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.

Evaluation of the Antiviral Activity against Infectious Pancreatic Necrosis Virus (IPNV) of a Copper (I) Homoleptic Complex with a Coumarin as Ligand

The aquatic infectious pancreatic necrosis virus (IPNV) causes a severe disease in farmed salmonid fish that generates great economic losses in the aquaculture industry. In the search for new tools to control the disease, in this paper we show the results obtained from the evaluation of the antiviral effect of [Cu(NN1)2](ClO4) Cu(I) complex, synthesized in our laboratory, where the NN1 ligand is a synthetic derivate of the natural compound coumarin. This complex demonstrated antiviral activity against IPNV at 5.0 and 15.0 µg/mL causing a decrease viral load 99.0% and 99.5%, respectively. The Molecular Docking studies carried out showed that the copper complex would interact with the VP2 protein, specifically in the S domain, altering the process of entry of the virus into the host cell.

Identification of a New Infectious Pancreatic Necrosis Virus (IPNV) Variant in Atlantic Salmon (Salmo salar L.) that can Cause High Mortality Even in Genetically Resistant Fish

Infectious pancreatic necrosis (IPN) is an important viral disease of salmonids that can affect fish during various life cycles. In Atlantic salmon, selecting for genetically resistant fish against IPN has been one of the most highly praised success stories in the history of fish breeding. During the late 2000s, the findings that resistance against this disease has a significant genetic component, which is mainly controlled by variations in a single gene, have helped to reduce the IPN outbreaks to a great extent. In this paper, we present the identification of a new variant of the IPN virus from a field outbreak in Western Norway that had caused mortality, even in genetically resistant salmon. We recovered and assembled the full-length genome of this virus, following the deep-sequencing of the head-kidney transcriptome. The comparative sequence analysis revealed that for the critical amino acid motifs, previously found to be associated with the degree of virulence, the newly identified variant is similar to the virus’s avirulent form. However, we detected a set of deduced amino acid residues, particularly in the hypervariable domain of the VP2, that collectively are unique to this variant compared to all other reference sequences assessed in this study. We suggest that these mutations have likely equipped the virus with the capacity to escape the host defence mechanism more efficiently, even in the genetically deemed IPN resistant fish.

Detections of Rainbow Trout Antibodies to Infectious Pancreatic Necrosis Virus and Viral Hemorrhagic Septicemia Virus via a Recombinant Protein-Based Enzyme-Linked Immunosorbent Assay

Infectious Pancreatic Necrosis Virus (IPNV) and Viral hemorrhagic septicemia virus (VHSV) cause significant losses in the aquaculture industry. There have been few reports of the use of screening rainbow trout for antibodies against IPNV and VHSV as an epidemiological tool. Several ELISAs using a whole virus or recombinant IPNV and VHSV proteins have been described. In this study, a recombinant protein-based enzyme-linked immunosorbent assay (ELISA) for the detection of IPNV and VHSV antibodies in rainbow trout (Oncorhynchus mykiss) was evaluated. To develop recombinant protein-based enzyme-linked immunosorbent assays, a fragment containing the entire length of the gG gene of VHSV and VP2 of IPNV was amplified by PCR using the viruses' genomic RNA and cloned in pET-28a(+) plasmid. Recombinant structural viral proteins (rVP2 and rgG) were expressed in the Escherichia coli BL21 (DE3). The rgG was extracted and purified. 96-well plates were coated with VP2 and gG separately. For VHSV, Assay could detect until 1/15625 dilution in VHSV positive fish serum. For IPNV, Assays could detect until 1/3125 dilution in IPNV positive fish serum. These results show rgG and rVP2, used in ELISA, are more sensitive than virus neutralization tests.

Identification of a new Infectious Pancreatic Necrosis Virus (IPNV) isolate in Atlantic salmon (Salmo salar L.) that causes mortality in resistant fish

Infectious pancreatic necrosis (IPN) is an important viral disease of salmonids that can affect fish during various life cycles. In Atlantic salmon, selecting for genetically resistant animals against IPN has been one of the most highly praised success stories in the history of fish breeding. The findings that resistance against this disease has a significant genetic component, which is mainly controlled by variations in a single gene, has helped to reduce the IPN outbreaks over the past decade to a great extent. In this paper, we present the identification of a new isolate of the IPN virus, from a field outbreak, that had caused mortality, even in the genetically resistant animals. We recovered and assembled the full-length genome of this virus, following deep-sequencing of an infected tissue. The comparative sequence analysis revealed that for the critical amino acid motifs, previously found to be associated with the degree of virulence, the newly identified isolate is similar to the virus's avirulent form. However, we detected a set of deduced amino acid residues, particularly in the hypervariable region of the polyprotein, that collectively are unique to this strain compared to all other reference sequences assessed in this study. We suggest that these mutations have likely equipped the virus with the capacity to escape the host defence mechanism more efficiently, even in the genetically deemed IPN resistant animals.

Small Incision Combined with Nephroscope Operation in the Treatment of Infectious Pancreatic Necrosis: A Single-Center Experience of 37 Patients

Objective. To explore the safety and efficacy of small incision combined with nephroscope surgery in the treatment of infectious pancreatic necrosis. Methods. A retrospective analysis of the clinical data of 37 patients with infectious pancreatic necrosis who underwent small incision combined with nephroscopy in the Department of Hepatobiliary Surgery of Hunan Provincial People’s Hospital from January 2018 to December 2019. Results. All 37 patients successfully completed small incision combined nephroscope surgery. The median time from the onset to the operation of all patients was 38 days (range: 29-80 days), and the hospital stay was 19 days (range: 3-95 days). The median number of drainage tubes placed during the operation was 4 (range: 2-8). According to the different surgical approaches, 13 cases were through the retroperitoneal approach, 11 cases were through the omental sac approach, 2 cases were through the intercostal approach, and 11 cases were combined approach. The operation time was 85.3 ± 31.6 min, and intraoperative bleeding was 63.1 ± 40.0 ml. The incidence of complications (Clavien-Dindo grade 3 and above) was 5.4%. Among them, 2 patients were admitted to the intensive care unit due to postoperative bleeding, 1 case was cured by conservative treatment, and 1 case was cured by interventional treatment. During the follow-up period, 2 patients developed colonic fistula at 2 weeks after operation, and 2 patients developed gastric fistula at 1 week and 3 weeks after operation; all were cured by conservative treatment. Conclusion. Small incision combined with nephroscope surgery is an effective treatment for patients with infectious pancreatic necrosis by removing necrotic tissue, unobstructed drainage, and reducing complications.

Molecular Evolution of Infectious Pancreatic Necrosis Virus in China

Passive virus surveillance was performed in twenty-nine salmon and trout farms from seven provinces and districts in China during the period 2017–2020. A total of 25 infectious pancreatic necrosis virus (IPNV) isolates were obtained, mainly from rainbow trout (Oncorhynchus mykiss). The molecular evolution of these Chinese IPNV isolates and the previously reported Chinese IPNV strains ChRtm213 and WZ2016 was analyzed, based on their VP2 gene coding region sequences (CDS). All 27 Chinese IPNV isolates clustered within genogroups I and V, with 24 of the IPNV isolates belonging to genogroup I (including ChRtm213 and WZ2016), and only three isolates clustering in genogroup V. The Chinese genogroup I IPNV isolates lacked diversity, composing six haplotypes with 41 polymorphic sites, and the identity of nucleotide and amino acid sequences among the entire VP2 gene CDS from these isolates was 97.44%–100% and 98.19%–100%, respectively. Divergence time analyses revealed that the Chinese genogroup I IPNV isolates likely diverged from Japanese IPNV isolates in 1985 (95% highest posterior density (HPD), 1965–1997), and diverged again in 2006 (95% HPD, 1996–2013) in China. Each of the three Chinese genogroup V IPNV isolates has a unique VP2 gene CDS, with a total of 21 polymorphic sites; the identity of nucleotide and amino acid sequences among all VP2 gene CDS from these isolates was 98.5%–99.5% and 98.6%–99.0%, respectively. The data demonstrate that genogroups I and V are more likely the currently prevalent Chinese IPNV genotypes.