Applications of simulation modelling to inform viral disease management in Canadian salmon aquaculture

Infectious diseases are responsible for substantial economic losses in salmon aquaculture due to production losses from mortality, morbidity and reduced growth rates, and costs of outbreak prevention and mitigation. Two of the most concerning viral diseases affecting farmed salmon in Canada are infectious salmon anaemia (ISA) and infectious hematopoietic necrosis (IHN). These are region-specific in Canada, as ISA occurs in the Atlantic coast, while IHN is present in the Pacific coast. Despite epidemiologic differences between the two viruses, both can be transmitted between marine salmon farms in the water column. However, limited research has been conducted on the transmission dynamics of ISA virus (ISAV) and IHN virus (IHNV) among marine farmed salmon populations in Canada. Furthermore, some aspects of ISAV epidemiology and cost- effectiveness of its mitigation in Atlantic Canada require further investigation. Research documented in this thesis aimed to provide additional insights about the epidemiology of ISAV in Atlantic Canada. A population-level descriptive study reported epidemiologic findings of an ISAV outbreak in the region. In two of the affected marine salmon farms both European and North American ISAV variants were simultaneously detected. In addition, we found presumptive evidence of emergence of a pathogenic ISAV variant from a non-pathogenic variant of the same genotype, based on detection of co- infection in one fish. A simulation modelling framework was developed for the purpose of investigating the dynamics of waterborne pathogen transmission in marine salmon aquaculture. This framework allowed for development of models that simulate waterborne infection spread within net-pens, and between net-pens (both within and between farm sites), as well as surveillance, detection, and depopulation measures. Technical characteristics and structure of the framework were described, and a case study demonstrated the framework functionalities. This simulation tool addresses the lack of simulation models intrinsically adapted to the aquaculture context. The newly-developed modelling framework was used to simulate IHNV incursions and subsequent spread along the coast of British Columbia and the implementation of a viral disease management plan (VDMP) by salmon companies. Different scenarios were explored to assess VDMP effectiveness compared with alternative mitigation measures. Research findings indicated that interventions crucial to contain IHN outbreaks were the use of an IHN vaccine with high population coverage and efficacy, the implementation of surveillance zones, and the pre-emptive depopulation of all net-pens in IHNV-infected farms. Comparisons between simulated scenarios indicated that the VDMP was effective in limiting IHNV spread and mitigating outbreaks across the region. Finally, to help the salmon aquaculture industry plan for expansion of production capacity in Atlantic Canada, a simulation modelling approach was used to assess the cost- effectiveness of ISAV outbreak mitigation strategies, considering different percentages of active licensed farms. For each model scenario, direct costs of ISAV mitigation interventions were estimated from model outputs. Results demonstrated the importance of pre-emptive depopulation of all net-pens in ISAV-positive farms to effectively limit ISAV spread; however, this strategy increased costs of ISAV mitigation as production capacity expanded, suggesting that a moderate capacity increase (65% compared with 40% active farms) would be more cost-effective than a high capacity increase (90% active farms). Nevertheless, a cost-benefit analysis should be explored to substantiate this recommendation. This research demonstrates the value of descriptive epidemiologic studies and simulation modelling in aquatic health management. Ultimately, research findings documented herein provide insights to inform policy and disease management decisions to reduce viral disease risk in Canadian salmon aquaculture