:
We thank Rose Marie Larios and Karen Chojnacki for cultivating the viruses in cell culture and performing viral DNA extractions, and Jenn Cundiff for advice on viral DNA extractions. We also thank Matt Settles for assistance with genome assembly, Jesse Brunner for assistance with collecting strains, and Omar Cornejo for helpful comments that have improved the manuscript. This work was supported by National Science Foundation (NSF) grants DEB 0548415 and 1316549 from the NSF, and by the Washington State University Eastlick Distinguished Professorship to AS.

Keywords

  • Ambystoma tigrinum virus
  • Ranavirus
  • Range expansion

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