CFIA scientists investigate “fruitful” technology

February 2020 | Canadian Food Inspection Agency | by Stefanie Sultmanis, Tracy Lawrence, Brittany Day and Anithra Selvakumar

Science at CFIA is ever-growing, always changing, and constantly improving. As our science changes, the tools, techniques and infrastructure must also evolve to meet the needs of our innovative scientists across the country. In 2017, the Government of Canada announced an investment of 80 million dollars to replace the current century old Centre for Plant Health on Vancouver Island, B.C.

“What does that have to do with me?” you may think to yourself.

Some of the fruit we eat begin their journey at the Centre for Plant Health. The Centre is an accredited laboratory for testing plant material that is imported and exported for fruit production, like apples or grapes. At the new facility, the scientists will be able to use innovative technology to strengthen the work that they are doing to help protect plant health in our country.

One of the most prominent up and coming technologies that is being tested at the Centre for Plant Health is high-throughput genome sequencing, or HTS. Despite the many applications of HTS, there are no countries that have yet defined standards surrounding its widespread use in diagnostic laboratories, nor developed the necessary criteria to have it accepted internationally. Although there are some challenges surrounding the development of standards for this new technology, research scientists at CFIA have made it their mission to take on the task of being a global leader and pursue research to support the creation of scientific standards that could allow HTS to become internationally accepted.

But what is HTS? Why doesn’t everyone use it? HTS is a method for sequencing genomes, the genetic code of a living thing, at a high speed and low cost. Essentially, we are revealing the code that allows scientists to identify organisms and learn more about their diversity at the genetic level. Why is this important in the context of plant health? Ultimately, this helps us determine if the pest in question is considered a threat to the plant. Canada has signed on to follow the International Plant Protection Convention (IPPC), the goal of which is to ensure that plant resources are protected from pests. One of the roles of the IPPC is to develop standards for testing. In order to reduce the risk of spreading pests, it is imperative that these possible contaminants are discovered as soon as possible so that scientists are able to prevent their spread. Currently, it can take years of testing using internationally accepted methods before a plant that is imported into, or to be exported from Canada can be certified free of regulated viruses. With the introduction of HTS, the time it takes for genome sequencing to produce the necessary results could be drastically decreased to only a few months. The speed and accuracy of this new tech would be a huge game changer for producing lab results faster and supporting the growth of Canada’s fruit industry.

Although HTS is appearing to be truly revolutionary in the world of diagnostics, there are some challenges that scientists will have to overcome in order for this technology to become internationally accepted. One of the biggest challenges is being able to interpret the complex results consistently across labs. Significant validation data and universally accepted criteria for interpreting HTS results are required in order to develop standards that will allow those results to inform decisions governing international trade of plant material. Scientists at the CFIA have been stepping up to the plate to address these challenges by conducting research that will help define this new era in plant health regulation.

Scientists at the Centre for Plant Health have been part of the effort by leading research that will help the CFIA to validate HTS. Dr. Stefanie Sultmanis started out exploring the potential for international acceptance of HTS. Starting as a MITACS science policy fellow, Stefanie went on to write successful research proposals which led to her present day research which is centred around determining the sensitivity and repeatability of HTS for the detection of viruses in tree fruit. The results of this work will be essential for producing the necessary data and moving one step closer towards developing international diagnostic standards. The Commission on Phytosanitary Measures (CPM) has adopted a list of recommendations on the use of HTS. For Canadians, the implementation of HTS in Sidney’s regular testing could mean faster, high-quality results so that imported plant material could be released to growers sooner; this would be a big competitive advantage for Canada’s fruit industry.

As with any new emerging technology, it is important to ensure that future steps are in place to make sure the work continues to advance. In the case of using HTS as a part of the IPPC’s standard-setting system, there are still a number of steps to take to accomplish this ultimate goal. International collaboration through sharing knowledge and expertise is necessary in order to develop a standard for HTS usage. In addition, more scientific evidence is still needed. A standardized set of detection criteria is needed in order to allow scientists to make a decision about whether or not a virus is found within a sample. Since genetic information is so variable, this becomes a challenge. The reliability and accuracy also has to be confirmed. With this in mind, the scientists are hard at work trying to tackle these challenges.

With 2020 being the United Nation’s International Year of Plant Health (IYPH), it is fitting that the CFIA’s work with HTS supports and aligns so well with its mission to promote plant health internationally.

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About the authors:

  • Stefanie Sultmanis, Science Analyst, Sidney Laboratory
  • Tracy Lawrence, Virology Technician, Sidney Laboratory
  • Brittany Day, A/Senior Science Advisor, Plant Health Science Directorate
  • Anithra Selvakumar, Coop Intern, Plant Health Science Directorate

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