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sector_ico_Agrifood_trans Agrifood

Evaluation of a Next Generation Sequencing Diagnostic Tool for Detection of Strawberry Viruses

  • Project Leaders: Michael Rott, Gerda de Villiers, Michael Dossett
  • Institutions: Canadian Food Inspection Agency (CFIA)
  • Budget: $100249
  • Program/Competition: User Partnership Program
  • Genome Centre(s): Genome British Columbia
  • Fiscal Year: 2016
  • Status: Closed

The USA is the world leader in strawberry production with about 1.3 million tons in 2009. A significant number of the strawberry plants grown in the USA are imported from Canadian nurseries, which are prized for improved fruit production. In 2017, the industry was worth about $17 million/year. In 2013 the Canadian government provided the Nova Scotia strawberry growers $2.3 million to replace diseased plants that died before they could bear fruit. Molecular testing of plants both in the US and from Canada were shown to be positive for several known strawberry viruses, Strawberry mild yellow edge virus (SMYEV), Strawberry mottle virus (SMoV) and Strawberry vein banding virus (SVBV). Complexes of these viruses are known to result in significant yield losses. It is believed that the plants were infected in Canadian nurseries before being shipped to the USA. Canadian strawberry growers have had to incorporate improved sanitary and virus testing methods to ensure that their product is virus free. US importers now request that plants be tested by a USDA qualified laboratory.

Phyto Diagnostics located in North Saanich, BC is a Canadian Food Inspection Agency (CFIA) accredited and private diagnostic laboratory specializing in the testing of plant viruses for many different commodities nationally and internationally and is working closely with Canadian strawberry growers and USA importers to ensure plants are virus-free. Phyto Diagnostics uses a combination of ELISA and PCR methods to test for 11 different virus species as requested by Canadian growers shipping plant material to the US. This is both labour intensive and time consuming, requiring individual testing for each species at a considerable cost to the client. An additional 11 virus species of strawberry are not tested for on a regular basis, due to their low prevalence and extra cost.

The project team achieved its objective to develop and validate next generation sequencing (NGS) method using strawberry plant tissue and to apply the method to test for strawberry viruses in plants exported to the USA. A reduction in costs associated with virus testing and an improved, more reliable test method for all known strawberry viruses, will result in an increased confidence from US strawberry growers to purchase virus free planting material from Canada, with freer trade for Canadian strawberry plant growers.

In addition, a prototype of a diagnostic tool, Virtool, was developed for use by commercial plant pathogen testing laboratories. This tool is also able to detect a strawberry virus that wasn’t being tested for by Phyto Diagnostics, as well as detect a potentially new novel virus of strawberry. The detection of all viruses present in a sample, standard and novel isolates as well as novel viruses are a clear advantage of NGS over all other methods.