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Öhlschuster M, Comiskey D, Kavanagh M, Kickinger F, Scaldaferri C, Sigler M, Nilsen P. On the prediction of SAV transmission among Norwegian aquaculture sites. Prev Vet Med 2024; 224:106095. [PMID: 38232517 DOI: 10.1016/j.prevetmed.2023.106095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 11/28/2023] [Accepted: 12/12/2023] [Indexed: 01/19/2024]
Abstract
Pancreas Disease (PD) is a viral disease that affects Atlantic salmon (Salmo salar) in Norwegian, Scottish and Irish aquaculture. It is caused by salmonid alphavirus (SAV) and represents a significant problem in salmonid farming. Infection with SAV leads to reduced growth, mortality, product downgrading, and has a significant financial impact for the farms. The overall aim of this study is to evaluate the effect of various factors on the transmission of SAV and to create a predictive model capable of providing an early warning system for salmon farms within the Norwegian waters. Using a combination of publicly available databases, specifically BarentsWatch, and privately held PCR analyses a feature set consisting of 11 unique features was created based on the input parameters of the databases. An ensemble model was developed based on this feature set using XG-Boost, Ada-Boost, Random Forest and a Multilayer Perceptron. It was possible to successfully predict SAV transmission with 94.4% accuracy. Moreover, it was possible to predict SAV transmission 8 weeks in advance of a 'PD registration' at individual aquaculture salmon farming sites. Important predictors included well boat movement, environmental factors, proximity to sites with a 'PD registration' and seasonality.
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Affiliation(s)
| | - D Comiskey
- Zoetis, Cherrywood Business Park, Loughlinstown, D18 T3Y1 Dublin, Ireland
| | - M Kavanagh
- Zoetis, Cherrywood Business Park, Loughlinstown, D18 T3Y1 Dublin, Ireland
| | | | | | - M Sigler
- Zoetis, Jutogasse 3, 4675 Weibern, Austria
| | - P Nilsen
- Pharmaq Analytiq, Thormøhlensgate 53D, Bergen 5006, Norway.
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2
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Dorotea T, Riuzzi G, Franzago E, Posen P, Tavornpanich S, Di Lorenzo A, Ferroni L, Martelli W, Mazzucato M, Soccio G, Segato S, Ferrè N. A Scoping Review on GIS Technologies Applied to Farmed Fish Health Management. Animals (Basel) 2023; 13:3525. [PMID: 38003143 PMCID: PMC10668695 DOI: 10.3390/ani13223525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/08/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
Finfish aquaculture, one of the fastest growing intensive sectors worldwide, is threatened by numerous transmissible diseases that may have devastating impacts on its economic sustainability. This review (2010-2022) used a PRISMA extension for scoping reviews and a text mining approach to explore the extent to which geographical information systems (GIS) are used in farmed fish health management and to unveil the main GIS technologies, databases, and functions used to update the spatiotemporal data underpinning risk and predictive models in aquatic surveillance programmes. After filtering for eligibility criteria, the literature search provided 54 records, highlighting the limited use of GIS technologies for disease prevention and control, as well as the prevalence of GIS application in marine salmonid farming, especially for viruses and parasitic diseases typically associated with these species. The text mining generated five main research areas, underlining a limited range of investigated species, rearing environments, and diseases, as well as highlighting the lack of GIS-based methodologies at the core of such publications. This scoping review provides a source of information for future more detailed literature analyses and outcomes to support the development of geospatial disease spread models and expand in-field GIS technologies for the prevention and mitigation of fish disease epidemics.
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Affiliation(s)
- Tiziano Dorotea
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy; (T.D.); (E.F.); (M.M.); (G.S.); (N.F.)
| | - Giorgia Riuzzi
- Department of Animal Medicine, Production and Health, University of Padova, 35020 Legnaro, Italy;
| | - Eleonora Franzago
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy; (T.D.); (E.F.); (M.M.); (G.S.); (N.F.)
| | - Paulette Posen
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset DT4 8UB, UK;
| | - Saraya Tavornpanich
- Department of Aquatic Animal Health and Welfare, Norwegian Veterinary Institute, 1433 Ås, Norway;
| | - Alessio Di Lorenzo
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, 64100 Teramo, Italy;
| | - Laura Ferroni
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, 06126 Perugia, Italy;
| | - Walter Martelli
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, 10154 Torino, Italy;
| | - Matteo Mazzucato
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy; (T.D.); (E.F.); (M.M.); (G.S.); (N.F.)
| | - Grazia Soccio
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy; (T.D.); (E.F.); (M.M.); (G.S.); (N.F.)
| | - Severino Segato
- Department of Animal Medicine, Production and Health, University of Padova, 35020 Legnaro, Italy;
| | - Nicola Ferrè
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Italy; (T.D.); (E.F.); (M.M.); (G.S.); (N.F.)
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3
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Nielsen SS, Alvarez J, Calistri P, Canali E, Drewe JA, Garin‐Bastuji B, Gonzales Rojas JL, Gortázar C, Herskin MS, Michel V, Miranda Chueca MÁ, Padalino B, Roberts HC, Spoolder H, Ståhl K, Velarde A, Viltrop A, Winckler C, Bron J, Olesen NJ, Sindre H, Stone D, Vendramin N, Antoniou SE, Broglia A, Karagianni AE, Papanikolaou A, Bicout DJ. Assessment of listing and categorisation of animal diseases within the framework of the Animal Health Law (Regulation (EU)2016/429): Infection with salmonid alphavirus (SAV). EFSA J 2023; 21:e08327. [PMID: 37908450 PMCID: PMC10613945 DOI: 10.2903/j.efsa.2023.8327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023] Open
Abstract
Infection with salmonid alphavirus (SAV) was assessed according to the criteria of the Animal Health Law (AHL), in particular the criteria of Article 7 on disease profile and impacts, Article 5 on its eligibility to be listed, Annex IV for its categorisation according to disease prevention and control rules as laid out in Article 9 and Article 8 for listing animal species related to infection with SAV. The assessment was performed following the ad hoc method on data collection and assessment developed by AHAW Panel and already published. The outcome reported is the median of the probability ranges provided by the experts, which indicates whether each criterion is fulfilled (lower bound ≥ 66%) or not (upper bound ≤ 33%), or whether there is uncertainty about fulfilment. Reasoning points are reported for criteria with an uncertain outcome. According to the assessment, it was uncertain whether infection with salmonid alphavirus can be considered eligible to be listed for Union intervention according to Article 5 of the AHL (50-80% probability). According to the criteria in Annex IV, for the purpose of categorisation related to the level of prevention and control as in Article 9 of the AHL, the AHAW Panel concluded that infection with salmonid alphavirus does not meet the criteria in Section 1 (Category A; 5-10% probability of meeting the criteria) and it is uncertain whether it meets the criteria in Sections 2, 3, 4 and 5 (Categories B, C, D and E; 50-90%, probability of meeting the criteria). The animal species to be listed for infection with SAV according to Article 8 criteria are provided.
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Tvete IF, Aldrin M, Jensen BB. Towards better survival: Modeling drivers for daily mortality in Norwegian Atlantic salmon farming. Prev Vet Med 2023; 210:105798. [PMID: 36402048 DOI: 10.1016/j.prevetmed.2022.105798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 11/07/2022] [Accepted: 11/10/2022] [Indexed: 11/13/2022]
Abstract
Mortality in the production of farmed salmonids is a major constraint to the sustainability of this form of animal husbandry. We have developed a model for the daily mortality in salmon farming over a full production cycle from stocking to harvest, considering different environmental and production factors. These factors included sea temperature, salinity, day within year, fish weight at stocking, stocking day, four types of lice treatments and the possible occurrence of pancreas disease (PD). We considered a generalized additive model following full production cycles, allowing for non-linear descriptions of how relevant factors relate to the daily mortality. We saw a high overall mortality rate immediately after stocking, which decreased the first three months in the cycle and thereafter increased. We found that the total mortality could be reduced by 21% if avoiding all lice treatments, and similarly reduced by 20% if no PD infections occurred. If avoiding jointly PD and all lice treatments, the accumulated mortality could be reduced by 34%. A single thermal or hydrogen peroxide treatment was associated with a mortality of around 1.6% and 1.3%, respectively. This modeling approach gave a unique opportunity to model how different factors interact on the overall global mortality and can easily be extended by other factors, such as additional fish diseases.
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Affiliation(s)
- Ingunn Fride Tvete
- The Norwegian Computing Center, Mailbox 114 Blindern, 0314 Oslo, Norway.
| | - Magne Aldrin
- The Norwegian Computing Center, Mailbox 114 Blindern, 0314 Oslo, Norway.
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5
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Okawa M, Iwata T, Tanaka Y, Kurashima T, Toda H, Kashima H. Context-aware spatio-temporal event prediction via convolutional Hawkes processes. Mach Learn 2022. [DOI: 10.1007/s10994-022-06136-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Bang Jensen B, Dean KR, Huseby RB, Aldrin M, Qviller L. Realtime case study simulations of transmission of Pancreas Disease (PD) in Norwegian salmonid farming for disease control purposes. Epidemics 2021; 37:100502. [PMID: 34610550 DOI: 10.1016/j.epidem.2021.100502] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 08/24/2021] [Accepted: 09/22/2021] [Indexed: 10/20/2022] Open
Abstract
Pancreas Disease (PD) is a viral disease caused by Salmonid Alphavirus (SAV). It affects farmed salmonids in the North Atlantic, and leads to reduced feed intake and increased mortality with reduced production and welfare as a consequence. In 2013, the estimated cost of an outbreak on an average salmon farm was about 6.6 mil €. In Norway, PD has been notifiable since 2008, and regulations to mitigate disease spread are in place. However, despite the regulations, 140-170 farms are affected by PD every year. The aquaculture industry is growing continuously, introducing farms in new geographical areas, and fish are moved between hydrographically separated zones for trade and slaughter. All such movements and relocations need to be approved by the competent authorities. Thus, there is a demand for support to farmers and competent authorities when making decisions on disease management and especially on the effect of moving infected fish. We have used a disease-transmission model for outbreak-simulation in real time for assessing the probability of disease transmission from a farm that gets infected with PD. We have also simulated the effects of three different control-regimes: no stamping-out, delayed stamping-out or immediate stamping-out, on the transmission of PD to surrounding farms. Simulations showed that the immediate stamping out of an infected farm led to effective containment of an outbreak. No stamping out led to up to 32.1% of farms within 100 km of the index farm to become effected. We have used real production data for the model building and the scenario simulations, and the results illustrate that a risk assessment of horizontal disease transmission must be undertaken on a case-by-case basis, because the time and place of the outbreak has a large influence on the risk of transmission.
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Affiliation(s)
| | | | | | - Magne Aldrin
- Norwegian Computing Center, P.O. Box 114 Blindern, N-0314 Oslo, Norway
| | - Lars Qviller
- Norwegian Veterinary Institute, PO Box 64, 1431 Ås, Norway
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7
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Bernhardt LV, Lillehaug A, Qviller L, Weli SC, Grønneberg E, Nilsen H, Myrmel M. Early detection of salmonid alphavirus in seawater from marine farm sites of Atlantic salmon Salmo salar. DISEASES OF AQUATIC ORGANISMS 2021; 146:41-52. [PMID: 34498609 DOI: 10.3354/dao03618] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The traditional strategy for national surveillance of salmonid alphavirus (SAV) infection in Norwegian fish farms relies on a costly, time-consuming, and resource-demanding approach based on the monthly sampling of fish from all marine farms with salmonids. In order to develop an alternative surveillance method, a water filtration method was tested in parallel with the ongoing surveillance program at 7 Norwegian marine farm sites of Atlantic salmon Salmo salar L. with no current suspicion of SAV infection. During the period from May 2019 to January 2020, seawater samples were collected from the top layer water inside all net-pens at these 7 sites. The samples were concentrated for SAV by filtration through an MF-Millipore™ electronegative membrane filter, followed by rinsing with NucliSENS® Lysis Buffer, before RNA extraction and analysis by RT-qPCR. SAV was detected from seawater at an earlier stage compared to traditional sampling methods, at all sites where the fish tested positive for SAV. A significant negative relationship was observed at all sites between the SAV concentration found in seawater samples and the number of days until SAV was detected in the fish. This means that the fewer the SAV particles in the seawater, the more days it took until SAV was detected in the fish samples. Based on this, sampling of seawater every month for the surveillance of SAV has a great potential as an alternative method for early detection of SAV in Atlantic salmon farms.
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8
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Romero JF, Gardner I, Price D, Halasa T, Thakur K. DTU-DADS-Aqua: A simulation framework for modelling waterborne spread of highly infectious pathogens in marine aquaculture. Transbound Emerg Dis 2021; 69:2029-2044. [PMID: 34152091 DOI: 10.1111/tbed.14195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/10/2021] [Accepted: 06/10/2021] [Indexed: 11/29/2022]
Abstract
Simulation models are useful tools to predict and elucidate the effects of factors influencing the occurrence and spread of epidemics in animal populations, evaluate the effectiveness of different control strategies and ultimately inform decision-makers about mitigations to reduce risk. There is a paucity of simulation models to study waterborne transmission of viral and bacterial pathogens in marine environments. We developed a stochastic, spatiotemporal hybrid simulation model (DTU-DADS-Aqua) that incorporates a compartmental model for infection spread within net-pens, an agent-based model for infection spread between net-pens within and between sites and uses seaway distance to inform farm-site hydroconnectivity. The model includes processes to simulate infection transmission and control over surveillance, detection and depopulation measures. Different what-if scenarios can be explored according to the input data provided and user-defined parameter values, such as daily surveillance and depopulation capacities or increased animal mortality that triggers diagnostic testing to detect infection. The latter can be easily defined in a software application, in which results are summarized after each simulation. To demonstrate capabilities of the model, we simulated the spread of infectious salmon anaemia virus (ISAv) for realistic scenarios in a transboundary population of farmed Atlantic salmon (Salmo salar L.) in New Brunswick, Canada and Maine, United States. We assessed the progression of infection in the different simulated outbreak scenarios, allowing for variation in the control strategies adopted for ISAv. Model results showed that improved disease detection, coupled with increasing surveillance visits to farm-sites and increased culling capacity for depopulation of infected net-pens reduced the number of infected net-pens and outbreak duration but the number of ISA-infected farm sites was minimally affected. DTU-DADS-Aqua is a flexible modelling framework, which can be applied to study different infectious diseases in the aquatic environment, allowing the incorporation of alternative transmission and control dynamics. The framework is open-source and available at https://github.com/upei-aqua/DTU-DADS-Aqua.
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Affiliation(s)
- João F Romero
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Ian Gardner
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Derek Price
- Aquaculture Environmental Operations, Aquaculture Management Division, Fisheries and Oceans Canada, Ottawa, Ontario, Canada
| | - Tariq Halasa
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Krishna Thakur
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
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Aldrin M, Huseby RB, Bang Jensen B, Jansen MD. Evaluating effects of different control strategies for Infectious Salmon Anaemia (ISA) in marine salmonid farming by scenario simulation using a disease transmission model. Prev Vet Med 2021; 191:105360. [PMID: 33989910 DOI: 10.1016/j.prevetmed.2021.105360] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/26/2021] [Accepted: 04/13/2021] [Indexed: 11/17/2022]
Abstract
Infectious salmon anaemia (ISA) is an important viral disease causing economic losses and reduced welfare in farmed Atlantic salmon. Here, we present a spatio-temporal stochastic model for the spread of ISA between and within marine aquaculture farms. The model is estimated on historical production data for all marine salmonid farms in Norway from 2004 to February 2019. In this time 142 outbreaks of ISA occurred. We find that transmission from infected neighbouring farms accounts for around 50% of the infections, whereas transmission from "non-specified sources" accounts for around 40%. We hypothesise that the most important of the latter are viruses mutating from the non-virulent ISAV HPR0 to the virulent ISAV HPRdel. The model is used for scenario simulation, or what-if analysis, to investigate the effects of potential strategies to combat ISA, including screening, vaccination and culling. Changing from the current strategy of culling farms with detected ISA-outbreaks to mandatory screening and culling when virus is detected will reduce the fraction of cohorts with a clinical ISA outbreak from 3.8 to 0.36%. Introducing mandatory vaccination would have approximately the same effect as the current stamping-out strategy. The scenario simulation is a useful tool for deciding on appropriate mitigation measures.
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Affiliation(s)
- M Aldrin
- Norwegian Computing Center, P.O.Box 114 Blindern, N-0314 Oslo, Norway
| | - R B Huseby
- Norwegian Computing Center, P.O.Box 114 Blindern, N-0314 Oslo, Norway
| | - B Bang Jensen
- Norwegian Veterinary Institute, P.O. Box 750 Sentrum, N-0106 Oslo, Norway.
| | - M D Jansen
- Norwegian Veterinary Institute, P.O. Box 750 Sentrum, N-0106 Oslo, Norway
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Lu TH, Chen CY, Yang YF, Liao CM. Modelling the effect of vaccination on transmission dynamics of nervous necrosis virus in grouper larvae Epinephelus coioides. JOURNAL OF FISH DISEASES 2020; 43:1155-1165. [PMID: 32720332 DOI: 10.1111/jfd.13225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/29/2020] [Accepted: 07/02/2020] [Indexed: 06/11/2023]
Abstract
Nervous necrosis virus (NNV) infection in susceptible grouper larvae has been reported to cause high mortalities, leading to great economic losses in aquaculture industry. Although the effects of NNV vaccines on grouper have been broadly investigated, vaccination strategies have not been fully established. To this end, we introduced the parsimonious epidemiological models that explored the assessment of key epidemiological parameters and how they changed when vaccinations showed the effects. We showed that the models capture the published cumulative mortality data accurately. We estimated a basic reproduction number R0 = 2.44 for NNV transmission in grouper larvae without vaccination. To effectively control NNV transmission by vaccination, a model for disease control was also generalized to attain the goals of controlled reproduction number less than 1. Our results indicated that at least 60% of grouper population needed to be immunized for ~75 min. Our data-driven modelling approach that links the transmission dynamics of NNV and vaccination strategies for grouper has the potential to support evidence-based planning and adaptation of integrated control measures. We encourage that the epidemiology-based framework introduced here can be further implemented for establishing effective vaccination and mitigation actions aimed at controlling diseases in fish farming practices.
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Affiliation(s)
- Tien-Hsuan Lu
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei, Taiwan
| | - Chi-Yun Chen
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei, Taiwan
| | - Ying-Fei Yang
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei, Taiwan
| | - Chung-Min Liao
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei, Taiwan
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Janssen K, Bijma P. The economic value of R 0 for selective breeding against microparasitic diseases. Genet Sel Evol 2020; 52:3. [PMID: 32005099 PMCID: PMC6993466 DOI: 10.1186/s12711-020-0526-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 01/23/2020] [Indexed: 02/06/2023] Open
Abstract
Background Microparasitic diseases are caused by bacteria and viruses. Genetic improvement of resistance to microparasitic diseases in breeding programs is desirable and should aim at reducing the basic reproduction ratio \documentclass[12pt]{minimal}
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\begin{document}$${\text{R}}_{0}$$\end{document}R0. Recently, we developed a method to derive the economic value of \documentclass[12pt]{minimal}
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\begin{document}$${\text{R}}_{0}$$\end{document}R0 for macroparasitic diseases. In epidemiological models for microparasitic diseases, an animal’s disease status is treated as infected or not infected, resulting in a definition of \documentclass[12pt]{minimal}
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\begin{document}$${\text{R}}_{0}$$\end{document}R0 that differs from that for macroparasitic diseases. Here, we extend the method for the derivation of the economic value of \documentclass[12pt]{minimal}
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\begin{document}$${\text{R}}_{0}$$\end{document}R0 to microparasitic diseases. Methods When \documentclass[12pt]{minimal}
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\begin{document}$${\text{R}}_{0} \le 1$$\end{document}R0≤1, the economic value of \documentclass[12pt]{minimal}
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\begin{document}$${\text{R}}_{0}$$\end{document}R0 is zero because the disease is very rare. When \documentclass[12pt]{minimal}
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\begin{document}$${\text{R}}_{0}$$\end{document}R0. is higher than 1, genetic improvement of \documentclass[12pt]{minimal}
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\begin{document}$${\text{R}}_{0}$$\end{document}R0 can reduce expenditures on vaccination if vaccination induces herd immunity, or it can reduce production losses due to disease. When vaccination is used to achieve herd immunity, expenditures are proportional to the critical vaccination coverage, which decreases with \documentclass[12pt]{minimal}
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\begin{document}$${\text{R}}_{0}$$\end{document}R0. The effect of \documentclass[12pt]{minimal}
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\begin{document}$${\text{R}}_{0}$$\end{document}R0 on losses is considered separately for epidemic and endemic disease. Losses for epidemic diseases are proportional to the probability and size of major epidemics. Losses for endemic diseases are proportional to the infected fraction of the population at the endemic equilibrium. Results When genetic improvement reduces expenditures on vaccination, expenditures decrease with \documentclass[12pt]{minimal}
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\begin{document}$${\text{R}}_{0}$$\end{document}R0 at an increasing rate. When genetic improvement reduces losses in epidemic or endemic diseases, losses decrease with \documentclass[12pt]{minimal}
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\begin{document}$${\text{R}}_{0}$$\end{document}R0 at an increasing rate. Hence, in all cases, the economic value of \documentclass[12pt]{minimal}
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\begin{document}$${\text{R}}_{0}$$\end{document}R0 increases as \documentclass[12pt]{minimal}
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\begin{document}$${\text{R}}_{0}$$\end{document}R0 decreases towards 1. Discussion \documentclass[12pt]{minimal}
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\begin{document}$${\text{R}}_{0}$$\end{document}R0 and its economic value are more informative for potential benefits of genetic improvement than heritability estimates for survival after a disease challenge. In livestock, the potential for genetic improvement is small for epidemic microparasitic diseases, where disease control measures limit possibilities for phenotyping. This is not an issue in aquaculture, where controlled challenge tests are performed in dedicated facilities. If genetic evaluations include infectivity, genetic gain in \documentclass[12pt]{minimal}
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\begin{document}$${\text{R}}_{0}$$\end{document}R0 can be accelerated but this would require different testing designs. Conclusions When \documentclass[12pt]{minimal}
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\begin{document}$${\text{R}}_{0} \le 1$$\end{document}R0≤1, its economic value is zero. The economic value of \documentclass[12pt]{minimal}
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\begin{document}$${\text{R}}_{0}$$\end{document}R0 is highest at low values of \documentclass[12pt]{minimal}
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\begin{document}$${\text{R}}_{0}$$\end{document}R0 and approaches zero at high values of \documentclass[12pt]{minimal}
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\begin{document}$${\text{R}}_{0}$$\end{document}R0.
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Affiliation(s)
- Kasper Janssen
- Animal Breeding and Genomics, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
| | - Piter Bijma
- Animal Breeding and Genomics, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
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12
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Robinson NA, Krasnov A, Burgerhout E, Johnsen H, Moghadam HK, Hillestad B, Aslam ML, Baranski M, Boison SA. Response of the Salmon Heart Transcriptome to Pancreas Disease: Differences Between High- and Low-Ranking Families for Resistance. Sci Rep 2020; 10:868. [PMID: 31964968 PMCID: PMC6972705 DOI: 10.1038/s41598-020-57786-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 01/07/2020] [Indexed: 12/30/2022] Open
Abstract
Pancreas disease caused by salmonid alphaviruses leads to severe losses in Atlantic salmon aquaculture. The aim of our study was to gain a better understanding of the biological differences between salmon with high and low genomic breeding values (H-gEBV and L-gEBV respectively) for pancreas disease resistance. Fish from H- and L-gEBV families were challenged by intraperitoneal injection of salmonid alphavirus or co-habitation with infected fish. Mortality was higher with co-habitation than injection, and for L- than H-gEBV. Heart for RNA-seq and histopathology was collected before challenge and at four- and ten-weeks post-challenge. Heart damage was less severe in injection-challenged H- than L-gEBV fish at week 4. Viral load was lower in H- than L-gEBV salmon after co-habitant challenge. Gene expression differences between H- and L-gEBV manifested before challenge, peaked at week 4, and moderated by week 10. At week 4, H-gEBV salmon showed lower expression of innate antiviral defence genes, stimulation of B- and T-cell immune function, and weaker stress responses. Retarded resolution of the disease explains the higher expression of immune genes in L-gEBV at week 10. Results suggest earlier mobilization of acquired immunity better protects H-gEBV salmon by accelerating clearance of the virus and resolution of the disease.
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Affiliation(s)
- N A Robinson
- Breeding and Genetics, Nofima, Ås, 1430, Norway. .,Sustainable Aquaculture Laboratory- Temperate and Tropical (SALTT), School of BioSciences, The University of Melbourne, Parkville, 3010, Australia.
| | - A Krasnov
- Breeding and Genetics, Nofima, Ås, 1430, Norway
| | | | - H Johnsen
- Breeding and Genetics, Nofima, Ås, 1430, Norway
| | | | | | - M L Aslam
- Breeding and Genetics, Nofima, Ås, 1430, Norway
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13
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Lu TH, Yang YF, Chen CY, Wang WM, Liao CM. Quantifying the impact of temperature variation on birnavirus transmission dynamics in hard clams Meretrix lusoria. JOURNAL OF FISH DISEASES 2020; 43:57-68. [PMID: 31691318 DOI: 10.1111/jfd.13105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/24/2019] [Accepted: 09/25/2019] [Indexed: 06/10/2023]
Abstract
Susceptibility of hard clams Meretrix lusoria to birnavirus (BV) infections caused by temperature variations, from a mechanistic perspective, has rarely been explored. We used a deterministic susceptible-infectious-mortality (SIM) model to derive temperature-dependent key epidemiologic parameters based on data sets of viral infections in hard clams subjected to acute temperature changes. To parameterize seasonal pattern dependence, we estimated monthly based cumulative mortality and basic reproduction numbers (R0 ) between 1997 and 2017 by way of statistical analysis. Two alternative disease control models were also proposed to assess status of controlled temperature-mediated BV infection by using, respectively, control reproduction number (RC )-control line criterion and removal strategy-based control measure. We showed that based on RC -control strategy, when temperatures ranged from 15 to 26.8°C, proportion of susceptible hard clams removed should be at least 0.22%. Based on removal-control strategy, we found that by limiting pond water temperature to 25-30°C, together with increased removal rates and periods to remove hard clams, it is better to remove hard clams from June and August to reduce both mortality rate and spread of BV. Our results can be used to monitor BV transmission potential in hard clams that will contribute to government control strategy to eradicate future BV epidemics.
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Affiliation(s)
- Tien-Hsuan Lu
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei, Taiwan
| | - Ying-Fei Yang
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei, Taiwan
| | - Chi-Yun Chen
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei, Taiwan
| | - Wei-Ming Wang
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei, Taiwan
| | - Chung-Min Liao
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei, Taiwan
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14
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Amirpour Haredasht S, Tavornpanich S, Jansen MD, Lyngstad TM, Yatabe T, Brun E, Martínez-López B. A stochastic network-based model to simulate the spread of pancreas disease (PD) in the Norwegian salmon industry based on the observed vessel movements and seaway distance between marine farms. Prev Vet Med 2019; 167:174-181. [DOI: 10.1016/j.prevetmed.2018.05.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 01/08/2018] [Accepted: 05/31/2018] [Indexed: 11/30/2022]
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15
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Røsaeg MV, Rimstad E, Guttvik A, Skjelstad B, Bendiksen EÅ, Garseth ÅH. Effect of pancreas disease caused by SAV 2 on protein and fat digestion in Atlantic salmon. JOURNAL OF FISH DISEASES 2019; 42:97-108. [PMID: 30370677 DOI: 10.1111/jfd.12914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 09/17/2018] [Accepted: 09/18/2018] [Indexed: 05/13/2023]
Abstract
Salmonid alphavirus (SAV) causes pancreas disease (PD) in farmed Atlantic salmon (Salmo salar L.), and exocrine pancreas tissue is a primary target of the virus. Digestive enzymes secreted by the exocrine pancreas break down macromolecules in feed into smaller molecules that can be absorbed. The effect of SAV infection on digestion has been poorly studied. In this study, longitudinal observations of PD outbreaks caused by SAV subtype 2 (SAV2) in Atlantic salmon at two commercial sea sites were performed. The development of PD was assessed by measurement of SAV2 RNA load and evaluation of histopathological lesions typical of PD. Reduced digestion of both protein and fat co-varied with the severity of PD lesions and viral load. Also, the study found that during a PD outbreak, the pen population comprise several subpopulations, with different likelihoods of being sampled. The body length of sampled fish deviated from the expected increase or steady state over time, and the infection status in sampled fish deviated from the expected course of infection in the population. Both conditions indicate that disease status of the individual fish influenced the likelihood of being sampled, which may cause sampling bias in population studies.
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Affiliation(s)
| | - Espen Rimstad
- Department of Food Safety and Infection Biology, Norwegian University of Life Sciences, Oslo, Norway
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16
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17
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Ferguson PF, Breyta R, Brito I, Kurath G, LaDeau SL. An epidemiological model of virus transmission in salmonid fishes of the Columbia River Basin. Ecol Modell 2018. [DOI: 10.1016/j.ecolmodel.2018.03.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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18
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Abstract
Salmonid alphavirus (SAV), genus Alphavirus, family Togaviridae, is a single-stranded RNA virus affecting Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss). It is known to be responsible for pancreas disease (PD) and sleeping disease (SD) which are increasing problems, causing high fish mortality and economic losses in the European aquaculture industry. Pancreas disease was first described in Atlantic salmon in Scotland in 1976 and a similar disease caused by the closely related sleeping disease virus was first described in rainbow trout in France. There have also been reports of salmonid alphavirus infections from other European countries, including Ireland, England, Norway, Germany, Italy, and Spain. Salmonid alphaviruses have been classified into six subtypes (SAV1–6). SAV1 and SAV4–6 cause pancreas disease in Atlantic salmon in Ireland or Scotland, SAV2 is the causative agent of sleeping disease in rainbow trout, and SAV3 has been detected in Atlantic salmon in Norway. The aim of this paper was to summarise current knowledge of infections caused by salmonid alphavirus and diagnostic methods including the newest techniques, and to briefly describe prevention from SAV infections by vaccination.
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19
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Aldrin M, Huseby R, Stien A, Grøntvedt R, Viljugrein H, Jansen P. A stage-structured Bayesian hierarchical model for salmon lice populations at individual salmon farms – Estimated from multiple farm data sets. Ecol Modell 2017. [DOI: 10.1016/j.ecolmodel.2017.05.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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20
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Jansen MD, Bang Jensen B, McLoughlin MF, Rodger HD, Taksdal T, Sindre H, Graham DA, Lillehaug A. The epidemiology of pancreas disease in salmonid aquaculture: a summary of the current state of knowledge. JOURNAL OF FISH DISEASES 2017; 40:141-155. [PMID: 27136332 DOI: 10.1111/jfd.12478] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 02/12/2016] [Accepted: 02/18/2016] [Indexed: 05/13/2023]
Abstract
Pancreas disease (PD) is a viral disease caused by Salmonid alphavirus (SAV) that affects farmed Atlantic salmon (Salmo salar L.) and rainbow trout (Oncorhynchus mykiss (Walbaum)) in the seawater phase. Since its first description in Scotland in 1976, a large number of studies have been conducted relating to the disease itself and to factors contributing to agent spread and disease occurrence. This paper summarizes the currently available, scientific information on the epidemiology of PD and its associated mitigation and control measures. Available literature shows infected farmed salmonids to be the main reservoir of SAV. Transmission between seawater sites occurs mainly passively by water currents or actively through human activity coupled with inadequate biosecurity measures. All available information suggests that the current fallowing procedures are adequate to prevent agent survival within the environment through the fallowing period and thus that a repeated disease outbreak at the same site is due to a new agent introduction. There has been no scientific evaluation of currently used on-site biosecurity measures, and there is limited information on the impact of available mitigation measures and control strategies.
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Affiliation(s)
- M D Jansen
- Norwegian Veterinary Institute, Oslo, Norway
| | | | | | - H D Rodger
- Vet-Aqua International, Oranmore, Ireland
| | - T Taksdal
- Norwegian Veterinary Institute, Oslo, Norway
| | - H Sindre
- Norwegian Veterinary Institute, Oslo, Norway
| | - D A Graham
- Animal Health Ireland, Carrick on Shannon, Ireland
| | - A Lillehaug
- Norwegian Veterinary Institute, Oslo, Norway
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21
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Pettersen J, Brynildsrud O, Huseby R, Rich K, Aunsmo A, Bang BJ, Aldrin M. The epidemiological and economic effects from systematic depopulation of Norwegian marine salmon farms infected with pancreas disease virus. Prev Vet Med 2016; 132:113-124. [DOI: 10.1016/j.prevetmed.2016.09.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 08/31/2016] [Accepted: 09/01/2016] [Indexed: 10/21/2022]
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