Molecular Responses of Sparus aurata to Nervous Necrosis Virus (NNV) Infection: A Bioinformatic Analysis of RNA Sequencing Data

Nervous necrosis virus (NNV) is a highly pathogenic virus affecting marine fish like Sparus aurata (gilt-head bream), causing viral encephalopathy and retinopathy (VER). Infected fish display severe neurological symptoms such as abnormal swimming, loss of equilibrium, lethargy, and skin darkening. The virus attacks the central nervous system, leading to tissue necrosis and high mortality rates, especially in larvae and juveniles. This results in significant economic losses in aquaculture, highlighting the need for advanced research to understand NNV mechanisms and develop effective control measures. This study analyzed RNA sequencing data from S. aurata larvae infected with NNV and mock-infected controls. The experimental data were sourced from a prior study where sea bream larvae, obtained from a virus-free hatchery, were acclimated in controlled conditions and divided into two groups: one exposed to NNV and the other serving as a control. Mortality and welfare were monitored, and samples were collected at various post-infection time points for molecular analysis. In this study, I focused on bioinformatics analysis; RNA sequencing data from the previous study were initially retrieved, then processed using a High-Performance Computing (HPC) server to process the data and iDEP to identify differentially expressed genes and significant biological pathways. The RNA sequencing analysis revealed numerous differentially expressed genes in NNV-infected larvae compared to controls. Key pathways involved in immune response, apoptosis, and neural functions were significantly impacted. Specifically, pathways related to visual perception and sensory perception of light stimuli were down-regulated, while those associated with positive regulation of cytokine production were up-regulated. These findings reflect the physiological and pathological changes induced by NNV infection, providing insights into the host-pathogen interactions and the molecular mechanisms underlying NNV pathogenesis in S. aurata. This study highlights its critical molecular responses to NNV infection, identifying potential genes causing this disease. The insights gained from differentially expressed genes and pathways can inform future research and interventions to mitigate the impact of NNV in aquaculture. Understanding these molecular responses is essential for developing effective disease management strategies and enhancing the resilience of marine fish species against viral infections.