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Rounsville TF, Polinski MP, Marini AG, Turner SM, Vendramin N, Cuenca A, Pietrak MR, Peterson BC, Bouchard DA. Rapid differentiation of infectious salmon anemia virus avirulent (HPR0) from virulent (HPRΔ) variants using multiplex RT-qPCR. J Vet Diagn Invest 2024:10406387231223290. [PMID: 38212882 DOI: 10.1177/10406387231223290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024] Open
Abstract
Infectious salmon anemia virus (ISAV; Isavirus salaris) causes an economically important disease of Atlantic salmon (Salmo salar L.). ISA outbreaks have resulted in significant losses of farmed salmon globally, often with a sudden onset. However, 2 phenotypically distinct variants of ISAV exist, each with divergent disease outcomes, associated regulations, and control measures. ISAV-HPRΔ, also known as ISAV-HPR deleted, is responsible for ISA outbreaks; ISAV-HPR0, is avirulent and is not known to cause fish mortality. Current detection methodology requires genetic sequencing of ISAV-positive samples to differentiate phenotypes, which may slow responses to disease management. To increase the speed of phenotypic determinations of ISAV, we developed a new, rapid multiplex RT-qPCR method capable of 1) detecting if a sample contains any form of ISAV, 2) discriminating whether positive samples contain HPRΔ or HPR0, and 3) validating RNA extractions with an internal control, all in a single reaction. Following assay development and optimization, we validated this new multiplex on 31 ISAV strains collected from North America and Europe (28 ISAV-HPRΔ, 3 ISAV-HPR0). Finally, we completed an inter-laboratory comparison of this multiplex qPCR with commercial ISAV testing and found that both methods provided equivalent results for ISAV detection.
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Affiliation(s)
- Thomas F Rounsville
- Pest Management Unit, University of Maine Cooperative Extension Diagnostic and Research Laboratory, Orono, ME, USA
| | - Mark P Polinski
- National Cold Water Marine Aquaculture Center, U.S. Department of Agriculture-Agricultural Research Service, Franklin, ME, USA
| | - Alyssa G Marini
- Pest Management Unit, University of Maine Cooperative Extension Diagnostic and Research Laboratory, Orono, ME, USA
- University of Maine School of Biology and Ecology, Orono, ME, USA
| | - Sarah M Turner
- Aquatic Animal Health Laboratory, University of Maine Cooperative Extension Diagnostic and Research Laboratory, Orono, ME, USA
| | - Niccolò Vendramin
- Unit for Fish and Shellfish Diseases, National Institute of Aquatic Resources, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Argelia Cuenca
- Unit for Fish and Shellfish Diseases, National Institute of Aquatic Resources, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Michael R Pietrak
- National Cold Water Marine Aquaculture Center, U.S. Department of Agriculture-Agricultural Research Service, Franklin, ME, USA
| | - Brian C Peterson
- National Cold Water Marine Aquaculture Center, U.S. Department of Agriculture-Agricultural Research Service, Franklin, ME, USA
| | - Deborah A Bouchard
- Aquatic Animal Health Laboratory, University of Maine Cooperative Extension Diagnostic and Research Laboratory, Orono, ME, USA
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Gautam M, Hammell KL, Burnley H, O'Brien N, Whelan D, Thakur KK. Description of spatiotemporal patterns of infectious salmon anemia virus (ISAV) detections in marine Atlantic Salmon farms in Newfoundland and Labrador. J Aquat Anim Health 2023; 35:296-307. [PMID: 38124493 DOI: 10.1002/aah.10205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 09/23/2023] [Accepted: 09/25/2023] [Indexed: 12/23/2023]
Abstract
OBJECTIVE The objectives of this study were to describe spatiotemporal patterns of infectious salmon anemia virus (ISAV) detections in marine salmonid production sites in the province of Newfoundland and Labrador in Canada. METHODS Infectious salmon anemia virus surveillance data between 2012 and 2020 from the province of Newfoundland and Labrador were used. Data comprised a total of 94 sampling events from 20 Atlantic Salmon Salmo salar production sites in which ISAV was detected. Using linear regression models, factors influencing time to detection (days from stocking to first ISAV detection) and time to depopulation (days from first detection to production site depopulation) were investigated. RESULT Based on 28 unique cases, site-level annual incidence risk of ISAV detection ranged from 3% to 29%. The proportion of ISAV detection by PCR in fish samples ranged from 2% to 45% annually. Overall, ISAV variants from the European clade were more common than variants from the North American clade. The type of ISAV clade, detections of ISAV in nearest production sites based on seaway distances, and year of infectious salmon anemia cases were not associated with time to first ISAV detection. Time to depopulation for sites infected with the ISAV-HPRΔ variant was not associated with ISAV North American or European clades. CONCLUSION Our results contribute to the further understanding of the changing dynamics of infectious salmon anemia detections in Newfoundland and Labrador since its first detection in 2012 and will likely assist in the design of improved disease surveillance and control programs in the province.
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Affiliation(s)
- Milan Gautam
- Centre for Veterinary Epidemiological Research and Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - K Larry Hammell
- Centre for Veterinary Epidemiological Research and Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Holly Burnley
- Centre for Veterinary Epidemiological Research and Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Nicole O'Brien
- Department of Fisheries, Forestry and Agriculture, Aquatic Animal Health Division, St. John's, Newfoundland and Labrador, Canada
| | - Daryl Whelan
- Department of Fisheries, Forestry and Agriculture, Aquatic Animal Health Division, St. John's, Newfoundland and Labrador, Canada
| | - Krishna Kumar Thakur
- Centre for Veterinary Epidemiological Research and Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
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Lyngstad TM, Qviller L, Sindre H, Brun E, Kristoffersen AB. Risk Factors Associated With Outbreaks of Infectious Salmon Anemia (ISA) With Unknown Source of Infection in Norway. Front Vet Sci 2018; 5:308. [PMID: 30574509 PMCID: PMC6292176 DOI: 10.3389/fvets.2018.00308] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 11/21/2018] [Indexed: 12/12/2022] Open
Abstract
The occurrence of infectious salmon anemia (ISA) outbreaks in marine farmed Atlantic salmon constitutes a recurring challenge in Norway. Here, we aim to identify risk factors associated with ISA outbreaks with an unknown source of infection (referred to as primary ISA outbreaks). Primary ISA outbreaks are here defined by an earlier published transmission model. We explored a wide range of possible risk factors with logistic regression analysis, trying to explain occurrence of primary ISA with available data from all Norwegian farm sites from 2004 to June 2017. Explanatory variables included site latitude and a range of production and disease data. The mean annual risk of having a primary outbreak of ISA in Norway was 0.7% during this study period. We identified the occurrence of infectious pancreatic necrosis (IPN), having a stocking period longer than 2 months, having the site located at high latitude and high fish density (biomass per cage volume) in the first six months after transfer to sea site as significant risk factors (p < 0.05). We have identified factors related to management routines, other disease problems, and latitude that may help to understand the hitherto unidentified drivers behind the emergence of primary ISA outbreaks. Based on our findings, we also provide management advice that may reduce the incidence of primary ISA outbreaks.
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Affiliation(s)
| | | | | | - Edgar Brun
- Norwegian Veterinary Institute, Oslo, Norway
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Li J, Boroevich KA, Koop BF, Davidson WS. Comparative genomics identifies candidate genes for infectious salmon anemia (ISA) resistance in Atlantic salmon (Salmo salar). Mar Biotechnol (NY) 2011; 13:232-41. [PMID: 20396924 PMCID: PMC3084937 DOI: 10.1007/s10126-010-9284-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2009] [Accepted: 03/04/2010] [Indexed: 05/25/2023]
Abstract
Infectious salmon anemia (ISA) has been described as the hoof and mouth disease of salmon farming. ISA is caused by a lethal and highly communicable virus, which can have a major impact on salmon aquaculture, as demonstrated by an outbreak in Chile in 2007. A quantitative trait locus (QTL) for ISA resistance has been mapped to three microsatellite markers on linkage group (LG) 8 (Chr 15) on the Atlantic salmon genetic map. We identified bacterial artificial chromosome (BAC) clones and three fingerprint contigs from the Atlantic salmon physical map that contains these markers. We made use of the extensive BAC end sequence database to extend these contigs by chromosome walking and identified additional two markers in this region. The BAC end sequences were used to search for conserved synteny between this segment of LG8 and the fish genomes that have been sequenced. An examination of the genes in the syntenic segments of the tetraodon and medaka genomes identified candidates for association with ISA resistance in Atlantic salmon based on differential expression profiles from ISA challenges or on the putative biological functions of the proteins they encode. One gene in particular, HIV-EP2/MBP-2, caught our attention as it may influence the expression of several genes that have been implicated in the response to infection by infectious salmon anemia virus (ISAV). Therefore, we suggest that HIV-EP2/MBP-2 is a very strong candidate for the gene associated with the ISAV resistance QTL in Atlantic salmon and is worthy of further study.
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Affiliation(s)
- Jieying Li
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC Canada V5A 1S6
| | - Keith A. Boroevich
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC Canada V5A 1S6
| | - Ben F. Koop
- Department of Biology, University of Victoria, Victoria, BC Canada V8W 3N5
| | - William S. Davidson
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC Canada V5A 1S6
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