1
|
Fontdevila Pareta N, Khalili M, Maachi A, Rivarez MPS, Rollin J, Salavert F, Temple C, Aranda MA, Boonham N, Botermans M, Candresse T, Fox A, Hernando Y, Kutnjak D, Marais A, Petter F, Ravnikar M, Selmi I, Tahzima R, Trontin C, Wetzel T, Massart S. Managing the deluge of newly discovered plant viruses and viroids: an optimized scientific and regulatory framework for their characterization and risk analysis. Front Microbiol 2023; 14:1181562. [PMID: 37323908 PMCID: PMC10265641 DOI: 10.3389/fmicb.2023.1181562] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 04/25/2023] [Indexed: 06/17/2023] Open
Abstract
The advances in high-throughput sequencing (HTS) technologies and bioinformatic tools have provided new opportunities for virus and viroid discovery and diagnostics. Hence, new sequences of viral origin are being discovered and published at a previously unseen rate. Therefore, a collective effort was undertaken to write and propose a framework for prioritizing the biological characterization steps needed after discovering a new plant virus to evaluate its impact at different levels. Even though the proposed approach was widely used, a revision of these guidelines was prepared to consider virus discovery and characterization trends and integrate novel approaches and tools recently published or under development. This updated framework is more adapted to the current rate of virus discovery and provides an improved prioritization for filling knowledge and data gaps. It consists of four distinct steps adapted to include a multi-stakeholder feedback loop. Key improvements include better prioritization and organization of the various steps, earlier data sharing among researchers and involved stakeholders, public database screening, and exploitation of genomic information to predict biological properties.
Collapse
Affiliation(s)
| | - Maryam Khalili
- Univ. Bordeaux, INRAE, UMR BFP, Villenave d'Ornon, France
- EGFV, Univ. Bordeaux, INRAE, ISVV, Villenave d’Ornon, France
| | | | - Mark Paul S. Rivarez
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
- College of Agriculture and Agri-Industries, Caraga State University, Butuan, Philippines
| | - Johan Rollin
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
- DNAVision (Belgium), Charleroi, Belgium
| | - Ferran Salavert
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Coline Temple
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Miguel A. Aranda
- Department of Stress Biology and Plant Pathology, Center for Edaphology and Applied Biology of Segura, Spanish National Research Council (CSIC), Murcia, Spain
| | - Neil Boonham
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Marleen Botermans
- Netherlands Institute for Vectors, Invasive Plants and Plant Health (NIVIP), Wageningen, Netherlands
| | | | - Adrian Fox
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
- Fera Science Ltd, York Biotech Campus, York, United Kingdom
| | | | - Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Armelle Marais
- Univ. Bordeaux, INRAE, UMR BFP, Villenave d'Ornon, France
| | | | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Ilhem Selmi
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Rachid Tahzima
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
- Plant Sciences Unit, Institute for Agricultural, Fisheries and Food Research (ILVO), Merelbeke, Belgium
| | - Charlotte Trontin
- European and Mediterranean Plant Protection Organization, Paris, France
| | - Thierry Wetzel
- DLR Rheinpfalz, Institute of Plant Protection, Neustadt an der Weinstrasse, Germany
| | - Sebastien Massart
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
- Bioversity International, Montpellier, France
| |
Collapse
|