Abstract
The IPN virus (IPNV) causes a highly contagious disease that affects farmed salmonids. IPNV isolates have been phylogenetically classified into seven genogroups, of which two are present in Chile, genogroups 1 and 5. This study aimed to compare the transcriptomic response of rainbow trout fry challenged with two Chilean isolates of IPNV, RTTX (genogroup 1), and ALKA (genogroup 5). Tissue samples from challenged individuals and controls were taken at 1, 7, and 20 days post-challenge and analyzed by RNA-Seq. The results revealed that infection with RTTX elicited a greater modulation of the trout transcriptome compared to ALKA infection, generating a greater number of highly differentially expressed genes in relation to the control fish. Gene Ontology enrichment indicated that functions related to the inflammatory and immune responses were modulated in fish challenged with both isolates throughout the trial, but with different regulation patterns. On day 1 post challenge, these functions were activated in those challenged with ALKA, but suppressed in RTTX-challenged fish. These results suggest that rainbow trout exhibit a differential transcriptomic response to infection with the two genetically distinct IPNV isolates, especially at early times post-infection.
Highlights
Rainbow trout (Oncorhynchus mykiss) is one of the most widely farmed finfish in the world
We showed that viral load and mortality varied in rainbow trout fry challenged with Chilean Infectious pancreatic necrosis (IPN) virus (IPNV) isolates from genogroups 1 and 5, more commonly known in the country as West Buxton (WB) and Sp strains, respectively [25]
At 7 dpc, viral load was detected only in fish challenged with RTTX, while at 20 dpc, IPNV was detected in trout challenged with both RTTX and ALKA
Summary
Rainbow trout (Oncorhynchus mykiss) is one of the most widely farmed finfish in the world. The species is cultivated in more than seventy countries and currently the main producers are Turkey, Iran, Norway, Chile, and Peru [1]. Infectious pancreatic necrosis (IPN), a highly contagious viral disease that affects salmonid fish in farming systems including rainbow trout [2,3], has been found in all major producer countries [4–8]. IPN outbreaks occur mainly during the freshwater stage in first-feeding fry, and to a lesser extent in post-smolts after transfer to the sea [9]. Cumulative mortalities during outbreaks can vary greatly, with reports of up to 100% in young fry, and between 10 to 20% in postsmolts [9]. Fish that survive can become asymptomatic carriers and transmit disease both horizontally to other susceptible fish or vertically to their offspring [10]
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