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ARS Home » Northeast Area » Orono, Maine » National Cold Water Marine Aquaculture Center » Research » Publications at this Location » Publication #405870

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 from virulent variants using Multiplex RT-qPCR

item ROUNSVILLE, THOMAS - University Of Maine
item Polinski, Mark
item TURNER, SARAH - University Of Maine
item Pietrak, Michael
item Peterson, Brian
item BOUNCHARD, DEBORAH - University Of Maine

Submitted to: Western Fish Disease Workshop
Publication Type: Abstract Only
Publication Acceptance Date: 6/15/2023
Publication Date: N/A
Citation: N/A

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 new rapid (one day) assay for detecting and differentiating these two ISAV variants and provide data for its utility in a diagnostic laboratory setting.

Technical Abstract: Infectious salmon anemia (ISA) is a serious disease of Atlantic salmon. The causative agent of ISA is infectious salmon anemia virus (ISAV), which belongs to the Orthomyxoviridae family and shares several properties with well-studied influenza viruses. Importantly, two phenotypically distinct variants of ISAV have been identified. One is the well characterized highly virulent ISAV-HPR' variant associated with ISA, commonly referred to as ISAV-HPR deleted. The second is the avirulent variant known as ISAV-HPR0 which is not associated with ISA or indeed any other notable disease pathology. Both ISAV phenotypes are commonly found in regions where Atlantic salmon farming occurs. Typical diagnostic steps used for confirming the presence of ISAV involve molecular methods for identifying virus genetic material (specifically ISAV segment 8) and then positive samples are subjected to Sanger sequencing (specifically ISAV segment 6) to differentiate HPR-delete from HPR0 phenotypes. Here we describe a new multiplex RT-qPCR method to rapidly differentiate ISAV HPR0 from HPR-delete without the need for follow-up sequencing. We defined the analytical specificity of the new assay using more than 30 genetically diverse ISAV isolates collected from North America and Europe. We further evaluated the new assay in three different laboratories and determined this assay has equivalent sensitivity to current molecular methods used to detect ISAV.