In 1935, 101 cane toads (Rhinella marina) were introduced into Queensland to control the cane beetle. Now in 2017, feral toads range over 1.2 million km2 of northern Australia and threaten native biodiversity. Viral biocontrol has successfully reduced the European rabbit population and remains a viable strategy to control the cane toad. Previous research involving the frog Bohle Iridovirus, a biocontrol candidate, was halted due to the virus’ ability to infect native species and thus a strong imperative exists to find new cane toad-specific viruses.
Here, we use bulk RNA sequencing and computational approaches to discover new cane toad-infecting viruses. RNA sequencing of 16 pooled cane toad livers was performed using the Illumina HiSeq2500 platform. The transcriptome was assembled de novo and screened for virus-like sequences using BLAST and Diamond tools. A full-length, novel, and abundant picornavirus was identified, which represents the first description of an RNA virus that infects cane toads.
Endogenous viral elements (EVEs) are genetic remnants of viruses that infected an organism’s germline in its history, often hundreds to thousands of years before, and have been used to expand the known host range of viral families and date host and viral species emergence. We searched for non-retroviral EVEs within the newly sequenced 2 Gb cane toad genome, using a similar discovery pipeline as for RNA sequencing. This revealed the first evidence of a cane toad circovirus (family Circoviridae) in the genome, suggesting possible long-term host-virus associations between circoviruses and Australian cane toads.
Our results uncover two new viruses that can infect the cane toad. Phylogenetic analysis suggests that these toad viruses are genetically distinct from known viruses and thus expands our knowledge of the amphibian virosphere. We are now using this virus sequence data to facilitate the isolation of viruses infecting toads from diverse locations in Australia.