First Complete Genome Sequence of Piscine Orthoreovirus Variant 3 Infecting Coho Salmon (Oncorhynchus kisutch) Farmed in Southern Chile

ABSTRACT We report here the complete genome of an isolate of piscine orthoreovirus variant 3 sequenced from a moribund coho salmon with jaundice that was reared in a seawater farm in southern Chile. The genome consists of 23,627 bp, including 10 segments that range from 1,052 bp (segment S4) to 4,014 bp (segment L1).

P iscine orthoreoviruses (PRVs) are a group of emerging fish viruses associated with myocardial and skeletal muscle disease and circulatory disorders in seawater-reared salmonids. PRVs belong to the genus Orthoreovirus, which is in the family Reoviridae, with virus particles that have an icosahedral symmetry and are nonenveloped and nonfusogenic. The genome of PRV consists of 10 segments of double-stranded RNA (1). PRVs are ubiquitous and have been reported in all main farming countries with a particularly high incidence in salmonids. PRV-linked diseases negatively impact the salmon industry in Norway (2), Japan (3), and Chile (4, 5) by causing mortality. In Chile, PRVs were detected for the first time in Atlantic salmon (4), and their prevalence has been increasing. Therefore, epidemiological data related to PRVs need to be updated, especially after the identification of distinct genotypes.
The most prevalent variant is PRV-1, the etiological agent of heart and skeletal muscle inflammation (HSMI) in Atlantic salmon, Salmo salar (6), and coho salmon, Oncorhynchus kisutch (5). Recently, PRV-2 was recognized as the cause of erythrocytic inclusion body syndrome in coho salmon (3). Another PRV variant (PRV-Om) was initially related to HSMI-like disease and was suggested to be species specific for rainbow trout, Oncorhynchus mykiss (7). To maintain taxonomic consistency, PRV-Om was later renamed PRV-3 (8). In sum, three variants of PRV have been distinguished to date, with PRV-1 and PRV-3 being closely related to each other.
Specimens were collected by the Servicio Nacional de Pesca y Acuicultura (Sernapesca) in the region of Los Lagos in 2017. Total RNA samples from a moribund coho salmon and a healthy control were purified from heart and kidney tissues. The removal of host rRNA was accomplished with a Ribo-Zero kit. TruSeq libraries were prepared to be run on an Illumina HiSeq 2500 platform, and high-throughput sequencing was performed at Macrogen, Inc. (Seoul, South Korea). From a total of 55,292,189 reads, 101 bp in length, 5,201 paired-end reads were assigned to PRV-3 with an N 50 value of 1,361 bp and 22ϫ coverage. All reads were de novo assembled with SOAPdenovo version 2.0. The selected viral contigs were reassembled and annotated with BLAST2go version 4.1 ( Table 1). The resulting S1 sequence of PRV-3 was highly homologous to the ones previously reported for PRV isolated from rainbow trout in Norway (7) and coho salmon in Chile (5) This complete genome sequence of PRV-3 will contribute to a better understanding of the epidemiology of PRV and allow for improvements in diagnostics.
Accession number(s). The sequences of segments comprising the PRV-3 genome reported here were deposited at DDBJ/EMBL/GenBank under the accession numbers listed in Table 1. The versions described here are the first versions.

ACKNOWLEDGMENTS
This work was performed at the Laboratorio de Diagnóstico y Biotecnología, ADL Diagnostic Chile SpA, Sector La Vara s/n, Camino a Alerce, Puerto Montt, Chile. We gratefully acknowledge the work done by Melanie Kaiser in editing the manuscript.
This study was supported by Servicio Nacional de Pesca y Acuicultura (Sernapesca), the regulatory agency for aquaculture and fisheries related to the Chilean government.