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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] [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.
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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
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Moubset O, François S, Maclot F, Palanga E, Julian C, Claude L, Fernandez E, Rott P, Daugrois JH, Antoine-Lorquin A, Bernardo P, Blouin AG, Temple C, Kraberger S, Fontenele RS, Harkins GW, Ma Y, Marais A, Candresse T, Chéhida SB, Lefeuvre P, Lett JM, Varsani A, Massart S, Ogliastro M, Martin DP, Filloux D, Roumagnac P. Virion-Associated Nucleic Acid-Based Metagenomics: A Decade of Advances in Molecular Characterization of Plant Viruses. PHYTOPATHOLOGY 2022; 112:2253-2272. [PMID: 35722889 DOI: 10.1094/phyto-03-22-0096-rvw] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Over the last decade, viral metagenomic studies have resulted in the discovery of thousands of previously unknown viruses. These studies are likely to play a pivotal role in obtaining an accurate and robust understanding of how viruses affect the stability and productivity of ecosystems. Among the metagenomics-based approaches that have been developed since the beginning of the 21st century, shotgun metagenomics applied specifically to virion-associated nucleic acids (VANA) has been used to disentangle the diversity of the viral world. We summarize herein the results of 24 VANA-based studies, focusing on plant and insect samples conducted over the last decade (2010 to 2020). Collectively, viruses from 85 different families were reliably detected in these studies, including capsidless RNA viruses that replicate in fungi, oomycetes, and plants. Finally, strengths and weaknesses of the VANA approach are summarized and perspectives of applications in detection, epidemiological surveillance, environmental monitoring, and ecology of plant viruses are provided. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Oumaima Moubset
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | | | - François Maclot
- Plant Pathology Laboratory, Terra, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | - Essowè Palanga
- Institut Togolais de Recherche Agronomique (ITRA-CRASS), B.P. 129, Kara, Togo
| | - Charlotte Julian
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Lisa Claude
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Emmanuel Fernandez
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Philippe Rott
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Jean-Heinrich Daugrois
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | | | | | - Arnaud G Blouin
- Plant Pathology Laboratory, Terra, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
- Plant Protection Department, Agroscope, 1260, Nyon, Switzerland
| | - Coline Temple
- Plant Pathology Laboratory, Terra, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, U.S.A
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, U.S.A
| | - Gordon W Harkins
- South African Medical Research Council Capacity Development Unit, South African National Bioinformatics, Institute, University of the Western Cape, South Africa
| | - Yuxin Ma
- Univ. Bordeaux, INRAE, UMR BFP, 33140 Villenave d'Ornon, France
| | - Armelle Marais
- Univ. Bordeaux, INRAE, UMR BFP, 33140 Villenave d'Ornon, France
| | | | | | | | | | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, U.S.A
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Sébastien Massart
- Plant Pathology Laboratory, Terra, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | | | - Darren P Martin
- Division of Computational Biology, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Denis Filloux
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Philippe Roumagnac
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
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3
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Kwibuka Y, Bisimwa E, Blouin AG, Bragard C, Candresse T, Faure C, Filloux D, Lett JM, Maclot F, Marais A, Ravelomanantsoa S, Shakir S, Vanderschuren H, Massart S. Novel Ampeloviruses Infecting Cassava in Central Africa and the South-West Indian Ocean Islands. Viruses 2021; 13:v13061030. [PMID: 34072594 PMCID: PMC8226816 DOI: 10.3390/v13061030] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/24/2021] [Accepted: 05/25/2021] [Indexed: 11/30/2022] Open
Abstract
Cassava is one of the most important staple crops in Africa and its production is seriously damaged by viral diseases. In this study, we identify for the first time and characterize the genome organization of novel ampeloviruses infecting cassava plants in diverse geographical locations using three high-throughput sequencing protocols [Virion-Associated Nucleotide Acid (VANA), dsRNA and total RNA], and we provide a first analysis of the diversity of these agents and of the evolutionary forces acting on them. Thirteen new Closteroviridae isolates were characterized in field-grown cassava plants from the Democratic Republic of Congo (DR Congo), Madagascar, Mayotte, and Reunion islands. The analysis of the sequences of the corresponding contigs (ranging between 10,417 and 13,752 nucleotides in length) revealed seven open reading frames. The replication-associated polyproteins have three expected functional domains: methyltransferase, helicase, and RNA-dependent RNA polymerase (RdRp). Additional open reading frames code for a small transmembrane protein, a heat-shock protein 70 homolog (HSP70h), a heat shock protein 90 homolog (HSP90h), and a major and a minor coat protein (CP and CPd respectively). Defective genomic variants were also identified in some cassava accessions originating from Madagascar and Reunion. The isolates were found to belong to two species tentatively named Manihot esculenta-associated virus 1 and 2 (MEaV-1 and MEaV-2). Phylogenetic analyses showed that MEaV-1 and MEaV-2 belong to the genus Ampelovirus, in particular to its subgroup II. MEaV-1 was found in all of the countries of study, while MEaV-2 was only detected in Madagascar and Mayotte. Recombination analysis provided evidence of intraspecies recombination occurring between the isolates from Madagascar and Mayotte. No clear association with visual symptoms in the cassava host could be identified.
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Affiliation(s)
- Yves Kwibuka
- Plant Pathology Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés, 2, 5030 Gembloux, Belgium; (A.G.B.); (F.M.)
- Faculté des Sciences Agronomiques, Université Catholique de Bukavu, BP 285 Bukavu, Democratic Republic of the Congo;
- Correspondence: (Y.K.); (S.M.)
| | - Espoir Bisimwa
- Faculté des Sciences Agronomiques, Université Catholique de Bukavu, BP 285 Bukavu, Democratic Republic of the Congo;
| | - Arnaud G. Blouin
- Plant Pathology Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés, 2, 5030 Gembloux, Belgium; (A.G.B.); (F.M.)
| | - Claude Bragard
- Earth and Life Institute, Applied Microbiology-Phytopathology, UCLouvain, 1348 Louvain-la-Neuve, Belgium;
| | - Thierry Candresse
- Université Bordeaux, INRAE, UMR BFP, CS20032, CEDEX, 33882 Villenave d’Ornon, France; (T.C.); (C.F.); (A.M.)
| | - Chantal Faure
- Université Bordeaux, INRAE, UMR BFP, CS20032, CEDEX, 33882 Villenave d’Ornon, France; (T.C.); (C.F.); (A.M.)
| | - Denis Filloux
- CIRAD, UMR PHIM, 34090 Montpellier, France;
- PHIM Plant Health Institute, Université Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34000 Montpellier, France
| | - Jean-Michel Lett
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, Saint-Pierre, F-97410 Ile de la Reunion, France;
| | - François Maclot
- Plant Pathology Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés, 2, 5030 Gembloux, Belgium; (A.G.B.); (F.M.)
| | - Armelle Marais
- Université Bordeaux, INRAE, UMR BFP, CS20032, CEDEX, 33882 Villenave d’Ornon, France; (T.C.); (C.F.); (A.M.)
| | | | - Sara Shakir
- Plant Genetics Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés, 2, 5030 Gembloux, Belgium; (S.S.); (H.V.)
| | - Hervé Vanderschuren
- Plant Genetics Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés, 2, 5030 Gembloux, Belgium; (S.S.); (H.V.)
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, Biosystems Department, KU Leuven, 3000 Leuven, Belgium
| | - Sébastien Massart
- Plant Pathology Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés, 2, 5030 Gembloux, Belgium; (A.G.B.); (F.M.)
- Correspondence: (Y.K.); (S.M.)
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Kutnjak D, Tamisier L, Adams I, Boonham N, Candresse T, Chiumenti M, De Jonghe K, Kreuze JF, Lefebvre M, Silva G, Malapi-Wight M, Margaria P, Mavrič Pleško I, McGreig S, Miozzi L, Remenant B, Reynard JS, Rollin J, Rott M, Schumpp O, Massart S, Haegeman A. A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses. Microorganisms 2021; 9:841. [PMID: 33920047 PMCID: PMC8071028 DOI: 10.3390/microorganisms9040841] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/09/2021] [Accepted: 04/10/2021] [Indexed: 12/12/2022] Open
Abstract
High-throughput sequencing (HTS) technologies have become indispensable tools assisting plant virus diagnostics and research thanks to their ability to detect any plant virus in a sample without prior knowledge. As HTS technologies are heavily relying on bioinformatics analysis of the huge amount of generated sequences, it is of utmost importance that researchers can rely on efficient and reliable bioinformatic tools and can understand the principles, advantages, and disadvantages of the tools used. Here, we present a critical overview of the steps involved in HTS as employed for plant virus detection and virome characterization. We start from sample preparation and nucleic acid extraction as appropriate to the chosen HTS strategy, which is followed by basic data analysis requirements, an extensive overview of the in-depth data processing options, and taxonomic classification of viral sequences detected. By presenting the bioinformatic tools and a detailed overview of the consecutive steps that can be used to implement a well-structured HTS data analysis in an easy and accessible way, this paper is targeted at both beginners and expert scientists engaging in HTS plant virome projects.
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Affiliation(s)
- Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Lucie Tamisier
- Plant Pathology Laboratory, Université de Liège, Gembloux Agro-Bio Tech, TERRA, Passage des Déportés, 2, 5030 Gembloux, Belgium; (L.T.); (J.R.); (S.M.)
| | - Ian Adams
- Fera Science Limited, York YO41 1LZ, UK; (I.A.); (S.M.)
| | - Neil Boonham
- Institute for Agri-Food Research and Innovation, Newcastle University, King’s Rd, Newcastle Upon Tyne NE1 7RU, UK;
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, 33140 Villenave d’Ornon, France; (T.C.); (M.L.)
| | - Michela Chiumenti
- Institute for Sustainable Plant Protection, National Research Council, Via Amendola, 122/D, 70126 Bari, Italy;
| | - Kris De Jonghe
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Burg. Van Gansberghelaan 96, 9820 Merelbeke, Belgium; (K.D.J.); (A.H.)
| | - Jan F. Kreuze
- International Potato Center (CIP), Avenida la Molina 1895, La Molina, Lima 15023, Peru;
| | - Marie Lefebvre
- UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, 33140 Villenave d’Ornon, France; (T.C.); (M.L.)
| | - Gonçalo Silva
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent ME4 4TB, UK;
| | - Martha Malapi-Wight
- Biotechnology Risk Analysis Programs, Biotechnology Regulatory Services, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Riverdale, MD 20737, USA;
| | - Paolo Margaria
- Leibniz Institute-DSMZ, Inhoffenstrasse 7b, 38124 Braunschweig, Germany;
| | - Irena Mavrič Pleško
- Agricultural Institute of Slovenia, Hacquetova Ulica 17, 1000 Ljubljana, Slovenia;
| | - Sam McGreig
- Fera Science Limited, York YO41 1LZ, UK; (I.A.); (S.M.)
| | - Laura Miozzi
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Strada delle Cacce 73, 10135 Torino, Italy;
| | - Benoit Remenant
- ANSES Plant Health Laboratory, 7 Rue Jean Dixméras, CEDEX 01, 49044 Angers, France;
| | | | - Johan Rollin
- Plant Pathology Laboratory, Université de Liège, Gembloux Agro-Bio Tech, TERRA, Passage des Déportés, 2, 5030 Gembloux, Belgium; (L.T.); (J.R.); (S.M.)
- DNAVision, 6041 Charleroi, Belgium
| | - Mike Rott
- Sidney Laboratory, Canadian Food Inspection Agency, 8801 East Saanich Rd, North Saanich, BC V8L 1H3, Canada;
| | - Olivier Schumpp
- Agroscope, Route de Duillier 50, 1260 Nyon, Switzerland; (J.-S.R.); (O.S.)
| | - Sébastien Massart
- Plant Pathology Laboratory, Université de Liège, Gembloux Agro-Bio Tech, TERRA, Passage des Déportés, 2, 5030 Gembloux, Belgium; (L.T.); (J.R.); (S.M.)
| | - Annelies Haegeman
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Burg. Van Gansberghelaan 96, 9820 Merelbeke, Belgium; (K.D.J.); (A.H.)
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Špak J, Koloniuk I, Tzanetakis IE. Graft-Transmissible Diseases of Ribes - Pathogens, Impact, and Control. PLANT DISEASE 2021; 105:242-250. [PMID: 32870112 DOI: 10.1094/pdis-04-20-0759-fe] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
This article provides an up-to-date review of disease-causing viruses and phytoplasmas of currants including symptoms, transmission, detection, economic impact, and control measures. Currants are widely cultivated in more than 30 countries in the temperate zones of Europe, Asia, South America, Australia, and New Zealand. Ribes spp. can be infected by more than 20 virus species and four Candidatus Phytoplasma species, with more to be described in the future. High-throughput sequencing opened a new era of deciphering virus variants and mixed infections, leading to the characterization of several new species. The use of clean propagation material is the basis for control of Ribes graft-transmissible diseases, but this has become a challenging task given the ever-growing number of newly discovered pathogens.
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Affiliation(s)
- Josef Špak
- Biology Centre, Czech Academy of Sciences, 37005 České Budějovice, Czech Republic
| | - Igor Koloniuk
- Biology Centre, Czech Academy of Sciences, 37005 České Budějovice, Czech Republic
| | - Ioannis E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701, U.S.A
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Hou W, Li S, Massart S. Is There a "Biological Desert" With the Discovery of New Plant Viruses? A Retrospective Analysis for New Fruit Tree Viruses. Front Microbiol 2020; 11:592816. [PMID: 33329473 PMCID: PMC7710903 DOI: 10.3389/fmicb.2020.592816] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/29/2020] [Indexed: 12/13/2022] Open
Abstract
High throughput sequencing technologies accelerated the pace of discovery and identification of new viral species. Nevertheless, biological characterization of a new virus is a complex and long process, which can hardly follow the current pace of virus discovery. This review has analyzed 78 publications of new viruses and viroids discovered from 32 fruit tree species since 2011. The scientific biological information useful for a pest risk assessment and published together with the discovery of a new fruit tree virus or viroid has been analyzed. In addition, the 933 publications citing at least one of these original publications were reviewed, focusing on the biology-related information provided. In the original publications, the scientific information provided was the development of a detection test (94%), whole-genome sequence including UTRs (92%), local and large-scale epidemiological surveys (68%), infectivity and indicators experiments (50%), association with symptoms (25%), host range infection (23%), and natural vector identification (8%). The publication of a new virus is cited 2.8 times per year on average. Only 18% of the citations reported information on the biology or geographical repartition of the new viruses. These citing publications improved the new virus characterization by identifying the virus in a new country or continent, determining a new host, developing a new diagnostic test, studying genome or gene diversity, or by studying the transmission. Based on the gathered scientific information on the virus biology, the fulfillment of a recently proposed framework has been evaluated. A baseline prioritization approach for publishing a new plant virus is proposed for proper assessment of the potential risks caused by a newly identified fruit tree virus.
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Affiliation(s)
- Wanying Hou
- Key Laboratory of Tobacco Pest Monitoring Controlling and Integrated Management, Institute of Tobacco Research, Chinese Academy of Agricultural Sciences, Qingdao, China
- Plant Pathology Laboratory, TERRA, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Shifang Li
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sebastien Massart
- Plant Pathology Laboratory, TERRA, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
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Gazel M, Roumi V, Ördek K, Maclot F, Massart S, Çağlayan K. Identification and molecular characterization of a novel foveavirus from Rubus spp. in Turkey. Virus Res 2020; 286:198078. [PMID: 32603671 DOI: 10.1016/j.virusres.2020.198078] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 06/23/2020] [Accepted: 06/26/2020] [Indexed: 02/02/2023]
Abstract
A novel plant virus was identified by high-throughput sequencing analysis from a raspberry plant showing slight mottling symptom. The complete genome sequence of this virus is 8645 nucleotides long, including the 5' and 3' UTRs. Its genome contains five ORFs and is very close to members of the genus Foveavirus (Quinvirinae, Betaflexiviridae) in terms of genome organization, TGB presence and the sizes of the RdRp and CP proteins. The novel virus shares 33.5-51.3 % and 23.3-41.3 % nucleotide identity to other genera of the Betaflexifiviridae family based on polymerase (RdRp) and CP genes, respectively. Compared to other foveavirus species, the RdRp protein showed the highest sequence identity (45.3 %) to the RdRp of peach chlorotic mottle virus (PCMV) while the maximal sequence identity for the CP protein was 33.9 % with grapevine rupestris stem pitting-associated virus (GRSPaV). The low nucleotide and amino acid sequence identity with known foveaviruses indicated that it was a novel virus, for which the provisional name "rubus virus 1 (RuV1)" is proposed. The phylogenetic analysis supports the assignment of this virus as a new species of the genus Foveavirus. A survey of 537 Rubus spp. samples grown in six provinces of Turkey, including some symptomatic samples, showed a RuV1 prevalence of 2.2 %, confirming its presence in both raspberry and blackberry plants in a single province, although no obvious association between virus infection and specific symptoms was found.
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Affiliation(s)
- Mona Gazel
- Department of Plant Protection, College of Agriculture, University of Hatay Mustafa Kemal, Hatay, Turkey
| | - Vahid Roumi
- Department of Plant Protection, College of Agriculture, University of Maragheh, Maragheh, Iran.
| | - Kivilcim Ördek
- Department of Plant Protection, College of Agriculture, University of Hatay Mustafa Kemal, Hatay, Turkey
| | - Francois Maclot
- Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liege, Passage des Deportes 2, 5030 Gembloux, Belgium
| | - Sebastien Massart
- Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liege, Passage des Deportes 2, 5030 Gembloux, Belgium
| | - Kadriye Çağlayan
- Department of Plant Protection, College of Agriculture, University of Hatay Mustafa Kemal, Hatay, Turkey
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Bragard C, Dehnen-Schmutz K, Gonthier P, Jacques MA, Jaques Miret JA, Justesen AF, MacLeod A, Magnusson CS, Milonas P, Navas-Cortes JA, Parnell S, Potting R, Reignault PL, Thulke HH, Van der Werf W, Civera AV, Yuen J, Zappalà L, Candresse T, Chatzivassiliou E, Finelli F, Winter S, Bosco D, Chiumenti M, Di Serio F, Ferilli F, Kaluski T, Minafra A, Rubino L. Pest categorisation of non-EU viruses of Ribes L. EFSA J 2019; 17:e05859. [PMID: 32626160 PMCID: PMC7008784 DOI: 10.2903/j.efsa.2019.5859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Following a request from the EU Commission, the Panel on Plant Health addressed the pest categorisation of the viruses of Ribes L. determined as being either non-EU or of undetermined standing in a previous EFSA opinion. These infectious agents belong to different genera and are heterogeneous in their biology. Alaska vitivirus 1 and Ribes virus F were excluded from categorisation because these are very poorly characterised viruses. The pest categorisation was completed for seven viruses with clear identity and for which detection methods are available. All these viruses are efficiently transmitted by vegetative propagation techniques, with plants for planting representing the major pathway for long-distance dispersal and thus considered as the major pathway for entry. Depending on the virus, additional pathway(s) can also be Ribes seeds, pollen and/or vector(s). Most of the viruses categorised here are known to infect only one or few plant genera, but tomato ringspot virus (ToRSV) has a wide host range, thus extending the possible entry pathways. ToRSV meets all the criteria evaluated by EFSA to qualify as potential Union quarantine pest (QP). With the exception of impact in the EU territory, on which the Panel was unable to conclude, Actinidia virus X, blackcurrant leaf chlorosis-associated virus, blackcurrant leafroll-associated virus, black currant-associated rhabdovirus, blackcurrant waikavirus A and Ribes americanum virus A satisfy all the other criteria to be considered as potential Union QPs. For several viruses, especially those recently discovered, the categorisation is associated with high uncertainties mainly because of the absence of data on their biology, distribution and impact. Since this opinion addresses specifically the non-EU viruses, in general these viruses do not meet the criteria assessed by EFSA to qualify as potential Union regulated non-quarantine pests.
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