Epidemiological Insights Into Infectious Pancreatic Necrosis Virus: Detection, Distribution and Persistence in Chilean Salmon Farms

This study presents a comprehensive molecular and epidemiological characterisation of infectious pancreatic necrosis virus (IPNV) in Chilean salmon aquaculture. Between 2015 and 2016, 26 sampling events were conducted in freshwater and seawater farms spanning a broad latitudinal gradient (30.3° S to 52.6° S). Three diagnostic methods were used: Quantitative real-time Polymerase Chain Reaction (PCR) (qRT-PCR) (targeting VP1 and VP2 protein coding genes), nested PCR and virus isolation in CHSE-214 cells. In addition, a 523-bp VP2 gene fragment was sequenced directly from samples. These approaches were employed to assess detection sensitivity and to explore IPNV genogroup distribution and persistence. Nested PCR and viral isolation detected IPNV in 50 of 53 samples, outperforming qRT-PCR, which detected only 39. Phylogenetic analysis of the 523-bp VP2 gene fragment classified the isolates into two genogroups-5 (Salmo salar) and 1 (Oncorhynchus spp.), confirming host-specific associations. Identical or near-identical sequences were identified in geographically distant farms and temporally spaced samples, suggesting persistent isolates and potential long-distance spread, likely via egg transfers or fish movement. The most severe mortality event (> 125,000 fish) occurred during a genogroup 1 outbreak (Isla del Rey, GMTS, O. kisutch), followed by genogroup 5 outbreaks documented in Molco Alto (PMLC, S. salar) and Chayahue (S. salar). Although less frequently detected, genogroup 1 was associated with higher virulence, particularly in coho salmon. These findings highlight the need of integrated diagnostic strategies, genogroup-specific monitoring and strengthened biosecurity to mitigate the impact of IPNV in Chilean salmon farming.