Emerging pathogens in the fish farming industry and sequencing-based pathogen discovery. (October 2017)

• Record Type: Journal Article
• Authors: Tengs, Torstein; Rimstad, Espen
• Is Part Of: Developmental and comparative immunology. Volume 75(2017)
• Page Start: 109
• Page End: 119
• Publication Date: 2017-10
• Subjects: Next generation sequencing -- Atlantic salmon -- Salmo salar -- PRV -- PMCV -- SGPV; CMS cardiomyopathy syndrome -- DDBJ DNA Data Bank of Japan -- ENA European Nucleotide Archive -- EST expressed sequence tags -- GSS genome survey sequence -- HSMI heart- and skeletal muscle inflammation -- HSS haemorrhagic smolt syndrome -- IPN infectious pancreatic necrosis -- IPNV Infectious pancreatic necrosis virus -- ISA infectious salmon anemia -- ISAV Infectious salmon anemia virus -- PD pancreas disease -- PDG proliferative gill disease -- PMCV Piscine myocarditis virus -- PRV Piscine orthoreovirus -- RACE rapid amplification of cDNA ends -- SAV Salmon alphavirus -- SGPV Salmon gill poxvirus -- SPDV Salmon pancreas disease virus -- SSH suppression subtractive hybridization -- VACV Vaccinia virus -- VHS viral hemorrhagic septicemia -- VHSV Viral hemorrhagic septicemia virus; Immunology -- Periodicals; Developmental immunology -- Periodicals; 616.079
• DOI: 10.1016/j.dci.2017.01.025
• Languages: English
• ISSNs: 0145-305X

Abstract

Abstract: The use of large scale DNA/RNA sequencing has become an integral part of biomedical research. Reduced sequencing costs and the availability of efficient computational resources has led to a revolution in how problems concerning genomics and transcriptomics are addressed. Sequencing-based pathogen discovery represents one example of how genetic data can now be used in ways that were previously considered infeasible. Emerging pathogens affect both human and animal health due to a multitude of factors, including globalization, a shifting environment and an increasing human population. Fish farming represents a relevant, interesting and challenging system to study emerging pathogens. This review summarizes recent progress in pathogen discovery using sequence data, with particular emphasis on viruses in Atlantic salmon ( Salmo salar ). Highlights: Large-scale sequencing makes pathogen discovery possible without culturing or visual identification. Outbreaks of both established and emerging pathogens are associated with significant losses in the fish farming industry. Sequencing-based pathogen discovery has led to the description of several important viruses affecting farmed Atlantic salmon.