A Framework for the Evaluation of Biosecurity, Commercial, Regulatory, and Scientific Impacts of Plant Viruses and Viroids Identified by NGS Technologies.
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.
Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège Gembloux, Belgium.
Sebastien
S
Massart
Institut National de la Recherche Agronomique (INRA), University of Bordeaux, CS20032 UMR 1332 BFP Villenave d'Ornon, France.
Thierry
T
Candresse
Plant Biology, Linnean Centre for Plant Biology, Uppsala BioCentre, Swedish University of Agricultural Sciences Uppsala, Sweden.
José
J
Gil
Virology and Zoology, Science and Advice for Scottish Agriculture Edinbourgh, UK.
Christophe
C
Lacomme
Department of Plant Virology, Institute of Virology, Biomedical Research Center, Slovak Academy of Science (SAS) Bratislava, Slovakia.
Lukas
L
Predajna
Department of Biotechnology and Systems Biology, National Institute of Biology Ljubljana, Slovenia.
Maja
M
Ravnikar
Virology, Agroscope Nyon, Switzerland.
Jean-Sébastien
JS
Reynard
Division Phytomedicine Lentzeallee, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-University of Berlin Berlin, Germany.
Artemis
A
Rumbou
National Research Council Institute for Sustainable Plant Protection Bari, Italy.
Pasquale
P
Saldarelli
Department of Biology, Faculty of Science, University of Zagreb Zagreb, Croatia.
Dijana
D
Škorić
Management and Production of Renewable Resources, Natural Resources Institute Finland (Luke) Helsinki, Finland.
Eeva J
EJ
Vainio
Department of Agricultural Sciences, University of Helsinki Helsinki, Finland.
Jari P T
JP
Valkonen
Plant Genetics, Gembloux Agro-Bio Tech, University of Liège Gembloux, Belgium.
Hervé
H
Vanderschuren
Department of Phytopathology, Benaki Phytopathological Institute Athens, Greece.
Christina
C
Varveri
DLR Rheinpfalz, Institute of Plant Protection, Neustadt an der Weinstrasse Germany.
Thierry
T
Wetzel
NGS; biological characterization; pest risk analysis; plant health; regulatory agencies; virus diseases