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Complete genome analysis of a frog virus 3 (FV3) isolate and sequence comparison with isolates of differing levels of virulence

Elizabeth A Morrison1, Shawn Garner12, Pierre Echaubard3, David Lesbarrères2, Christopher J Kyle1 and Craig R Brunetti1*

Author Affiliations

1 Department of Biology, Trent University, 1600 East Bank Dr., Peterborough, Ontario K9J 7B8, Canada

2 Current address: Department of Biology, Western University, 1151 Richmond Street, London, Ontario N6A 5B7, Canada

3 Genetics and Ecology of Amphibians Research Group (GEARG), Department of Biology, Laurentian University, Sudbury, Ontario P3E 2C6, Canada

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Virology Journal 2014, 11:46  doi:10.1186/1743-422X-11-46

Published: 12 March 2014

Abstract

Background

Frog virus 3 (FV3) is the type species of the genus Ranavirus, and in the past few decades, FV3 infections have resulted in considerable morbidity and mortality in a range of wild and cultivated amphibian species in the Americas, Europe, and Asia. The reasons for the pathogenicity of FV3 are not well understood.

Findings

We investigated three FV3 isolates designated SSME, wt-FV3, and aza-Cr, and reported that our wt-FV3 and aza-Cr strains showed similar levels of virulence, while SSME was the least virulent in an in vivo study with Lithiobates pipiens tadpoles. Using 454 GS-FLX sequencing technology, we sequenced SSME and compared it to the published wt-FV3 genome. SSME had multiple amino acid deletions in ORFs 49/50L, 65L, 66L, and 87L, which may explain its reduced virulence. We also investigated repeat regions and found that repeat copy number differed between isolates, with only one group of 3 isolates and 1 pair of isolates being identical at all 3 locations.

Conclusions

In this study we have shown that genetic variability is present between closely related FV3 isolates, both in terms of deletions/insertions, and even more so at select repeat locations. These genomic areas with deletions/insertions may represent regions that affect virulence, and therefore require investigation. Furthermore, we have identified repeat regions that may prove useful in future phylogeographical tracking and identification of ranaviral strains across different environmental regions.

Keywords:
FV3; 454 GS-FLX technology; Viral isolates; Genetic variation; Virulence