Current impact and future direction of High Throughput Sequencing in plant virus diagnostics: the drivers of COST Action FA1407

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Nancy Clark
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drivers of COST Action FA1407 THIERRY CANDRESSE,

FELIX, ISABEL FONT, MIROSLAV GLASA, RISTO JALKANEN,

VARVARA MALIOGKA, ANGELANOTIO MINAFRA, NELIA ORTEGA

SAFAROVA, RENE VANDERVLUGT, CHRISTINA VARVERI,

SEBASTIEN MASSART Laboratoire de Phytopathologie

1 Current impact and future direction of High Throughput Sequencing in plant virus diagnostics: the drivers of COST Action FA1407 THIERRY CANDRESSE, ANTONIO OLMOS, NEIL BOONHAM, CARMEN BÜTTNER, ROSARIO FELIX, ISABEL FONT, MIROSLAV GLASA, RISTO JALKANEN, PETR KOMINEK, MARGIT LAIMER, TADEUSZ MALINOWSKI, VARVARA MALIOGKA, ANGELANOTIO MINAFRA, NELIA ORTEGA PARRA, ANNALISA POLIVERARI, MAJA RAVNIKAR, DANA SAFAROVA, RENE VANDERVLUGT, CHRISTINA VARVERI, JOHANNA WITZELL, IOAN ZAGRAI, THIERRY WETZEL and SEBASTIEN MASSART Laboratoire de Phytopathologie Gembloux Agro-Bio Tech Université de Liège Belgique Driving factors 1

Taxonomy Viral population genetics Expectedimpact

2 NGS & Viruses Plant-virus interaction Etiology Viral ecology Currentimpact on R&D Plant resistance Taxonomy Viral population genetics Expectedimpact on diagnostics Diagnostic & Etiology Before NGS With NGS 2

3 Diagnostic & Etiology LES VIRUS More than 50 publications with new virus identification Diagnostic & Etiology New virus 3

Diagnostic & Etiology Host range Transmission? Plant-virus interaction?

diagnostic and eradication CLEAN UPSTREAM Improvedand standardized NGS

4 Diagnostic & Etiology Host range Transmission? Plant-virus interaction? New virus Viral population genetics???? Plant resistance Symptomatology? Threatto the plants & control measures? Diagnostic & NGS Certification, sanitation and quarantine Field diagnostic and eradication CLEAN UPSTREAM Improvedand standardized NGS methodologies for indexing IMPROVE DOWNSTREAM Deluge of sequences to accelerate and improve rapid-testing 4

5 Technical Cost evolution Challenges 1. Preparation& sequencing strategies? Extraction protocol DNA, total RNA, particle isolation, small RNA, dsrna 2. Sensitivity? Dependent on sequencing depth Similar to PCR Whatabout a single or a couple of viral reads? 3. Reproducibility and repeatability? Intra and inter-laboratory comparison 4. Contaminations? Technical Cost evolution Challenges Human& beefcontigs -> whatabout viruses? Partial or total genome coverage Strict confinement needed! 5. Adapatation to host species? Virus titre and extraction method Practical and technical challenges requiring both fundamental and applied research 5

6 Practical impact Identification of a new virus or a poorly characterized virus by a diagnostician? Halt the distribution of the plant material? Confirmatory assays (Molecular Koch postulate)? Long-term experiment on virus biology? Technical framework and decision schemes are needed Latent (or symbiotic )viruses discovered? Probability of discovering non pathogenic viruses is high Re-think trophic relationships? Adaptation of regulatory framework? NGS & Viruses Plant-virus interaction Etiology Viral ecology Currentimpact on R&D Plant resistance Taxonomy Viral population genetics Expectedimpact on diagnostics 6

7 COST Action FA1407 Deep DIVAS Investigation on Virus Associated Sequences DIVAS Fundamental virologists Industries Applied virologists Coordinate and raise the European capacity to apply NGS technologies for the study and diagnosis of viral diseases in vegetatively propagated plants, seeds and seedlings. Diagnostician NPPO/EPPO Regulatory authorities 7

Objectives of DIVAS COST Action for leveragingplant virus control throughngs Consolidate basic knowledge Improved Pest Risk Assessment and Control Transversal

8 Objectives of DIVAS COST Action for leveragingplant virus control throughngs Consolidate basic knowledge Improved Pest Risk Assessment and Control Transversal Action bridging various stakeholders Structure of DIVAS 1. Technological improvement 2. New scientific Knowledge 3. Societal innovations Societal innovations 8

9 Structure of DIVAS 25 European countries 10 additional countries outside Europe 50 people involved Activities: Conference Training schools Scientific missions Large impact in R&D Conclusion Impact ongoing in diagnostic Scientific & regulatory consequences Feedback loop to fundamental research Long term : Safer movement and trade Better understanding of the virus threat and biology (including the Pathovirome) 9

10 Thank you for your attention For more information: Massart et al., Virus Research, 188: Getin touchwithcost Action : Any inquiry: sebastien.massart@ulg.ac.be 10

Framework for the evaluation of. and scientific impacts of plant viruses. technologies.

Framework for the evaluation of biosecurity, commercial, regulatory and scientific impacts of plant viruses and viroids identified by NGS technologies. Sebastien Massart, Thierry Candresse, José Gil, Christophe