Perspectives on Salmon Aquaculture: Current Status, Challenges and Genetic Improvement for Future Growth

With an estimated global value of US$15.6 billion, farmed salmonids represent a precious food resource, which is also the fastest increasing food producing industry with annual growth of 7% in production. A total average of 3,594,000 metric tonnes was produced in 2020, behind Chinese and Indian carps, tilapias and catfishes. Lead producers of farmed salmonids are Norway, Chile, Faroe, Canada and Scotland, stimulated by increasing global demand and market. However, over the last 2 years, production has been declining, occasioned by effects of diseases as well as rising feed costs. Over the last year, production has declined sharply due to effects of covid-19. This chapter reviews the species in culture, systems of culture, environmental footprints of salmon culture, and market trends in salmon culture. Burden of diseases, especially Infectious pancreatic Necrosis, Infectious salmon anemia and furunculosis, as well as high cost of feed formulation, key challenges curtailing growth of the salmon production industry, are discussed. A review is made of the international salmon genome sequencing effort, selective breeding for disease resistance, and the use of genomics to mitigate challenges of diseases that stifle higher production of salmonids globally.

Transcriptome Analysis of Atlantic Salmon (Salmo salar) Skin in Response to Sea Lice and Infectious Salmon Anemia Virus Co-Infection Under Different Experimental Functional Diets

Sea lice (Lepeophtheirus salmonis) are ectoparasitic copepods that cause significant economic loss in marine salmoniculture. In commercial salmon farms, infestation with sea lice can enhance susceptibility to other significant pathogens, such as the highly contagious infectious salmon anemia virus (ISAv). In this study, transcriptomic analysis was used to evaluate the impact of four experimental functional feeds (i.e. 0.3% EPA/DHA+high-ω6, 0.3% EPA/DHA+high-ω6+immunostimulant (IS), 1% EPA/DHA+high-ω6, and 1% EPA/DHA+high-ω3) on Atlantic salmon (Salmo salar) during a single infection with sea lice (L. salmonis) and a co-infection with sea lice and ISAv. The overall objectives were to compare the transcriptomic profiles of skin between lice infection alone with co-infection groups and assess differences in gene expression response among animals with different experimental diets. Atlantic salmon smolts were challenged with L. salmonis following a 28-day feeding trial. Fish were then challenged with ISAv at 18 days post-sea lice infection (dpi), and maintained on individual diets, to establish a co-infection model. Skin tissues sampled at 33 dpi were subjected to RNA-seq analysis. The co-infection’s overall survival rates were between 37%-50%, while no mortality was observed in the single infection with lice. With regard to the infection status, 756 and 1303 consensus differentially expressed genes (DEGs) among the four diets were identified in “lice infection vs. pre-infection” and “co-infection vs. pre-infection” groups, respectively, that were shared between the four experimental diets. The co-infection groups (co-infection vs. pre-infection) included up-regulated genes associated with glycolysis, the interferon pathway, complement cascade activity, and heat shock protein family, while the down-regulated genes were related to antigen presentation and processing, T-cell activation, collagen formation, and extracellular matrix. Pathway enrichment analysis conducted between infected groups (lice infection vs. co-infection) resulted in several immune-related significant GO terms and pathways unique to this group, such as “autophagosome”, “cytosolic DNA-sensing pathway” and “response to type I interferons”. Understanding how experimental functional feeds can impact the host response and the trajectory of co-infections will be an essential step in identifying efficacious intervention strategies that account for the complexities of disease in open cage culture.

Infectious Salmon Anemia Virus Shedding from Infected Atlantic Salmon (Salmo salar L.)—Application of a Droplet Digital PCR Assay for Virus Quantification in Seawater

Infectious salmon anemia virus (ISAV) infection is currently detected by fish sampling for PCR and immunohistochemistry analysis. As an alternative to sampling fish, we evaluated two different membrane filters in combination with four buffers for elution, concentration, and detection of ISAV in seawater, during a bath challenge of Atlantic salmon (Salmo salar L.) post-smolts with high and low concentrations of ISAV. Transmission of ISAV in the bath challenge was confirmed by a high mortality, clinical signs associated with ISA disease, and detection of ISAV RNA in organ tissues and seawater samples. The electronegatively charged filter, combined with lysis buffer, gave significantly higher ISAV RNA detection by droplet digital PCR from seawater (5.6 × 104 ISAV RNA copies/L; p < 0.001). Viral shedding in seawater was first detected at two days post-challenge and peaked on day 11 post-challenge, one day before mortalities started in fish challenged with high dose ISAV, demonstrating that a large viral shedding event occurs before death. These data provide important information for ISAV shedding that is relevant for the development of improved surveillance tools based on water samples, transmission models, and management of ISA.

Anti-Viral microRNAs Profiling in Infectious Salmon Anemia Virus (ISAV)-Infected Atlantic Salmon Kidney (ASK) Cells

Infectious salmon anemia virus (ISAV) is an orthomyxovirus causing fetal disease of farmed Atlantic salmon, leading to considerable financial losses farmers around the world. In the present study, we sequenced and identified microRNAs (miRNAs) from Atlantic salmon kidney (ASK) cells infected with ISAV. Based on initial experimental data derived from RNA-Seq analysis, a group of differentially expressed (DE) miRNAs from the infected ASK cells were selected for expression analysis and to identify their mRNA targets. Among the DE miRNAs, highest-ranked 19 up-or down-regulated miRNAs stood out as attractive candidates for a role in ISAV-related function, which displayed a clear tendency to be continuously upregulated or downregulated during viral infection. Interestingly, these miRNAs displayed significant relationships with immune system processes based on their mRNA targets. Besides, miR-148a/b and miR-152 can be putative anti-viral miRNAs by directly targeting viral genes such as HA, P3, and NP genes which are required for viral infection. Taken together, these data may provide new clues to understanding the molecular framework of immune defense response during viral infection.

Antioxidant Effect of A. chilensis on the Production of Infectious Viral Particles of ISAv and Its Consequences on the SUMOylation of NP Protein

Infectious salmon anemia virus (ISAv) is a pathogen of high economic importance worldwide; it produces a highly fatal clinical symptomatology called infectious salmon anemia (ISA), which is one of the main causes of economic loss in Chilean aquaculture, specifically in Chilean salmon, being responsible for a mortality rate greater than 80% when outbreaks of this pathogen occur in fish farms. ISAv dramatically increases levels of reactive oxygen species (ROS) by increasing the activity of the p38MAPK protein, which activates p47phox, by phosphorylation, allowing its binding to the membrane subunits of the NADPH oxidase complex, which is an important positive regulator of ROS levels in cells. Further, it is known that oxidative stress is able to regulate the SUMOylation machinery, producing an increase in SUMOylated proteins. Together with this background and various bioinformatic analyses, it was found that the ISAv nucleoprotein (NP) has a highly conserved capacity for SUMOylation, and this protein alone is capable of causing strong oxidative stress in transfected cells and is therefore able to regulate the SUMOylation machinery. Immunoprecipitation assays confirmed the bioinformatic analyses, where NP was seen to be SUMOylated, and this signal decreased considerably when cells were treated with a p38MAPK inhibitor. Together with this, the number of copies of NP and the viability in cells infected with ISAv were also evaluated, where it was observed that there was a strong increase in the number of copies of NP and a marked decrease in cell viability, this being in contrast to when, in addition to the infection, the cells were treated with a natural product “maqui” (A. chilensis), which, due to its high content of polyphenolic compounds, has been shown to have a high antioxidant capacity, greatly reducing the number of copies of NP and the percentage of mortality compared to cells that are only infected with ISAv.

Interaction of the Amino-Terminal Domain of the ISAV Fusion Protein with a Cognate Cell Receptor

The infectious salmon anemia virus (ISAV), etiological agent of the disease by the same name, causes major losses to the salmon industry. Classified as a member of the Orthomyxoviridae family, ISAV is characterized by the presence of two surface glycoproteins termed hemagglutinin esterase (HE) and fusion protein (F), both of them directly involved in the initial interaction of the virus with the target cell. HE mediates receptor binding and destruction, while F promotes the fusion process of the viral and cell membranes. The carboxy-terminal end of F (F2) possesses canonical structural characteristics of a type I fusion protein, while no functional properties have been proposed for the amino-terminal (F1) region. In this report, based on in silico modeling, we propose a tertiary structure for the F1 region, which resembles a sialic acid binding domain. Furthermore, using recombinant forms of both HE and F proteins and an in vitro model system, we demonstrate the interaction of F with a cell receptor, the hydrolysis of this receptor by the HE esterase, and a crucial role for F1 in the fusion mechanism. Our interpretation is that binding of F to its cell receptor is fundamental for membrane fusion and that the esterase in HE modulates this interaction.

Chitosan-Based Nanoparticles for Intracellular Delivery of ISAV Fusion Protein cDNA into Melanoma Cells: A Path to Develop Oncolytic Anticancer Therapies

Oncolytic virus therapy has been tested against cancer in preclinical models and clinical assays. Current evidence shows that viruses induce cytopathic effects associated with fusogenic protein-mediated syncytium formation and immunogenic cell death of eukaryotic cells. We have previously demonstrated that tumor cell bodies generated from cells expressing the fusogenic protein of the infectious salmon anemia virus (ISAV-F) enhance crosspriming and display prophylactic antitumor activity against melanoma tumors. In this work, we evaluated the effects of the expression of ISAV-F on the B16 melanoma model, both in vitro and in vivo, using chitosan nanoparticles as transfection vehicle. We confirmed that the transfection of B16 tumor cells with chitosan nanoparticles (NP-ISAV) allows the expression of a fusogenically active ISAV-F protein and decreases cell viability because of syncytium formation in vitro. However, the in vivo transfection induces a delay in tumor growth, without inducing changes on the lymphoid populations in the tumor and the spleen. Altogether, our observations show that expression of ISAV fusion protein using chitosan nanoparticles induces cell fusion in melanoma cells and slight antitumor response.