Draft Genome Sequence of a Picorna-Like Virus Associated with Gill Tissue in Clinically Normal Brook Trout, Salvelinus fontinalis.

Here, we report a draft genome sequence of a picorna-like virus associated with brook trout, Salvelinus fontinalis, gill tissue. The draft genome comprises 8,681 nucleotides, excluding the poly(A) tract, and contains two open reading frames. It is most similar to picorna-like viruses that infect invertebrates.

GENOME ANNOUNCEMENT

Brook trout, Salvelinus fontinalis, are coldwater salmonids that inhabit pristine headwater streams and are native to eastern North America (1). Introductions of nonnative salmonids, changing thermal conditions, and land use characteristics of headwater streams have led to extirpation or population reduction throughout much of their native range (2, 3). Given the ecological and cultural importance of this fish, active restoration efforts are in progress by state agencies to revitalize this federal trust species. Here, we describe a novel picorna-like virus identified from brook trout transcriptomic data that were collected for health biomarker discovery in that species.

Brook trout were obtained from a hatchery located in east-central Pennsylvania and then maintained in recirculating tanks at the U.S. Geological Survey, Northern Appalachian Research Laboratory in Wellsboro, Tioga County, Pennsylvania, USA. Gill tissue from clinically normal fish was stabilized in RNAlater and stored at −20°C. Total RNA was extracted, and rRNA was depleted. Stranded RNA-Seq libraries were prepared for sequencing on an Illumina HiSeq 4000 platform. Sequence quality checking, trimming, and de novo assembly of paired-end reads into putative transcripts were performed with CLC Genomics Workbench version 7.5.1. Contigs were queried against an in-house curated UniRef90 database of viral sequences with BLASTx.

A candidate picorna-like virus was identified from this analysis that was close to full length based on homology to other complete genomes. In order to generate the best consensus sequence model, all reads were mapped to this contig using CLC Genomics Workbench version 9.5.3. A total of 747,900 reads were mapped (average coverage, 12,289×) and accounted for 0.11% of the total reads. The final draft genome comprised 8,681 nucleotides (nt), excluding the 3′-terminal poly(A) tract and was most similar to unclassified RNA viruses that infect invertebrates. In silico translation of the sequence identified two open reading frames. The first open frame (+3) comprised 4,791 nt and encoded a predicted polypeptide of 1,569 amino acids (aa) with an expected molecular mass of 180.5 kDa. Alignment of this protein with hypothetical protein 1 of the Sanxia picorna-like virus 9 (GenBank accession number YP_009337755) indicated that 59% of the residues were identical. Hypothetical protein 1 contained conserved domains for RNA-dependent RNA polymerase (pfam0080) and RNA helicase. The second open reading frame (+2) comprised 2,454 nt and encoded a predicted polypeptide of 817 aa with an expected molecular mass of 89.2 kDa and a theoretical pI of 5.43. Alignment of this protein to hypothetical protein 2 of the Sanxia picorna-like virus 9 (YP_009337756) indicated identity at 51% of sites. It contained conserved picornavirus capsid protein domains (cd00205) and the cricket paralysis virus, as well as a VP4 conserved domain (pfam0073).

Here, we name this novel virus Tioga picorna-like virus 1. It is most similar to the Sanxia picorna-like virus 9 that infects freshwater atyid shrimp (4). It is not known if brook trout is the authentic host of this virus or if this virus is associated with disease. Further taxonomic and functional studies are necessary to identify the definitive host and ecological relevance of this novel member of the Picornavirales order.

Accession number(s).

The genome sequence of Tioga picorna-like virus 1 was submitted to GenBank under accession number MF669547.