Temporal profiling of host transcriptome highlights time- and tissue-dependent Interferon pathway activation in NNV-infected European sea bass

Nervous Necrosis Virus (NNV) is a major threat to aquaculture, causing high mortality in farmed fish, including European sea bass. The genetic basis of host response to NNV has been well characterised, suggesting the potential role of interferon-induced genes in resistance to the virus, although the molecular mechanisms underlying NNV infection in sea bass are still debated. The time- and tissue-specific dynamics of gene expression is crucial for understanding host response to NNV. Here, we report on a time-course transcriptome analysis of brain and head kidney in NNV-infected bass that integrated the statistical evidence of differential expression with the information on temporal profiles (i.e. 6, 12, 24, 48, and 72 h post-infection (hpi)) compared to mock-infected controls. Results revealed substantial changes in gene expression over time, particularly for brain, with downregulation of genes involved in nervous system functions and upregulation of immune and inflammatory response genes from 24 to 48 hpi onwards, mostly associated with the interferon (IFN) response. The study highlights tissue-specific differences in the timing and magnitude of the innate immune response compared to other fish species and provides a comprehensive view of the dynamic host response, emphasizing the need for time-course studies in understanding viral pathogenesis.