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Development of rapid typing methods for teleost pathogens



Many factors are contributing to the development of disease in living organisms such as fishes. Finding a pathogen in a fish does not imply that disease has or could have occurred. To provide better definition of laboratory results, distinctions need to be made for pathogen strain variation with reference to host specificity. Some diseases of concern in Atlantic Provinces are viruses such as infectious salmon anemia virus (ISAV), nervous necrosis virus (NNV), and infectious pancreatic necrosis (IPN). While information on their host specificity and factors affecting their virulence is still partial, molecular characterisation of some of the strains isolated in Atlantic Provinces is in progress. This type of information is helping us understand the spread and diversity of viral strains present in the environment and help us predict the possible outcome of infected species.

Strain identification can be done by diverse methods, such as viral genome sequencing, viral serum neutralization assays, etc. RT-PCR is a powerful and rapid method that is used routinely to detect the presence of virus genomic material in fish samples, but does not distinguish viral strains. Combining RT-PCR results with a method that allows separation of results at the strain level can be done using a technique called denaturing gradient gel electrophoresis (DGGE). Well-characterized sequence variants or strains are initially used to set up DGGE conditions that will allow clear separation of these variants. These are then becoming standards. New isolates are compared to the migration pattern of standards. Their identification is possible based on the identity of their migration to one of the standard, or if they are new strain, they will migrate differently than known strains, prompting the need to better characterise them.

The project objectives are to determine conditions for RT-PCR and DGGE that will allow separation of currently known ISAV, NNV and IPN strains. This RT-PCR/DGGE assay will then be used to rapidly screen unknown isolates of these viruses and assign them a strain identity or discover new strains, which is not currently possible with RT-PCR alone.

Program Name

Aquaculture Collaborative Research and Development Program (ACRDP)


2001 - 2004


Atlantic: Gulf of Maine, Scotian Shelf

Principal Investigator(s)

Nellie Gagné

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