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Meyer A, Faverjon C, Hostens M, Stegeman A, Cameron A. Systematic review of the status of veterinary epidemiological research in two species regarding the FAIR guiding principles. BMC Vet Res 2021; 17:270. [PMID: 34380468 PMCID: PMC8355576 DOI: 10.1186/s12917-021-02971-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 07/06/2021] [Indexed: 01/08/2023] Open
Abstract
Background The FAIR (Findable, Accessible, Interoperable, Reusable) principles were proposed in 2016 to set a path towards reusability of research datasets. In this systematic review, we assessed the FAIRness of datasets associated with peer-reviewed articles in veterinary epidemiology research published since 2017, specifically looking at salmonids and dairy cattle. We considered the differences in practices between molecular epidemiology, the branch of epidemiology using genetic sequences of pathogens and hosts to describe disease patterns, and non-molecular epidemiology. Results A total of 152 articles were included in the assessment. Consistent with previous assessments conducted in other disciplines, our results showed that most datasets used in non-molecular epidemiological studies were not available (i.e., neither findable nor accessible). Data availability was much higher for molecular epidemiology papers, in line with a strong repository base available to scientists in this discipline. The available data objects generally scored favourably for Findable, Accessible and Reusable indicators, but Interoperability was more problematic. Conclusions None of the datasets assessed in this study met all the requirements set by the FAIR principles. Interoperability, in particular, requires specific skills in data management which may not yet be broadly available in the epidemiology community. In the discussion, we present recommendations on how veterinary research could move towards greater reusability according to FAIR principles. Overall, although many initiatives to improve data access have been started in the research community, their impact on the availability of datasets underlying published articles remains unclear to date. Supplementary Information The online version contains supplementary material available at 10.1186/s12917-021-02971-1.
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Affiliation(s)
- Anne Meyer
- Ausvet Europe, 3 rue Camille Jordan, 69001, Lyon, France. .,Department of Farm Animal Health, Utrecht University, 3512 JE, Utrecht, the Netherlands.
| | | | - Miel Hostens
- Department of Farm Animal Health, Utrecht University, 3512 JE, Utrecht, the Netherlands
| | - Arjan Stegeman
- Department of Farm Animal Health, Utrecht University, 3512 JE, Utrecht, the Netherlands
| | - Angus Cameron
- Ausvet Europe, 3 rue Camille Jordan, 69001, Lyon, France
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Mordecai GJ, Miller KM, Bass AL, Bateman AW, Teffer AK, Caleta JM, Di Cicco E, Schulze AD, Kaukinen KH, Li S, Tabata A, Jones BR, Ming TJ, Joy JB. Aquaculture mediates global transmission of a viral pathogen to wild salmon. SCIENCE ADVANCES 2021; 7:7/22/eabe2592. [PMID: 34039598 PMCID: PMC8153721 DOI: 10.1126/sciadv.abe2592] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 04/07/2021] [Indexed: 05/07/2023]
Abstract
Global expansion of aquaculture and agriculture facilitates disease emergence and catalyzes transmission to sympatric wildlife populations. The health of wild salmon stocks critically concerns Indigenous peoples, commercial and recreational fishers, and the general public. Despite potential impact of viral pathogens such as Piscine orthoreovirus-1 (PRV-1) on endangered wild salmon populations, their epidemiology in wild fish populations remains obscure, as does the role of aquaculture in global and local spread. Our phylogeographic analyses of PRV-1 suggest that development of Atlantic salmon aquaculture facilitated spread from Europe to the North and South East Pacific. Phylogenetic analysis and reverse transcription polymerase chain reaction surveillance further illuminate the circumstances of emergence of PRV-1 in the North East Pacific and provide strong evidence for Atlantic salmon aquaculture as a source of infection in wild Pacific salmon. PRV-1 is now an important infectious agent in critically endangered wild Pacific salmon populations, fueled by aquacultural transmission.
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Affiliation(s)
- Gideon J Mordecai
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada.
| | - Kristina M Miller
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada.
- Department of Forest and Conservation Sciences, Forest Sciences Centre, 3041 2424 Main Mall, Vancouver, BC V6T 1Z4, Canada
| | - Arthur L Bass
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Andrew W Bateman
- Pacific Salmon Foundation, 1682 W 7th Ave., Vancouver, BC V6J 4S6, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Room 3055, Toronto, ON M5S 3B2, Canada
- Salmon Coast Field Station General Delivery, Simoom Sound, BC V0P 1S0, Canada
| | - Amy K Teffer
- David H. Smith Conservation Research Fellowship, Society for Conservation Biology, Washington, DC, USA
| | - Jessica M Caleta
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Emiliano Di Cicco
- Pacific Salmon Foundation, 1682 W 7th Ave., Vancouver, BC V6J 4S6, Canada
| | - Angela D Schulze
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Karia H Kaukinen
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Shaorong Li
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Amy Tabata
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Brad R Jones
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
- Bioinformatics Programme, University of British Columbia, Vancouver, BC, Canada
| | - Tobi J Ming
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Jeffrey B Joy
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
- Bioinformatics Programme, University of British Columbia, Vancouver, BC, Canada
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Piscine Orthoreovirus (PRV)-3, but Not PRV-2, Cross-Protects against PRV-1 and Heart and Skeletal Muscle Inflammation in Atlantic Salmon. Vaccines (Basel) 2021; 9:vaccines9030230. [PMID: 33800725 PMCID: PMC8001985 DOI: 10.3390/vaccines9030230] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/26/2021] [Accepted: 03/02/2021] [Indexed: 02/06/2023] Open
Abstract
Heart and skeletal muscle inflammation (HSMI), caused by infection with Piscine orthoreovirus-1 (PRV-1), is a common disease in farmed Atlantic salmon (Salmo salar). Both an inactivated whole virus vaccine and a DNA vaccine have previously been tested experimentally against HSMI and demonstrated to give partial but not full protection. To understand the mechanisms involved in protection against HSMI and evaluate the potential of live attenuated vaccine strategies, we set up a cross-protection experiment using PRV genotypes not associated with disease development in Atlantic salmon. The three known genotypes of PRV differ in their preference of salmonid host species. The main target species for PRV-1 is Atlantic salmon. Coho salmon (Oncorhynchus kisutch) is the target species for PRV-2, where the infection may induce erythrocytic inclusion body syndrome (EIBS). PRV-3 is associated with heart pathology and anemia in rainbow trout, but brown trout (S. trutta) is the likely natural main host species. Here, we tested if primary infection with PRV-2 or PRV-3 in Atlantic salmon could induce protection against secondary PRV-1 infection, in comparison with an adjuvanted, inactivated PRV-1 vaccine. Viral kinetics, production of cross-reactive antibodies, and protection against HSMI were studied. PRV-3, and to a low extent PRV-2, induced antibodies cross-reacting with the PRV-1 σ1 protein, whereas no specific antibodies were detected after vaccination with inactivated PRV-1. Ten weeks after immunization, the fish were challenged through cohabitation with PRV-1-infected shedder fish. A primary PRV-3 infection completely blocked PRV-1 infection, while PRV-2 only reduced PRV-1 infection levels and the severity of HSMI pathology in a few individuals. This study indicates that infection with non-pathogenic, replicating PRV could be a future strategy to protect farmed salmon from HSMI.
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Polinski MP, Vendramin N, Cuenca A, Garver KA. Piscine orthoreovirus: Biology and distribution in farmed and wild fish. JOURNAL OF FISH DISEASES 2020; 43:1331-1352. [PMID: 32935367 DOI: 10.1111/jfd.13228] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/06/2020] [Accepted: 07/08/2020] [Indexed: 06/11/2023]
Abstract
Piscine orthoreovirus (PRV) is a common and widely distributed virus of salmonids. Since its discovery in 2010, the virus has been detected in wild and farmed stocks from North America, South America, Europe and East Asia in both fresh and salt water environments. Phylogenetic analysis suggests three distinct genogroups of PRV with generally discrete host tropisms and/or regional patterns. PRV-1 is found mainly in Atlantic (Salmo salar), Chinook (Oncorhynchus tshawytscha) and Coho (Oncorhynchus kisutch) Salmon of Europe and the Americas; PRV-2 has only been detected in Coho Salmon of Japan; and PRV-3 has been reported primarily in Rainbow Trout (Oncorhynchus mykiss) in Europe. All three genotypes can establish high-load systemic infections by targeting red blood cells for principal replication. Each genotype has also demonstrated potential to cause circulatory disease. At the same time, high-load PRV infections occur in non-diseased salmon and trout, indicating a complexity for defining PRV's role in disease aetiology. Here, we summarize the current body of knowledge regarding PRV following 10 years of study.
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Affiliation(s)
- Mark P Polinski
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Niccoló Vendramin
- National Institute of Aquatic Resources, Technical University of Denmark, Lyngby, Denmark
| | - Argelia Cuenca
- National Institute of Aquatic Resources, Technical University of Denmark, Lyngby, Denmark
| | - Kyle A Garver
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
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Siah A, Breyta RB, Warheit KI, Gagne N, Purcell MK, Morrison D, Powell JFF, Johnson SC. Genomes reveal genetic diversity of Piscine orthoreovirus in farmed and free-ranging salmonids from Canada and USA. Virus Evol 2020; 6:veaa054. [PMID: 33381304 PMCID: PMC7751156 DOI: 10.1093/ve/veaa054] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Piscine orthoreovirus (PRV-1) is a segmented RNA virus, which is commonly found in salmonids in the Atlantic and Pacific Oceans. PRV-1 causes the heart and skeletal muscle inflammation disease in Atlantic salmon and is associated with several other disease conditions. Previous phylogenetic studies of genome segment 1 (S1) identified four main genogroups of PRV-1 (S1 genogroups I–IV). The goal of the present study was to use Bayesian phylogenetic inference to expand our understanding of the spatial, temporal, and host patterns of PRV-1 from the waters of the northeast Pacific. To that end, we determined the coding genome sequences of fourteen PRV-1 samples that were selected to improve our knowledge of genetic diversity across a broader temporal, geographic, and host range, including the first reported genome sequences from the northwest Atlantic (Eastern Canada). Nucleotide and amino acid sequences of the concatenated genomes and their individual segments revealed that established sequences from the northeast Pacific were monophyletic in all analyses. Bayesian inference phylogenetic trees of S1 sequences using BEAST and MrBayes also found that sequences from the northeast Pacific grouped separately from sequences from other areas. One PRV-1 sample (WCAN_BC17_AS_2017) from an escaped Atlantic salmon, collected in British Columbia but derived from Icelandic broodstock, grouped with other S1 sequences from Iceland. Our concatenated genome and S1 analysis demonstrated that PRV-1 from the northeast Pacific is genetically distinct but descended from PRV-1 from the North Atlantic. However, the analyses were inconclusive as to the timing and exact source of introduction into the northeast Pacific, either from eastern North America or from European waters of the North Atlantic. There was no evidence that PRV-1 was evolving differently between free-ranging Pacific Salmon and farmed Atlantic Salmon. The northeast Pacific PRV-1 sequences fall within genogroup II based on the classification of Garseth, Ekrem, and Biering (Garseth, A. H., Ekrem, T., and Biering, E. (2013) ‘Phylogenetic Evidence of Long Distance Dispersal and Transmission of Piscine Reovirus (PRV) between Farmed and Wild Atlantic Salmon’, PLoS One, 8: e82202.), which also includes North Atlantic sequences from Eastern Canada, Iceland, and Norway. The additional full-genome sequences herein strengthen our understanding of phylogeographical patterns related to the northeast Pacific, but a more balanced representation of full PRV-1 genomes from across its range, as well additional sequencing of archived samples, is still needed to better understand global relationships including potential transmission links among regions.
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Affiliation(s)
- A Siah
- British Columbia Centre for Aquatic Health Sciences, 871A Island Highway, V9W 2C2, Campbell River, BC, Canada
| | - R B Breyta
- School of Aquatic Fisheries Sciences, University of Washington, Western Fisheries Research Center, USGS, 6505 NE 65th Street Seattle, WA 98115-5016, USA
| | - K I Warheit
- Washington Department of Fish and Wildlife PO Box 43200, Olympia, WA 98504-3200, USA
| | - N Gagne
- Gulf Fisheries Center, Fisheries & Oceans, 343 Université Ave, Moncton, NB E1C 5K4, Canada
| | - M K Purcell
- Western Fisheries Research Center, U.S. Geological Survey, 56505 NE 65th Street Seattle, WA 98115-5016, USA
| | - D Morrison
- Mowi Canada West, Campbell River, BC, Canada
| | - J F F Powell
- British Columbia Centre for Aquatic Health Sciences, 871A Island Highway, V9W 2C2, Campbell River, BC, Canada
| | - S C Johnson
- Fisheries & Oceans Canada, Nanaimo, British Columbia, Canada
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Teffer AK, Carr J, Tabata A, Schulze A, Bradbury I, Deschamps D, Gillis CA, Brunsdon EB, Mordecai G, Miller KM. A molecular assessment of infectious agents carried by Atlantic salmon at sea and in three eastern Canadian rivers, including aquaculture escapees and North American and European origin wild stocks. Facets (Ott) 2020. [DOI: 10.1139/facets-2019-0048] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Infectious agents are key components of animal ecology and drivers of host population dynamics. Knowledge of their diversity and transmission in the wild is necessary for the management and conservation of host species like Atlantic salmon ( Salmo salar). Although pathogen exchange can occur throughout the salmon life cycle, evidence is lacking to support transmission during population mixing at sea or between farmed and wild salmon due to aquaculture exposure. We tested these hypotheses using a molecular approach that identified infectious agents and transmission potential among sub-adult Atlantic salmon at marine feeding areas and adults in three eastern Canadian rivers with varying aquaculture influence. We used high-throughput qPCR to quantify infection profiles and next generation sequencing to measure genomic variation among viral isolates. We identified 14 agents, including five not yet described as occurring in Eastern Canada. Phylogenetic analysis of piscine orthoreovirus showed homology between isolates from European and North American origin fish at sea, supporting the hypothesis of intercontinental transmission. We found no evidence to support aquaculture influence on wild adult infections, which varied relative to environmental conditions, life stage, and host origin. Our findings identify research opportunities regarding pathogen transmission and biological significance for wild Atlantic salmon populations.
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Affiliation(s)
- Amy K. Teffer
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4, Canada
| | - Jonathan Carr
- Atlantic Salmon Federation, Chamcook, NB E5B 3A9, Canada
| | - Amy Tabata
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC V9T 6N7, Canada
| | - Angela Schulze
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC V9T 6N7, Canada
| | - Ian Bradbury
- Salmonids Section, Fisheries and Oceans Canada, St. John’s, NF A1C 5X1, Canada
| | - Denise Deschamps
- Ministère des Forêts, de la Faune et des Parcs du Québec, Direction de l’expertise sur la faune aquatique, Quebec, QC G1S 4X4, Canada
| | | | | | - Gideon Mordecai
- Department of Medicine, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Kristina M. Miller
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC V9T 6N7, Canada
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Kibenge MJT, Wang Y, Gayeski N, Morton A, Beardslee K, McMillan B, Kibenge FSB. Correction to: Piscine orthoreovirus sequences in escaped farmed Atlantic salmon in Washington and British Columbia. Virol J 2019; 16:60. [PMID: 31064382 PMCID: PMC6503429 DOI: 10.1186/s12985-019-1166-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 04/22/2019] [Indexed: 11/10/2022] Open
Abstract
In the original publication of the article [1], as the quotation below was included without specific permission from Dr. Gary Marty, which is against the Virology Journal guidelines for the citation of unpublished data, all authors request to delete it from their article.
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Affiliation(s)
- Molly J T Kibenge
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave, Charlottetown, P.E.I C1A 4P3, Canada
| | - Yingwei Wang
- School of Mathematical and Computational Sciences, University of Prince Edward Island, 550 University Ave, Charlottetown, P.E.I C1A 4P3, Canada
| | - Nick Gayeski
- Wild FishConservancy, PO Box 402, 15629 Main St. NE, Duvall, WA, 98019, USA
| | - Alexandra Morton
- RaincoastResearch Society, Box 399, Sointula, BC V0N 3E0, Canada
| | - Kurt Beardslee
- Wild FishConservancy, PO Box 402, 15629 Main St. NE, Duvall, WA, 98019, USA
| | - Bill McMillan
- Wild FishConservancy, PO Box 402, 15629 Main St. NE, Duvall, WA, 98019, USA
| | - Frederick S B Kibenge
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave, Charlottetown, P.E.I C1A 4P3, Canada.
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