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Prosjektnummer: 901832
Status: Pågår
Startdato: 02.05.2023
Sluttdato: 02.05.2025

Generation of new knowledge on disease risk in cod farming

A​tlantic cod (Gadus morhua L. hereafter referred to as cod) is an economically important fish species in the North Atlantic. In addition to providing export earning, cod provide high-value nutrients that represent valuable part of a healthy diet to the people in Norway. During the last century, the cod industry experienced decline in stocks, which was partly due to early sexual maturation problems and strict regulation in cod fishing in Russian and other nations in the North Atlantic. In an effort to fill the gaps in the stock decline in Norway, the Norwegian National Cod Breeding Program (NCBP) initiated and produced a fifth generation-domesticated cod for breeding high quality cod juveniles. The production of quality cod juveniles triggered renewed interest in cod farming. In 2021, there were approximately eight active cod farms in Norway, with total cod production of 6500 tons. This number is expected to increase to 25,000 tons in 2025, as new cod farming licences for seabased farms are being issued. Given that, these new cod farms will have to coexist with other sea-based fish farms, wild Atlantic cod and other marine fish species, it is important to generate new knowledge on the risk of disease spread. 

The project will see the combined effort of researchers from Institute for Marine Research (IMR) and Norwegian Veterinary Institute (NVI), along with three industrial partners, working closely together to provide new knowledge on the risk of infection of diseases between farmed cod, other farmed fish and wild marine fish population. Disease surveillance, models for spread of pathogens, and disease control strategies are all- important tools in fish health management. The project group will perform extensive review of cod diagnostic database in NVI dating back to early 1990 in order to map different cod diseases in Norway. It will follow cod development from hatchery all through to sea, collecting biological- and environmental samples over time, for analysis of known and potential new infectious pathogens. The material will supply the biobank for future in vitro and in vivo studies. Sequential sampling of water and fish (from hatchery to sea phase) will ensure that the project obtains ‘up to date’ material for genetic and biological characterization of pathogens in the cod farm. The project will also include experimental pathogen transmission study, to understand how pathogen can transfer and adapting into new host. The focus of the project will be to establish new knowledge that will allow cod farmers and food safety authority to make informed decisions on potential disease transmission within and between Norwegian aquaculture farms.
Main objective
To generate new knowledge for use in monitoring spread of pathogens between farmed cod, other farmed fish and wild marine species.

• To map existing data on diseases and pathogens in cod, with a focus on understanding the risk of spread between farmed cod, other farmed species and marine fish.
• To map the prevalence and spread of pathogens that cause disease in land and sea-based cod farms.
• To establish experimental test regimes in fish to understand the risks of amplification and spread of the different pathogens to environment and wild marine populations. 
• To produce a knowledge-based risk analysis for spread of various infectious diseases between farmed cod, other farmed species and wild marine species.  
Expected project impact
The project will employ new methods for detection of various cod pathogens from water, to provide new knowledge on different pathogens that exist in land and sea-based cod farms. Such analysis (also named e-DNA or e-RNA methods) will be beneficial for the cod industry, as to avoid handling and killing of individual fish for sampling. This new knowledge that will be obtained on pathogen distribution, will then be used to assess risk of pathogen transmission between farms, which are important information to farmers as well as competent authorities when establishing new farms, transporting fish etc.
Project design and implementation
The project will follow four lines of work, where work package 1 (WP1) will map current and past literature work on disease spread and pathogen transmission in cod. This will provide input into field and experimental work to obtain new knowledge about the risk of infection of various diseases between farmed cod and other marine fish (WP2 and WP3); and perform a knowledge-based risk analysis of pathogen transmission between farmed cod and other farmed species and wild marine populations (WP4). 

The work packages has the following tasks: 

WP 1: Literature review of existing knowledge on cod diseases
Work package leader: Simon Weli (the Norwegian Veterinary Institute (NVI)) in collaboration with Mona Gjessing (NVI), Sonal Patel (NVI) Nina Sandlund and Pål Arne Bjørn (Institute for Marine Research (IMR)).
Objective: To produce a written document based on existing data on the diseases and pathogens in cod, with a focus on the significance of spread between farmed cod, other farmed species and marine fish.
Rational: Currently, cod farmers are finding it difficult to secure locations for sea-based cod farming due to the fear of disease spread (particularly VHSV) from cod to salmonids or other marine fish. Thus, the generation of new knowledge/guidance on the risks posed by diseased cod to other marine fish, may guide the food safety authorities in deciding where new cod farm sites can be located.

WP1 will be a collaboration between NVI and the IMR, and will use data mining technique to identification possible cod pathogen and disease with significant risk to other marine fish in the environment.

A detailed literature review map of existing cod diseases will be performed to increase knowledge about disease prevention: 
• PubMed and ISI Web of Knowledge will be searched for articles published from 1980 to date using the search terms ‘cod’ AND (separately) ‘disease’ or 'pathogen’, or ‘transmission’ or ‘risks using the ‘all fields option to allow for the retrieval of articles in which the search terms appeared in the titles, abstracts, or keywords;
• NVI has fish diagnostic database hosting up 1800 cod disease cases dating back to the early 1990s. This database will be searched, to increase knowledge on the different cod diseases;
• The project group will have interviews with the industrial partners, other Norwegian cod breeders and the Norwegian Food Safety Authority, to get their description of the biosecurity aspects and challenges with disease problems in the cod farm industry;
• A one-time international Teams® meeting will be organized with cod disease experts (for example, from Canada, USA, UK, Denmark, and Norway) to get up to date knowledge of disease prevention in cod and risk factors.

WP 2 Mapping of pathogen and disease distribution in land and sea-based cod farms.
Work package leader: Mona Gjessing (NVI), in collaboration with Ingunn Sommerset, Hilde Sindre and Hanne Nilsen (all NVI) and fish health personnel from the industry partners.
Objective: Map pathogen distribution in land and sea-based farms, in order to produce necessary new knowledge on the risk of transmission of various diseases between farmed cod, other farmed species and wild marine populations. Knowledge generated in WP2 will argument the knowledge gaps identified in WP1 as well as input to WP4.

One land based (hatchery) and two sea-based cod farms industrial partners, have agreed to allow us take relevant samples from their farms. In WP2, the project group will collect fish and water samples from relevant parts of the farm facility for a period of 12 months. These samples will be used to map pathogen distribution in the farms. The sizes of fish to be sampled will be determined according to the sizes in each facility and the sampling time points will adapted as far as possible to some assumed risk periods (e.g., 2–3 weeks after transportation, at high sea water temperature) and to cover different stages in production.

The following sampling schedule is planned at the site: 
• Water samples will be collected from the farm facility containing fish of the same size from parallel tanks/cages;
• Three (5 x 1 L) random water samples will be collected at selected sampling points from the farms;
• The samples will be concentrated and qPCR analyzed for Francisella noatunesis subsp. noatunensis, Aeromonas spp., Vibrio anguillarum and viral nervous necrosis virus (VNNV). In addition, if the industrial partners are interested in screening other pathogens, the project group will be willing to consider such request;
• In addition, 3 x 30 random fish sampling will be sampled at each farm and preferably from each fish group (if more than one). If disease outbreaks are reported in the hatchery or in sea-based farms during the sampling period, risk based (disease fish and water) sampling can be performed if the farmers agree to an extended sample schedule (ref. industrial partners signed agreement);
• In addition to fish samples (heart, brain, gills, kidney, spleen, muscle tissue and water) for qPCR, samples for bacteriology, histology and RNAscope in situ hybridization analysis will be collected;
• Next generation sequencing (NGS) will be performed on limited number of tissues and water samples to have an overview of pathogens present in the sea compared to the land-based farms and to get knowledge about microflora in healthy cod. In addition, archival wild cod samples collected by IMR dating back 15 years, will be analysed as described below. 

WP 3: Experimental studies
Work package leader: Simon Weli, with Sonal Patel NVI responsible for challenge experiments and sample analysis while IMR will be responsible for wet-lab, fish, and logistics).
Objective: Fill the knowledge gaps identified in WP1 and 2. This will be done to generate data on the risk of amplification and spread of the pathogens from diseased cod to wild marine populations in order to cover the knowledge gaps identified in WP1 and WP2.

WP3 will investigate whether a cod infected with pathogen X can a) transfer infection from the primary host (cod 1) to secondary host (cod 2) and b) act as a transporter/vector of the pathogen from the primary outbreak to secondary fish species (spread). In addition, it will investigate pathogen shedding from infectious cod in water, data that can be used for the risk analysis in WP4. A field situation will be simulated, where different fish species will be exposed to cod infected with pathogen X, to assess possible pathogen transmission from cod to other species in the environment. The project group has knowledge of the susceptibility of some the chosen fish species to most of the important cod pathogens (e.g., Francisella noatunesis subsp. noatunensis, Aeromonas spp., Vibrio anguillarum, and viral nervous necrosis virus (VNNV).

The choice of pathogen X in this study, will depend on the data obtained from samples from pathogen distribution study in WP2 and relevant info obtained in WP1. If no new unknown pathogen with potential threat to cod is uncovered in WP2, material from NVI and IMRs biobank (e.g., Francisella noatunesis subsp. noatunensis, Aeromonas spp., Vibrio anguillarum and viral nervous necrosis virus (VNNV). can be used for the experimental challenge trial. Infection model for these pathogens are already established at NVI and IMR, and there are experienced researchers with knowledge and expertise in specific cod pathogen in the project team.  

Experimental setup
• Cod will be infected with the pathogen X (with potential threat);
• The infected cod will cohabitate with other fish species identified at being at risk from WP1, e.g., Atlantic halibut Hippoglossus hippoglossus, Atlantic salmon (Salmo Salar) and/or lumpfish (Cyclopterus lumpus);
• Experiments will be performed in tanks with several partitions or other type of water connection, which will allow for waterborne transmission of pathogens to different fish;
• At various times post challenge, fish heart, brain, gills, kidney, spleen, muscle tissue and water samples from the tanks will be process for qPCR, histology, immunohistochemistry and RNAscope in situ hybridization analysis;
• If the strategy of the cohabitation challenge experiment is successful, this will allow the project group to examine pathogen amplification, shedding and transmission in different scenarios, which is important to understanding risk of transmission to wild fish. 

WP4. Development of a knowledge-based risk assessment of infection of various diseases between farmed cod, other farmed species and wild marine stocks
Work package leader: Nina Sandlund (IMR), collaboration with Pål Arne Bjørn (IMR) and Lars Qviller (NVI).
Objective: Currently, updated knowledge for farmers and decision-making authorities on disease transmission within and between existing aquaculture farms and from farmed to wild fish is lacking. The objective of WP4 is to use the updated literature review from WP1 and the cod disease-transmission data from WP2 and WP3 to conduct a knowledge-based environmental risk assessment to where risk factors, events and consequences associated with the transmission of disease from a cod farm to surrounding farms and wild fish are described and analysed. To perform this risk assessment, the project group will use the recently published methodology on environmental risk assessments in aquaculture by project partner Nina Sandlund and colleagues.

The methodology is based on the latest thinking in risk science and has been tested thoroughly through the work on environmental risks related to Norwegian fish farming published annually in the IMR report series ‘Risikorapport norsk fiskeoppdrett’. The risk assessment process is made up of three main steps (1) defining the problem and identifying risk sources, events, and consequences; (2) measuring the uncertainties related to risk sources, events, and consequences in terms of subjective probabilities and strength of knowledge; and (3) aggregating the uncertainty measurements.

The uncertainty is measured by subjective/knowledge-based probabilities, the judgements of the strength of knowledge supporting the probabilities, and the knowledge that the subjective probabilities and strength of knowledge are based on. Risk-contributing factors are visualized in graphical cause-and-effect structures (Bayesian belief networks) to enhance risk understanding and help structuring discussions on risk. To ensure that the risk assessment covers as many aspects of disease transmission as possible, the expert group performing the risk assessment will include people of various expertise such as wild cod and wild fish in general (population structure, behaviour, and diseases), epidemiology, general fish health, pathogen specific knowledge, etc.

The goal of the risk assessment is to contribute to mutual risk understanding and risk acknowledgement among decision making authorities, farmers, and other stakeholders, and thus to common perspectives on measures and governance. The risk assessment will also include more specific suggestions for disease reducing measures. In addition to communicate this risk assessment through a written report, the project will aim to communicate findings through other channels as well, such as Norsk Fiskeoppdrett and the conferences ‘Sats Marint’ and ‘Frisk Fisk’. 
Dissemination of project results
Scientific results and breakthroughs will continuously be communicated to the scientific community through research presentations and publications in international journals with peer-review. A total of three journal publications are planned, and will be co-publications with the collaboration partners. Scientific presentations will be given at the biannually alternating conferences ‘Frisk fisk’ and ‘Havbrukskonferansen’. Dissemination of project information, aims and results will also be targeted to parties in the fish farming industry by publishing in national papers such as Norsk Fiskeoppdrett or similar. In the last year, a workshop or webinar will be organized either in connection with our industrial partners where the results are will be presented and discussed at other meetings with regulatory bodies (the Food Safety Authority), fish health professionals and aquaculture industry.