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

• Published in: Journal of Veterinary Diagnostic Investigation
• Main Authors: Rounsville, Thomas F., Polinski, Mark P., Marini, Alyssa G., Turner, Sarah M., Vendramin, Niccolò, Cuenca, Argelia, Pietrak, Michael R., Peterson, Brian C., Bouchard, Deborah A.
• Other Authors: agricultural research service
• Format: Article in Journal/Newspaper
• Language: English
• Published: SAGE Publications 2024
• Subjects: Atlantic salmon; Salmo salar
• Online Access: http://dx.doi.org/10.1177/10406387231223290; https://journals.sagepub.com/doi/pdf/10.1177/10406387231223290; https://journals.sagepub.com/doi/full-xml/10.1177/10406387231223290

Infectious salmon anemia virus (ISAV; Isavirus salaris) causes an economically important disease of Atlantic salmon ( Salmo salar L.). ISA outbreaks have resulted in significant losses of farmed salmon globally, often with a sudden onset. However, 2 phenotypically distinct variants of ISAV exist, each with divergent disease outcomes, associated regulations, and control measures. ISAV-HPRΔ, also known as ISAV-HPR deleted, is responsible for ISA outbreaks; ISAV-HPR0, is avirulent and is not known to cause fish mortality. Current detection methodology requires genetic sequencing of ISAV-positive samples to differentiate phenotypes, which may slow responses to disease management. 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 contains any form of ISAV, 2) discriminating whether positive samples contain HPRΔ 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 ISAV strains collected from North America and Europe (28 ISAV-HPRΔ, 3 ISAV-HPR0). Finally, we completed an inter-laboratory comparison of this multiplex qPCR with commercial ISAV testing and found that both methods provided equivalent results for ISAV detection.