Transcriptomic response to ISAV infection in the gills, head kidney and spleen of resistant and susceptible Atlantic salmon

Abstract

Background Infectious Salmon Anaemia virus (ISAV) is an orthomyxovirus responsible for large losses in Atlantic salmon (Salmo salar) aquaculture. Current available treatments and vaccines are not fully effective, and therefore selective breeding to produce ISAV-resistant strains of Atlantic salmon is a high priority for the industry. Genomic selection and potentially genome editing can be applied to enhance the disease resistance of aquaculture stocks, and both approaches can benefit from increased knowledge on the genomic mechanisms of resistance to ISAV. To improve our understanding of the mechanisms underlying resistance to ISAV in Atlantic salmon we performed a transcriptomic study in ISAV-infected salmon with contrasting levels of resistance to this virus. Results Three different tissues (gills, head kidney and spleen) were collected on 12 resistant and 12 susceptible fish at three timepoints (pre-challenge, 7 and 14 days post challenge) and RNA sequenced. The transcriptomes of infected and non-infected fish and of resistant and susceptible fish were compared at each timepoint. The results show that the responses to ISAV are organ-specific; an important response to the infection was observed in the head kidney, with up-regulation of immune processes such as interferon and NLR pathways, while in gills and spleen the response was more moderate. In addition to immune related genes, our results suggest that other processes such as ubiquitination and ribosomal processing are important during early infection with ISAV. Moreover, the comparison between resistant and susceptible fish has also highlighted some interesting genes related to ubiquitination, intracellular transport and the inflammasome. Conclusions Atlantic salmon infection by ISAV revealed an organ-specific response, implying differential function during the infection. An immune response was observed in the head kidney in these early timepoints, while gills and spleen showed modest responses in comparison. Comparison between resistance and susceptible samples have highlighted genes of interest for further studies, for instance those related to ubiquitination or the inflammasome.

Proteomic and phosphoproteomic profilings reveal distinct cellular responses during Tilapinevirus tilapiae entry and replication

“…In our study, we observed an increase in RPL17 and GIMAP7 in the infected RHTiB cells at 24 hpi. The phosphorylation of these proteins is associated with the concentration of infectious salmon anemia virus in the head kidney of infected salmon 81 , whereas the phosphorylation of GIMAPs plays a crucial role in the antiviral response in zebrafish 82 . These findings suggest that TiLV modulates the host immune response and promotes significant viral replication in RHTiB cells (Fig.…”

A Review of Factors Affecting Farmed Atlantic Salmon (Salmo salar) Welfare in Australia and Beyond

“…For example, transcriptome analysis has been used to characterise gene expression patterns involved in immune responses to microbial infections, e.g., detecting pilchard orthomyxovirus, a virus of vital concern in Tasmania (Samsing et al 2022). Such approaches can be used to examine physiological responses to abiotic and biotic stressors (Alipio et al 2022, Gervais et al 2022, determine optimal rearing conditions for promoting immunocompetence (Ellison et al 2020), help reduce disease outbreaks, (Ajasa et al 2024) and develop more efficacious vaccines against infection (Fu et al 2022). Genetic techniques also have demonstrated that quantifying hormone expression can guide the determination of optimal stocking densities, by using peptide hormones as biomarkers to analyse the physiological response of Atlantic salmon to population densities (Alvarez et al 2022).…”