Topic_Description_A-207

Transcription

1 1.1Topic area Diagnostics, field detection and surveillance. 1. Content of the Topic Description document 1.2 Topic title Development of detection methods for viruses on potato (PVT, APMoV) and APLV/APMMV test performance study. 1.3 Description of the problem the research should solve Potatoes are high value cash crop in Europe, the Americas and other parts of the world. Numerous diseases affect potato production negatively, therefore quarantine regulations are in place to prevent introduction of quarantine pests and diseases into areas where these pathogens are currently not present. Import controls and NPPOs need reliable, quick and sensitive detection methods to prevent the introduction of these pathogens. Potato virus T (PVT), Andean potato mottle virus (APMoV) and Andean potato latent virus/andean potato mild mottle virus (APLV/APMMV) are quarantine viruses listed by EPPO. For APLV/APMMV, RT-PCR tests have been developed recently for detection and identification. This project aims to validate these tests in test performance studies. However, no detection nor identification protocols are available for PVT and APMoV. Therefore, adequate detection methods will be developed during this project. The detection method of next generation sequencing (NGS) offers the potential to detect all viruses, both known and currently unknown in a single assay, thus reducing the costs of quarantine testing and the risk of not detecting a virus using current EPPO recommended detection methods for viruses e.g. ELISA, bioassay and RT-PCR/PCR (PM 3/21(2) Post-entry quarantine for potato). NGS however requires to be validated and costs reduced before it can enter mainstream use. This proposal aims to initially concentrate on APLV/APMMV, APMoV and PVT but to quickly extend the validation to other potato viruses and viroids. NGS will be validated (small RNAs v Total RNA) and also various sequencing platforms (Illumina-MiSeq, MinION). Where relevant extraction procedures will be simplified and bioinformatics pipelines improved. The validation process will involve testing known infected / healthy potato material and therefore collections identified in the Euphresco VirusCollect project will be important as a source of reference material. All NGS results will be confirmed using RT-PCR (PCR) /sequencing and this may require the development of new assays (for new viruses) or for known viruses that currently do not currently have a molecular assay. 1.4 Description of the expected results Existing diagnostic protocols for detection and identification of APLV/APMMV will be validated in test performance studies. For PVT and APMoV, quick, reliable and sensitive detection methods will be developed. Standard protocols of RT-PCR and real-time (q) RT-PCR have been developed by partner CFIA-CL for the detection of PVT in various potato tissues. The protocols can be shared in the collaboration. A validated NGS method for detection of potato viruses and RT-PCR (PCR) assays for confirmation of NGS results. Identification of new potato infecting viruses. Improved characterisation of potato viruses in current collections (feeds into Virus Collect II) 1

2 1.5 Beneficiaries of this research product Researchers: This project will generate standardized guidelines for detection and identification of quarantine potato viruses (APLV/APMMV, APMoV and PVT), a validated NGS method and new RT-PCR/PCR assays for confirmation of NGS results where these are currently lacking. This will allow researchers to carry out systematic surveys in the areas of origin to investigate ecology and epidemiology of these viruses. Diagnostic laboratories and inspection bodies will be able to apply validated standard protocols for detection and identification of quarantine viruses of potato crops. This will allow sound decisions on import or rejection of potatoes. In addition, NGS technology will be able to be used by laboratories producing pathogen tested nuclear potato stocks the starting point for potato certification. NPPO will be required to adapt their policies for quarantine testing based on this scientifically validated scheme. Industry will benefit from the availability of better controlled plants and of an adapted regulatory framework allowing them to explore new markets for their potato crops. 1.6 Research funders and research contribution/ distribution Funding organisation 1. Science and Advice for Scottish Agriculture, United Kingdom David Kenyon david.kenyon@sasa.gsi.gov.uk Research activity and researchers involved -Validation of RT-PCR assays for the specific detection of APLV /APMMV, but may also include a generic Tymovirus assay. -Development and validation of RT-PCR assays for the specific detection of for PVT and APMoV, but may also include a generic assay. -Participation in the proficiency tests if organised. -Validation of NGS including development of RT-PCR/PCR assays Information gained from a NGS project will be applied to this project. Coordinator name: Wendy Monger wendy.monger@sasa.gsi.gov.uk 2. Ministry of Agriculture and Forestry, Environment and Water Management, Austria Sylvia Blümel sylvia.bluemel@ages.at 3. Canadian Food Inspection Agency- Plant Research & Strategies, Canada Contact: C Jeffries colin.jeffries@sasa.gsi.gov.uk -Participation in PCR performance studies. Contact: Sabine Grausgruber-Gröger sabine.grausgruber-groeger@ages.at -Development of diagnostic procedures for APMoV. 2

3 Cheryl Dollard 4. French Agency for Food, Environmental and Occupational Health & Safety, France Geraldine Anthoine 5. Federal Ministry of Food and Agriculture, Germany Bettina Beerbaum 6. Netherlands Food and Consumer Products Safety Authority, the Netherlands Martijn Schenk -Validation of the standard diagnostic protocols for APLV and APMMV. -Implementation of RT-PCR/RT-qPCR for PVT. -Evaluation and validation of NGS procedures for potato quarantine testing. Contact: Huimin Xu -Participation in the test performance studies for the detection and identification of APLV/APMMV. Contact : Jean-Philippe Renvoisé jean-philippe.renvoise@anses.fr -Participation in test performance studies; potentially provision of APLV/APMMV isolates for test performance study. Contact: Heiko Ziebell Heiko.ziebell@julius-kuehn.de -Application and validation of NGS as a generic method for screening potato for quarantine viruses. Contact: Bart van de Vossenberg b.t.l.h.vandevossenberg@nvwa.nl -Extending Q-bank Plant Viruses and Viroids database so that it can be used for reference assembly for potato quarantine viruses. 7. US Department of Agriculture, Animal and Plant Health Inspection Service, United States of America Laurene Levy Laurene.Levy@aphis.usda.gov 8. International Potato Center, Peru Jan Kreuze J.kreuze@cgiar.org Contact: Annelien Roenhorst j.w.roenhorst@nvwa.nl -Participation in the test methods validation (end-point RT-PCR and real-time RT-PCR), possible ring test. Contact: Vessela Mavrodieva Vessela.A.Mavrodieva@aphis.usda.gov -Participation in the inter-laboratory testing of potato viruses included in this project (PVT, APMoV and APLV/APMMV) to validate diagnostic methods. Contact person: Jan Kreuze J.kreuze@cgiar.org Contact person: Giovanna Müller g.muller@cgiar.org 3

4 1.7 Research project partnership outside Euphresco Euphresco funding ensures a certain level of transnational collaboration among Euphresco member countries. It is possible, if the funding consortium is interested, to contact funding organisations or research groups outside the geographical area covered by Euphresco members. The Euphresco coordinator could advertise the research topic in order to have an enlarged collaboration. If funders are interested in this possibility, please check the case below: The funding consortium of the topic mentioned in section 1.2 requires to advertise the topic outside the Euphresco network 1.8 Any other relevant information on content 4

5 2. Euphresco management aspects of the project 2.1. Indication of the topic budget Funding organisation a Mechanism b Total Budget c 1. SASA (GB) NC AGES (AT) NC CFIA (CA) NC ANSES (FR) NC BMEL/JKI (DE) NC NVWA (NL) NC APHIS (USA) NC CIP (PE) NC total Expected duration of the project (only for non-competitive topics) months Any other relevant information on topic organisation and management a First member is project coordinator. A minimum of two partners are necessary for each proposal. Add lines as needed. b Please indicate the preferred mechanism (e.g. real pot RP; virtual pot VP; non-competitive NC), or several mechanisms if there is flexibility. c Optional, as this amount can still change in the next phase. In-kind contribution should also be indicated in this column. 5