Isolation and molecular characterization of a novel infectious pancreatic necrosis virus strain in returning Atlantic salmon Salmo salar from the Connecticut River, USA.

After 22 years of negative viral screening results, the viral pathogen infectious pancreatic necrosis virus (IPNV) was isolated from the ovarian fluid of two pooled samples of returning Connecticut River Atlantic salmon Salmo salar during the 2007 spawning season at Richard Cronin National Salmon Station (RCNSS), Hadley, Massachusetts. Cytopathic effect was observed in Chinook salmon embryo (CHSE-214) cells, and IPNV was confirmed by reverse transcriptase-polymerase chain reaction (RT-PCR). Sequence analysis conducted by the U.S. Geological Survey's Western Fisheries Research Center determined that the isolate closely resembled the Canada_3 strain, falling into Genogroup 4 rather than Genogroup 1, which is more common in the United States. This allowed us to speculate that the Atlantic salmon were not infected during their freshwater life stage in the Connecticut River watershed but somewhere on their migratory route or feeding grounds in the Northwest Atlantic. On November 20, 2007, the Connecticut River Atlantic Salmon Commission voted to depopulate the infected stock at RCNSS and the entire suspect egg lots held at White River National Fish Hatchery, Vermont. Approximately one and a half months later, the 121 Connecticut River Atlantic salmon were euthanized and sampled for a follow-up investigation to determine the prevalence of infection. Only one kidney-spleen homogenate (male) was confirmed IPNV positive via cell culture and RT-PCR. A total of 2,983 base pairs from segment A of the RNA genome were sequenced from this fish and determined to be from a new strain (Connecticut-1) of IPNV that closely resembles Canada_2 and Canada_3 in Genogroup 4. The new strain is genetically identical to one of the first ovarian fluid isolates over a shared 130-nucleotide region, possibly indicating original transmission from a single source. The absence of IPNV from the Connecticut River's subsequent four returning Atlantic salmon year-classes may indicate that the aggressive corrective action was prudent.