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Massart S, Candresse T, Gil J, et al. A Framework for the Evaluation of Biosecurity, Commercial, Regulatory, and Scientific Impacts of Plant Viruses and Viroids Identified by NGS Technologies. Front Microbiol. 2017;8:45doi: 10.3389/fmicb.2017.00045.
Massart, S., Candresse, T., Gil, J., Lacomme, C., Predajna, L., Ravnikar, M., Reynard, J. S., Rumbou, A., Saldarelli, P., Škorić, D., Vainio, E. J., Valkonen, J. P., Vanderschuren, H., Varveri, C., & Wetzel, T. (2017). A Framework for the Evaluation of Biosecurity, Commercial, Regulatory, and Scientific Impacts of Plant Viruses and Viroids Identified by NGS Technologies. Frontiers in microbiology, 845. https://doi.org/10.3389/fmicb.2017.00045
Massart, Sebastien, et al. "A Framework for the Evaluation of Biosecurity, Commercial, Regulatory, and Scientific Impacts of Plant Viruses and Viroids Identified by NGS Technologies." Frontiers in microbiology vol. 8 (2017): 45. doi: https://doi.org/10.3389/fmicb.2017.00045
Massart S, Candresse T, Gil J, Lacomme C, Predajna L, Ravnikar M, Reynard JS, Rumbou A, Saldarelli P, Škorić D, Vainio EJ, Valkonen JP, Vanderschuren H, Varveri C, Wetzel T. A Framework for the Evaluation of Biosecurity, Commercial, Regulatory, and Scientific Impacts of Plant Viruses and Viroids Identified by NGS Technologies. Front Microbiol. 2017 Jan 24;8:45. doi: 10.3389/fmicb.2017.00045. eCollection 2017. PMID: 28174561; PMCID: PMC5258733.
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Front Microbiol. 2017 Jan 24;8:45. doi: 10.3389/fmicb.2017.00045. eCollection 2017.

A Framework for the Evaluation of Biosecurity, Commercial, Regulatory, and Scientific Impacts of Plant Viruses and Viroids Identified by NGS Technologies.

Frontiers in microbiology

Sebastien Massart, Thierry Candresse, José Gil, Christophe Lacomme, Lukas Predajna, Maja Ravnikar, Jean-Sébastien Reynard, Artemis Rumbou, Pasquale Saldarelli, Dijana Škorić, Eeva J Vainio, Jari P T Valkonen, Hervé Vanderschuren, Christina Varveri, Thierry Wetzel

Affiliations

  1. Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège Gembloux, Belgium.
  2. Institut National de la Recherche Agronomique (INRA), University of Bordeaux, CS20032 UMR 1332 BFP Villenave d'Ornon, France.
  3. Plant Biology, Linnean Centre for Plant Biology, Uppsala BioCentre, Swedish University of Agricultural Sciences Uppsala, Sweden.
  4. Virology and Zoology, Science and Advice for Scottish Agriculture Edinbourgh, UK.
  5. Department of Plant Virology, Institute of Virology, Biomedical Research Center, Slovak Academy of Science (SAS) Bratislava, Slovakia.
  6. Department of Biotechnology and Systems Biology, National Institute of Biology Ljubljana, Slovenia.
  7. Virology, Agroscope Nyon, Switzerland.
  8. Division Phytomedicine Lentzeallee, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-University of Berlin Berlin, Germany.
  9. National Research Council Institute for Sustainable Plant Protection Bari, Italy.
  10. Department of Biology, Faculty of Science, University of Zagreb Zagreb, Croatia.
  11. Management and Production of Renewable Resources, Natural Resources Institute Finland (Luke) Helsinki, Finland.
  12. Department of Agricultural Sciences, University of Helsinki Helsinki, Finland.
  13. Plant Genetics, Gembloux Agro-Bio Tech, University of Liège Gembloux, Belgium.
  14. Department of Phytopathology, Benaki Phytopathological Institute Athens, Greece.
  15. DLR Rheinpfalz, Institute of Plant Protection, Neustadt an der Weinstrasse Germany.

PMID: 28174561 PMCID: PMC5258733 DOI: 10.3389/fmicb.2017.00045

Abstract

Recent advances in high-throughput sequencing technologies and bioinformatics have generated huge new opportunities for discovering and diagnosing plant viruses and viroids. Plant virology has undoubtedly benefited from these new methodologies, but at the same time, faces now substantial bottlenecks, namely the biological characterization of the newly discovered viruses and the analysis of their impact at the biosecurity, commercial, regulatory, and scientific levels. This paper proposes a scaled and progressive scientific framework for efficient biological characterization and risk assessment when a previously known or a new plant virus is detected by next generation sequencing (NGS) technologies. Four case studies are also presented to illustrate the need for such a framework, and to discuss the scenarios.

Keywords: NGS; biological characterization; pest risk analysis; plant health; regulatory agencies; virus diseases

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