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ARS Home » Northeast Area » Orono, Maine » National Cold Water Marine Aquaculture Center » Research » Publications at this Location » Publication #405549
Research Project: Genetic Improvement of North American Atlantic Salmon and the Eastern Oyster for Aquaculture Production

Location: National Cold Water Marine Aquaculture Center

Title: Rapid differentiation of infectious salmon anemia virus avirulent (HPR0) from virulent (HPR) variants using multiplex RT-qPCR

Author
item ROUNSVILLE, THOMAS - University Of Maine
item Polinski, Mark
item MARINI, ALYSSA - University Of Maine
item TURNER, SARAH - University Of Maine
item VENDRAMIN, NICCOLO - Technical University Of Denmark
item CUENCA, ARGELIA - Technical University Of Denmark
item Pietrak, Michael
item Peterson, Brian
item BOUCHARD, DEBORAH - University Of Maine

Submitted to: Journal of Veterinary Diagnostic Investigation
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/11/2024
Publication Date: 1/11/2024
Citation: Rounsville, T., Polinski, M.P., Marini, A., Turner, S., Vendramin, N., Cuenca, A., Pietrak, M.R., Peterson, B.C., Bouchard, D. 2024. Rapid differentiation of infectious salmon anemia virus avirulent (HPR0) from virulent (HPR) variants using multiplex RT-qPCR. Journal of Veterinary Diagnostic Investigation. 36(3):329-337. https://doi.org/10.1177/10406387231223290.
DOI: https://doi.org/10.1177/10406387231223290

Interpretive Summary: There are two phenotypic forms of the salmon virus known as Infectious salmon anemia virus (ISAV) - one form that causes serious disease and one that is benign. International regulations regarding ISAV differ based on phenotype and the current method used to distinguish the two variants is partial genome sequencing - a costly and typically time-consuming process. Here we describe a rapid assay for detecting and differentiating these two ISAV variants without the need for genome sequencing and provide data for its utility in a diagnostic laboratory setting.

Technical Abstract: Infectious salmon anemia (ISA) is an economically important disease of Atlantic salmon (Salmo salar L.) and the causative agent is the infectious salmon anemia virus (ISAV), also known as salmon Isavirus. ISA outbreaks have resulted in significant losses of farmed salmon globally, often with a sudden onset. However, two different phenotypically distinct variants of ISAV exist, each with divergent disease outcomes, associated regulations, and control measures. ISAV-HPR', also known as ISAV-HPR deleted, is responsible for ISA outbreaks, while ISAV-HPR0, is avirulent and is not known to cause fish mortality. Current diagnostic methodology requires genetic sequencing of ISAV positive samples to differentiate phenotypes, which may slow down responses to surveillance diagnosis. To increase the speed of phenotypic determinations of ISAV, we developed a new, rapid multiplex RT-qPCR method capable of 1) detecting if a sample is infected with any form of ISAV, 2) discriminating whether positive samples are infected with HPR' or HPR0, and 3) validating RNA extractions with an internal control, all in a single reaction. Following assay development and optimization, we validated this new multiplex on 31 different ISAV strains collected from North America and Europe (28 ISAV-HPR' and 3 ISAV-HPR0). Finally, we completed an inter-laboratory comparison of this multiplex with commercially available ISAV testing and found both methods provided equivocal results for ISAV detection.