The Future of Post Entry Quarantine: Canadian National Clean Plant Program

Transcription

1 The Future of Post Entry Quarantine: Canadian National Clean Plant Program Dr. Michael Rott, Canadian Food Inspection Agency (CFIA) Sidney, BC, Canada Her Majesty the Queen in right of Canada (Canadian Food Inspection Agency), all rights reserved. Use without permission is prohibited.

2 Overview What is a National Clean Plant Program (NCPP) A model: US Clean National Clean Plant Network Canadian Imported material: what is required Time Line illustration and explanations Current approaches Testing technologies Advances in testing Model for the implementation of NCPP What we need to get there Benefits 2

3 What is a National Clean Plant Program (NCPP) Goal: To promote the production and use of pathogen-free, healthy plant material for food crops in Canada Framework: A set of rules/regulations to govern the maintenance, testing, propagation and distribution of pest and disease free plant material from nuclear generation 1 material to generation 4 material grown for retail. Enabler: A lab network and testing technology to support the Program 3

4 A good model: US National Clean Plant Network (NCPN) 2005: Idea initiated by grape and tree fruit industries 2008: Grape and fruit tree networks developed by stakeholders, industry members, scientists and other interested parties 2009: NCPN created as a voluntary association of specialty crop networks to promote pathogen-tested, healthy plant material United States Department of Agriculture Animal and Plant Health Inspection Service (APHIS) Agricultural Research Service (ARS) National Institute of Food and Agriculture (NIFA) 2010: berries, citrus and hops programs added 2016: US Farm Bill: invested XXXX$ in program 4

5 US NCPN: Grapes New, state-of-the-art facility, Foundation Plant Service, Davis CA Regulates importation of grapevine material Provides tested, clean material, using latest equipment and techniques Manage Russell Ranch: foundation material for pathogen-tested US grapevine material 5

6 The Canadian Situation: Imported material Currently, propagative tissues of tree fruit, grapevines and small fruit imported into Canada must be held in post entry quarantine to ensure they are free from disease and pests of concern. This includes: Foreign material from non-certified sources Audit samples from approved certified sources Domestic material from plant breeding programs and nurseries

7 Time line: Import of new cultivar from a noncertified source 6 12 years!! 7

8 Why so long? Current Testing Methods Molecular and Serological Tests: Virus specific PCR and ELISA 1-3 days to complete Bioassay Tests: Herbaceous bioassay Nonspecific, 2-3 weeks to complete Woody field and greenhouse bioassay* Nonspecific, up to 3 years to complete *International Gold Standard 8

9 Until now: Canadian Situation: Canada does not currently have a NCPP due to several challenges: Additional costs: to the public to growers Reluctance to increase regulatory burden Requires a willingness from industry stakeholders and government 9

10 What is different now? Technological Advances and Novel Applications DNA sequencing: today a generally accepted a way to ID an organism e.g. DNA Barcoding 1st generation sequencing technology: - laborious, slow, $$$ human genome: 13yrs, $3B Next Generation Sequencing (NGS) - faster, cheaper, automatable human genome: 1-2 days, <$5K Metagenomics: use of NGS technology to ID multiple species in a single sample detect multiple viral infections in plants! 10

11 Small samples produce big data! Tissue Types: bark/cambium, leaf Tissue Amount: 1-5 g sample (individual/composite) DNA extraction: manual/automated Genomic Libraries DNA that has been Prepped for sequencing all genetic material from the sample Next Generation Sequencing: various systems Reads Gigabytes of data in <12h Cost: $150/sample/test includes above steps Data analysis: Bioinformatics processes computational advances allow for Computer facilitated analysis of data i.e. easier to find detection targets! 11

12 Other Benefits of NGS: Samples processed in months vs years Less expensive: 1/10 th the cost/sample. Or, 10x as many samples for the same cost. As sensitive or more sensitive than conventional More accurate Greater specificity Greater ability to detect new viruses Replace the bioassay? 12

13 Example: 2013 grapevine audit imports Approximately 2.5 million vines imported Center for Plant Health in Sidney receives 1800 vines for testing (0.07%) Samples are: inoculated to 5 indicator plants rub inoculated onto 3 herbaceous indicators tested by PCR for 12 virus tested by ELISA for 5 virus > 5200 individual tests are performed on these samples over 3 years!! 13

14 Example: 2013 grapevine audit imports vines imported: 2.5 million vines tested by CPH: 1800 Traditional tests: >5200 tests in 3 years The future: using NGS, metagenomics and bioinformatics approaches: NGS tests + Confirmatory testing (PCR or ELISA) IN 4 8 months 14

15 CFIA Programs that could be modernized through a NCPP: Export Certification Programs: Canadian Fruit Tree Export Program (CFTEP) for Malus, Pyrus, Chaenomeles and Prunus (D-08-05) Plant Protection Export Certification Program for Grapevine Nursery Stock, Vitis spp. (D-97-06) Import Programs: Post Entry Quarantine To prevent introduction of plant viruses/virus-like diseases in tree fruit, grapevines & small fruit. Other activities: Viral elimination, maintenance of clean stock 15

16 NCPP Vision: Harmonize with Canadian National Import and Export Programs new test methods based on NGS Harmonize with USA North American Plant Protection Organization (NAPPO) USA National Clean Plant Network (NCPN) Harmonize Internationally International Plant Protection Convention (IPPC) EUPHRESCO Network for Phytosanitary research coordination and funding 16

17 Supporting Research: Current, Next, Future. NGS validation & Generation 1 nuclear repository Re-test current grapevine and tree fruit export repository by NGS Validate NGS for plant viruses Develop NGS methods for grape fungal pathogens NGS Tech transfer to 3 rd party diagnostic lab Testing need for strawberry plant exports Methods for Curating Gen 1 nuclear material

18 18 Research: Current, Next, Future. Viral Elimination: Heat therapy Meristem culture Chemotherapy Cryotherapy Micrografting Others Plant Propagation In vitro cultures micropropagation Micrografting Others

19 Go from this: 6 12 years.to this: Imported material to CPH. Negative released to importer (4 plants) Virus free material released to importer (4 plants) 4-6 years Viruses testing program (4-8 months) Positive Virus elimination program (1-2 years) Micropropagation (1-1/2 years) First crop (2 years) 19

20 Benefits to Canada establishing a NCPP Help maintain the highest standards for Canadian food production while improving competitiveness of the Canadian Agro-Foods Sector Facilitate access to new material to Industry while reducing the reliance on imported and potentially infected material Provide protection to production systems and to farms, nurseries, and orchards while promoting trade Help prevent the introduction and spread of potentially harmful plant pests and diseases in Canada An integrated consortium of laboratory expertise linking university, AAFC, CFIA and the various industry sectors

21 Acknowledgements Funding Genomic R&D Initiative: Protection of Canadian biodiversity and trade from the impacts of global change through improved ability to monitor invasive alien and quarantine species Canadian Safety and Security Programs: CSSP-2014-TA CSSP-2015-TA

22 2007 Her Majesty the Queen in right of Canada (Canadian Food Inspection Agency), all rights reserved. Use without permission is prohibited. 22