Abstract Pacific cod (Gadus macrocephalus), as one of the most important economic fish, was seriously infected by the nervous necrosis virus (NNV), especially in the larvae stage. PolyI:C is an effective stimulus of the antivirus system, but whether it can work in the larvae stage is still unknown. In this study, the transcriptomic profiles of 10 day‐post hatching (dph) cod larvae challenged with polyI:C was analysed using next‐generation sequencing technology. After assembly and annotation, a total of 77,562 unigenes were acquired and 780 differentially expressed genes (DEGs) were identified, including 508 upregulated and 272 downregulated genes. The DEGs were involved in diverse pathways including protein processing in endoplasmic reticulum, peroxisome, carbon metabolism, fatty acid metabolism, and PPAR signaling pathway. Gene expression patterns of five immune relevant genes belonging to IFN signal pathway, such as TLR3, IRF3, MDA5, IPS1 and ATG5, were detected using qPCR. The transcript levels of TLR3, IRF3, MAD5 and IPS1 in cod larvae seems very low, but these genes were upregulated significantly 48h post‐challenged with polyI:C, while ATG5 was downregulated 12h after polyI:C challenged. The results indicated that IFN system of cod larvae can be induced by polyI:C, thus considering polyI:C as a potential antivirus agent for cod larvae.
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