First Isolation of a Novel Aquatic Flavivirus from Chinook Salmon (Oncorhynchus tshawytscha) and Its In Vivo Replication in a Piscine Animal Model

Abstract

The first isolation of a flavivirus from fish was made from moribund Chinook salmon Oncorhynchus tshawytscha from the Eel River, California, USA. Following observation of cytopathic effect in a striped snakehead-fish cell line, 35-nm virions with flaviviral morphology were visualized using electron microcopy. Next generation sequencing and rapid amplification of cDNA ends obtained the complete genome. Reverse transcriptase quantitative PCR (RT-qPCR) confirmed the presence of viral RNA in formalin-fixed tissues from the wild salmon. For the first time, in vivo replication of an aquatic flavivirus was demonstrated following intracoelomic injection in a Chinook salmon model of infection. RT-qPCR demonstrated viral replication in salmon brains up to 15 days post-injection. Infectious virus was then re-isolated in culture fulfilling Rivers' Postulates. Only limited replication occurred in the kidneys of Chinook salmon or in tissues of rainbow trout Onchorhynchus mykiss. The proposed salmon flavivirus (SFV) has a 10.3 kb genome that encodes a rare dual open reading frame uncharacteristic of classical flaviviruses. Phylogenetic analysis places SFV in a basal position among a new subgroup of recently recognized aquatic and bat flaviviruses distinct from the established mosquito-borne, tick-borne, insect only, and unknown vector flavivirus groups. While the pathogenic potential of the virus remains to be fully elucidated, its basal phylogeny and the in vivo infection model will allow SFV to serve as a prototype for aquatic flaviviruses. Ongoing field and laboratory studies will facilitate a better understanding of the potential impacts of SFV infection on ecologically and economically important salmonid species. IMPORTANCE Chinook salmon are a keystone fish species of great ecological and commercial significance in their native northern Pacific range and where they have been introduced. Threats to salmon populations include habitat degradation, climate change, and infectious agents, including viruses. While the first isolation of a flavivirus from wild migrating salmon may indicate an emerging disease threat, characterization of the genome provides insights into the ecology and long evolutionary history of this important group of viruses affecting humans and other animals, as well as an expanding group of recently discovered aquatic flaviviruses.