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1. Semi-artificial datasets as a resource for validation of bioinformatics pipelines for plant virus detection

Author

Tamisier, Lucie, Haegeman, Annelies, Foucart, Yoika, Fouillien, Nicolas, Al Rwahnih, Maher, Buzkan, Nihal, Candresse, Thierry, Chiumenti, Michela, De Jonghe, Kris, Lefebvre, Marie, Margaria, Paolo, Reynard, Jean Sébastien, Stevens, Kristian, Kutnjak, Denis, and Massart, Sébastien

Subjects
Archaeology, CC1-960, Science
Abstract

The widespread use of High-Throughput Sequencing (HTS) for detection of plant viruses and sequencing of plant virus genomes has led to the generation of large amounts of data and of bioinformatics challenges to process them. Many bioinformatics pipelines for virus detection are available, making the choice of a suitable one difficult. A robust benchmarking is needed for the unbiased comparison of the pipelines, but there is currently a lack of reference datasets that could be used for this purpose. We present 7 semi-artificial datasets composed of real RNA-seq datasets from virus-infected plants spiked with artificial virus reads. Each dataset addresses challenges that could prevent virus detection. We also present 3 real datasets showing a challenging virus composition as well as 8 completely artificial datasets to test haplotype reconstruction software. With these datasets that address several diagnostic challenges, we hope to encourage virologists, diagnosticians and bioinformaticians to evaluate and benchmark their pipeline(s).

Published
2021
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3. Contributors

Author

Adkar-Purushothama, Charith Raj, primary, Bardani, Irene, additional, Beltrán, M. Francisca, additional, Bolduc, François, additional, Chiumenti, Michela, additional, Cueto, C.A., additional, Daròs, José-Antonio, additional, de la Peña, Marcos, additional, Di Serio, Francesco, additional, Elleuch, Amine, additional, Fiore, Nicola, additional, Gómez, Gustavo, additional, Hamdi, Imen, additional, Hammond, Rosemarie W., additional, Hanold, D., additional, Harper, Scott, additional, Iftikhar, Y., additional, Jakše, Jernej, additional, Kalantidis, Kriton, additional, Krueger, Robert, additional, Kryovrysanaki, Nikoleta, additional, Lavagi-Craddock, Irene, additional, Li, Shifang, additional, Lisón, Purificación, additional, López-Galiano, Maria José, additional, Marquez-Molins, Joan, additional, Martinez, German, additional, Matoušek, Jaroslav, additional, Navarro, Beatriz, additional, Nie, Xianzhou, additional, Owens, Robert A., additional, Pallás, Vicente, additional, Perreault, Jean-Pierre, additional, Quijia-Lamiña, Paulina, additional, Randles, J.W., additional, Riesner, Detlev, additional, Rodrigo, Ismael, additional, Sano, Teruo, additional, Shruthi, B., additional, Škorić, Dijana, additional, Steger, Gerhard, additional, Thanarajoo, S.S., additional, Vadamalai, G., additional, Vázquez-Prol, Francisco, additional, Vidalakis, Georgios, additional, Wang, Ying, additional, Yanjarappa, Sreenivasa Marikunte, additional, and Zhang, Zhixiang, additional

Published
2024
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6. 2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

Author

Kuhn, Jens H, Adkins, Scott, Alioto, Daniela, Alkhovsky, Sergey V, Amarasinghe, Gaya K, Anthony, Simon J, Avšič-Županc, Tatjana, Ayllón, María A, Bahl, Justin, Balkema-Buschmann, Anne, Ballinger, Matthew J, Bartonička, Tomáš, Basler, Christopher, Bavari, Sina, Beer, Martin, Bente, Dennis A, Bergeron, Éric, Bird, Brian H, Blair, Carol, Blasdell, Kim R, Bradfute, Steven B, Breyta, Rachel, Briese, Thomas, Brown, Paul A, Buchholz, Ursula J, Buchmeier, Michael J, Bukreyev, Alexander, Burt, Felicity, Buzkan, Nihal, Calisher, Charles H, Cao, Mengji, Casas, Inmaculada, Chamberlain, John, Chandran, Kartik, Charrel, Rémi N, Chen, Biao, Chiumenti, Michela, Choi, Il-Ryong, Clegg, J Christopher S, Crozier, Ian, da Graça, John V, Dal Bó, Elena, Dávila, Alberto MR, de la Torre, Juan Carlos, de Lamballerie, Xavier, de Swart, Rik L, Di Bello, Patrick L, Di Paola, Nicholas, Di Serio, Francesco, Dietzgen, Ralf G, Digiaro, Michele, Dolja, Valerian V, Dolnik, Olga, Drebot, Michael A, Drexler, Jan Felix, Dürrwald, Ralf, Dufkova, Lucie, Dundon, William G, Duprex, W Paul, Dye, John M, Easton, Andrew J, Ebihara, Hideki, Elbeaino, Toufic, Ergünay, Koray, Fernandes, Jorlan, Fooks, Anthony R, Formenty, Pierre BH, Forth, Leonie F, Fouchier, Ron AM, Freitas-Astúa, Juliana, Gago-Zachert, Selma, Gāo, George Fú, García, María Laura, García-Sastre, Adolfo, Garrison, Aura R, Gbakima, Aiah, Goldstein, Tracey, Gonzalez, Jean-Paul J, Griffiths, Anthony, Groschup, Martin H, Günther, Stephan, Guterres, Alexandro, Hall, Roy A, Hammond, John, Hassan, Mohamed, Hepojoki, Jussi, Hepojoki, Satu, Hetzel, Udo, Hewson, Roger, Hoffmann, Bernd, Hongo, Seiji, Höper, Dirk, Horie, Masayuki, Hughes, Holly R, Hyndman, Timothy H, Jambai, Amara, Jardim, Rodrigo, Jiāng, Dàohóng, Jin, Qi, and Jonson, Gilda B

Subjects
Biotechnology, Mononegavirales, Terminology as Topic, Biological Sciences, Agricultural and Veterinary Sciences, Medical and Health Sciences, Virology
Abstract

In March 2020, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. At the genus rank, 20 new genera were added, two were deleted, one was moved, and three were renamed. At the species rank, 160 species were added, four were deleted, ten were moved and renamed, and 30 species were renamed. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.

Published
2020

9. Draft Genome Sequence of CO33, a Coffee-Infecting Isolate of Xylella fastidiosa

Author

Giampetruzzi, Annalisa, Loconsole, Giuliana, Boscia, Donato, Calzolari, Alessandra, Chiumenti, Michela, Martelli, Giovanni P, Saldarelli, Pasquale, Almeida, Rodrigo PP, and Saponari, Maria

Subjects
Microbiology, Biological Sciences, Genetics, Biochemistry and Cell Biology
Abstract

The draft genome sequence of Xylella fastidiosa CO33 isolate, retrieved from symptomatic leaves of coffee plant intercepted in northern Italy, is reported. The CO33 genome size is 2,681,926 bp with a GC content of 51.7%.

Published
2015

17. Commodity risk assessment of Prunus persica and P. dulcis plants from Türkiye

Author

Bragard, Claude, Baptista, Paula, Chatzivassiliou, Elisavet, Gonthier, Paolo, Jaques Miret, Josep Anton, Justesen, Annemarie Fejer, Macleod, Alan, Magnusson, Christer Sven, Milonas, Panagiotis, Navas-Cortes, Juan A, Parnell, Stephen, Potting, Roel, Reignault, Philippe Lucien, Stefani, Emilio, Thulke, Hans-Hermann, Van der Werf, Wopke, Civera, Antonio Vicent, Zappalà, Lucia, Lucchi, Andrea, Gómez, Pedro, Urek, Gregor, Bernardo, Umberto, Bubici, Giovanni, Carluccio, Anna Vittoria, Chiumenti, Michela, Di Serio, Francesco, Fanelli, Elena, Kaczmarek, Agata, Marzachì, Cristina, Mosbach-Schulz, Olaf, and Yuen, Jonathan

Subjects
Veterinary (miscellaneous), quarantine, Plant Science, rootstock, Peach, Microbiology, almond, pathway risk assessment, plant pest, Animal Science and Zoology, Parasitology, European Union, plant health, Food Science
Published
2023

18. Commodity risk assessment of Malus domestica plants from United Kingdom

Author

Bragard, Claude, Baptista, Paula, Chatzivassiliou, Elisavet, Gonthier, Paolo, Jaques Miret, Josep Anton, Justesen, Annemarie Fejer, Macleod, Alan, Magnusson, Christer Sven, Milonas, Panagiotis, Navas-Cortes, Juan A, Parnell, Stephen, Potting, Roel, Reignault, Philippe Lucien, Stefani, Emilio, Thulke, Hans-Hermann, Van der Werf, Wopke, Civera, Antonio Vicent, Zappalà, Lucia, Lucchi, Andrea, Gómez, Pedro, Urek, Gregor, Bernardo, Umberto, Bubici, Giovanni, Carluccio, Anna Vittoria, Chiumenti, Michela, Di Serio, Francesco, Fanelli, Elena, Marzachì, Cristina, Kaczmarek, Agata, Mosbach-Schulz, Olaf, and Yuen, Jonathan

Subjects
pathway risk assessment, plant pest, quarantine, apple, European Union, plant health
Published
2023

19. Pest categorisation of cowpea mosaic virus

Author

Bragard, Claude, Baptista, Paula, Chatzivassiliou, Elisavet, Gonthier, Paolo, Jaques Miret, Josep Anton, Justesen, Annemarie Fejer, Macleod, Alan, Magnusson, Christer Sven, Milonas, Panagiotis, Navas-Cortes, Juan A, Parnell, Stephen, Potting, Roel, Stefani, Emilio, Thulke, Hans-Hermann, Van der Werf, Wopke, Civera, Antonio Vicent, Yuen, Jonathan, Zappalà, Lucia, Streissl, Franz, Carluccio, Anna Vittoria, Chiumenti, Michela, Di Serio, Francesco, Rubino, Luisa, and Reignault, Philippe Lucien

Subjects
pest risk, Veterinary (miscellaneous), Comovirus, quarantine, Fabaceae, Plant Science, CPMV, Diabrotica virgifera virgifera, plant health, Microbiology, Animal Science and Zoology, Parasitology, Food Science
Published
2023

20. Pest categorisation of chickpea chlorotic dwarf virus

Author

Bragard, Claude, Baptista, Paula, Chatzivassiliou, Elisavet, Di Serio, Francesco, Gonthier, Paolo, Jaques Miret, Josep Anton, Justesen, Annemarie Fejer, Macleod, Alan, Magnusson, Christer Sven, Milonas, Panagiotis, Navas-Cortes, Juan A, Parnell, Stephen, Potting, Roel, Stefani, Emilio, Thulke, Hans-Hermann, Van der Werf, Wopke, Vicent Civera, Antonio, Yuen, Jonathan, Zappalà, Lucia, Migheli, Quirico, Vloutoglou, Irene, Czwienczek, Ewelina, Streissl, Franz, Carluccio, Anna Vittoria, Chiumenti, Michela, Rubino, Luisa, and Reignault, Philippe Lucien

Subjects
pest risk, leafhopper transmission, Veterinary (miscellaneous), Mastrevirus, quarantine, Plant Science, CpCDV, plant health, plant pest, Microbiology, Animal Science and Zoology, Parasitology, Food Science
Abstract

The EFSA Panel on Plant Health conducted a pest categorisation of chickpea chlorotic dwarf virus (CpCDV) for the EU territory. The identity of CpCDV, a member of the genus

Published
2022

21. Plant Health Bioinformatics Network (PHBN)

Author

Haegeman, Annelies, Rott, Michael, Nicolaisen, Morgen, Remenant, Benoît, Candresse, Thierry, Sela, Noa, Kutnjak, Denis, De Cal, Antonieta, Margaria, Paolo, Miozzi, Laura, Chiumenti, Michela, Okinyi Sewe, Steven, van Duivenbode, Inge, van Gurp, Thomas, and Schumpp, Olivier

Subjects
Euphresco, plant health, bioinformatics, high-throughput sequencing, HTS, training, validation
Abstract

Plant disease detection by high-throughput sequencing (HTS) is a relatively new and fast developing discipline, with very variable levels of expertise in phytopathology and diagnostics laboratories across the world. The overall goal of the “Plant Health Bioinformatics Network” project (PHBN) was to join different laboratories working with HTS applied to plant disease diagnostics problems and stimulate the exchange of information regarding HTS data analysis, as well as on the interpretation of the results of HTS data in a plant diagnostic context. In a collaborative effort of > 20 scientists from 11 different countries, open source training materials were developed. This resulted in the guide ‘A primer on the analysis of high-throughput sequencing data for detection of plant viruses‘, which is useful for both beginners and experts. This guide includes a glossary of terms, a flowchart (showing the typical workflow of an analysis), a checklist with things to keep in mind during data processing, a checklist with points of consideration during taxonomic classification and a quick-start guide. Data analysis pipelines were converted to training materials and compiled with other already well-documented pipelines to make them publicly available. Training people alone is not sufficient to develop good bioinformatics skills. People may follow a tutorial meticulously, but if the steps/parameters used are not suited for the specific case they investigate, they might misinterpret the results. In order to make virologists and bioinformaticians more aware of the strengths and weaknesses of their pipeline, (semi-)artificial datasets were designed and tested. Nine challenges in data analysis that can occur when analyzing HTS datasets for the detection and identification of plant viruses were identified. Based on these challenges, several plant-derived Illumina RNA-seq datasets were selected from different international partners. Three of them showed already one of the challenges and were not modified. For 7 other datasets, artificial reads were added as spike-in, with known read numbers, to mimic one of the challenges. Finally, 8 completely artificial datasets were made for haplotype reconstruction. The (semi-)artificial datasets were made publicly available and recommended by “Peer Community in Genomics”. A VIROMOCK challenge was then launched to encourage scientists to analyze the data and upload their results. Although only 29 reports were received (i.e. on average 3 per dataset), we were able to observe that most differences between the participants were due to mapping settings and the choice of the reference genome(s). Finally, we wanted to demonstrate the potential of HTS in the detection of (non-viral) plant pathogens and pests by re-analyzing existing RNA-seq datasets in an RNA-seq screening effort. More specifically, we asked the plant virology community to re-analyze some of their existing datasets, in order to check if traces could be found of non-viral pathogens. This is often overlooked since most virologists only compare the reads or contigs with plant virus sequence databases. In total 15 scientists participated in the screening, together analyzing 101 datasets of which 37 datasets were selected for detailed analysis at ILVO (BE). 29 of the 37 datasets revealed the potential presence of non-viral plant pathogens, with fungi, insects and mites the most observed organism categories. These results show that RNA-seq data generated by virologists can be used to investigate the potential presence of other potentially harmful organisms or potential virus vectors., Report of the Euphresco project 2018-A-289 'Plant Health Bioinformatics Network (PHBN)'

Published
2022
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23. Pest survey card on Tobacco ringspot virus.

Author

Chiumenti, Michela and Camilleri, Melanie

Subjects
*TOBACCO ringspot virus
Abstract

This document provides the conclusions of the pest survey card that was prepared in the context of the EFSA mandate on plant pest surveillance (M‐2020‐0114) at the request of the European Commission. The full pest survey card for tobacco ringspot virus (TRSV) is published and available online in the EFSA Plant Pest Survey Cards Gallery at the following link and will be updated whenever new information becomes available: https://efsa.europa.eu/plants/planthealth/monitoring/surveillance/tobacco-ringspot-virus [ABSTRACT FROM AUTHOR]

Published
2023
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24. Pest survey card on coconut cadang‐cadang viroid.

Author

Chiumenti, Michela and Graziosi, Ignazio

Subjects
*COCONUT
Abstract

This document provides the conclusions of the pest survey card that was prepared in the context of the EFSA mandate on plant pest surveillance (M‐2020‐0114) at the request of the European Commission. The full pest survey card for coconut cadang‐cadang viroid (CCCVd) is published and available online in the EFSA Plant Pest Survey Cards Gallery at the following link and will be updated whenever new information becomes available: https://efsa.europa.eu/plants/planthealth/monitoring/surveillance/coconut-cadang-cadang-viroid [ABSTRACT FROM AUTHOR]

Published
2023
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25. Commodity risk assessment of Prunus domestica plants from Ukraine

Author

Bragard, Claude, Chatzivassiliou, Elisavet, Dehnen-Schmutz, Katharina, Baptista, Paula, Gonthier, Paolo, Jacques, Marie-Agnès, Jaques Miret, Josep Anton, Justesen, Annemarie Fejer, Macleod, Alan, Magnusson, Christer Sven, Milonas, Panagiotis, Navas-Cortes, Juan A, Parnell, Stephen, Potting, Roel, Reignault, Philippe L, Stefani, Emilio, Thulke, Hans-Hermann, Van der Werf, Wopke, Vicent, Antonio, Zappalà, Lucia, Lucchi, Andrea, Gómez, Pedro, Urek, Gregor, Bernardo, Umberto, Bubici, Giovanni, Carluccio, Anna Vittoria, Chiumenti, Michela, Di Serio, Francesco, Fanelli, Elena, Marzachì, Cristina, Gardi, Ciro, Mosbach-Schulz, Olaf, de la Peña, Eduardo, and Yuen, Jonathan

Subjects
Plum, Veterinary (miscellaneous), quarantine, Plant Science, rootstock, Microbiology, pathway risk assessment, plant pest, European Union, plant health, Animal Science and Zoology, Parasitology, Food Science
Published
2022

26. Pest categorisation of Capsicum chlorosis virus

Author

Bragard, Claude, Baptista, Paula, Chatzivassiliou, Elisavet, Gonthier, Paolo, Jaques Miret, Josep Anton, Justesen, Annemarie Fejer, MacLeod, Alan, Magnusson, Christer Sven, Milonas, Panagiotis, Navas‐Cortes, Juan A, Parnell, Stephen, Potting, Roel, Reignault, Philippe Lucien, Stefani, Emilio, Thulke, Hans‐Hermann, Van der Werf, Wopke, Vicent Civera, Antonio, Yuen, Jonathan, Zappalà, Lucia, Dehnen‐Schmutz, Katharina, Migheli, Quirico, Vloutoglou, Irene, Czwienczek, Ewelina, Streissl, Franz, Carluccio, Anna Vittoria, Chiumenti, Michela, Di Serio, Francesco, Rubino, Luisa, and UCL - SST/ELI/ELIM - Applied Microbiology

Subjects
pest risk, thrips transmission, Veterinary (miscellaneous), quarantine, CaCV, Orthotospovirus, plant health, plant pest, Plant Science, Microbiology, Animal Science and Zoology, Parasitology, Food Science
Abstract

The EFSA Panel on Plant Health conducted a pest categorisation of Capsicum chlorosis virus (CaCV) for the EU territory. The identity of CaCV, a member of the genus Orthotospovirus (family Tospoviridae), is established and reliable detection and identification methods are available. The pathogen is not included in the EU Commission Implementing Regulation 2019/2072. CaCV has been reported in Australia, China, India, Iran, Taiwan, Thailand and USA (Hawaii). In the EU, it has been reported once in Greece (Crete Island). The NPPO of Greece reported that CaCV is no longer present in Greece. CaCV infects plant species in the family Solanaceae (i.e. pepper, tomato) and several species of other families, including ornamentals. It may induce severe symptoms on its hosts, mainly on leaves and fruits, which may become unmarketable. The virus is transmitted in a persistent propagative mode by the thrips Ceratothripoides claratris, Frankliniella schultzei, Microcephalothrips abdominalis and Thrips palmi. C. claratris and T. palmi are EU quarantine pests. M. abdominalis is known to be present in several EU member states and it is not regulated in the EU. Plants for planting, parts of plants, fruits and cut flowers of CaCV hosts, and viruliferous thrips were identified as the most relevant pathways for the entry of CaCV into the EU. Cultivated and wild hosts of CaCV are distributed across the EU. Should the pest enter and establish in the EU territory, impact on the production of cultivated hosts is expected. Phytosanitary measures are available to prevent entry and spread of the virus in the EU. CaCV fulfils the criteria that are within the remit of EFSA to assess for it to be regarded as a potential Union quarantine pest.

Published
2022

28. 2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

Author

National Institute of Allergy and Infectious Diseases (US), National Cancer Institute (US), National Institutes of Health (US), Frederick National Laboratory for Cancer Research (US), US Department of Homeland Security, National Institute of Food and Agriculture (US), Kuhn, Jens H. [0000-0002-7800-6045], Adkins, Scott [0000-0003-0095-8414], Alioto, Daniela [0000-0002-4954-8363], Alkhovsky, Sergey V. [0000-0001-6913-5841], Amarasinghe, Gaya K. [0000-0002-0418-9707], Avsic-Zupanc, Tatjana [0000-0001-6243-0688], Ayllón, María A. [0000-0001-7893-6106], Bahl, Justin [0000-0001-7572-4300], Balkema-Buschmann, A. [0000-0001-7613-9592], Ballinger, Matthew J. [0000-0001-7453-8725], Bartonička, Tomáš [0000-0001-7335-2435], Basler, Christopher F. [0000-0003-4195-425X], Bavari, Sina [0000-0001-8424-5635], Beer, Martin [0000-0002-0598-5254], Bente, Dennis A. [0000-0002-5150-7368], Bergeron, Éric [0000-0003-3398-8628], Bird, Brian H. [0000-0001-8170-8710], Blair, Carol D. [0000-0002-2803-0354], Blasdell, Kim R. [0000-0003-2121-0376], Bradfute, Steven B. [0000-0002-1985-751X], Breyta, Rachel [0000-0002-9106-1014], Briese, Thomas [0000-0002-4819-8963], Brown, Paul A. [0000-0002-6697-7688], Buchholz, Ursula J. [0000-0002-2329-3198], Buchmeier, Michael J. [0000-0002-2387-9287], Bukreyev, Alexander [0000-0002-0342-4824], Burt, Felicity [0000-0002-7238-7799], Buzkan, Nihal [0000-0002-0428-0447], Calisher, Charles H. [0000-0003-0213-294X], Cao, Mengji [0000-0003-0396-262X], Casas, Inmaculada [0000-0003-1840-1198], Chamberlain, John [0000-0002-7387-6420], Chandran, Kartik [0000-0003-0232-7077], Charrel, Rémi N. [0000-0002-7675-8251], Chen, Biao [0000-0002-2450-9296], Chiumenti, Michela [0000-0002-8412-3037], Choi, Il-Ryong [0000-0002-8035-7573], Clegg, J Christopher S. [0000-0003-3765-1862], Crozier, Ian [0000-0003-2485-4011], da Graça, John V. [0000-0003-0743-1519], Dávila, Alberto M.R. [0000-0002-6918-7673], de la Torre, J. C. [0000-0002-8171-8115], de Lamballerie, Xavier [0000-0001-7895-2720], De Swart, Rik L. [0000-0003-3599-8969], Di Bello, Patrick L. [0000-0002-4773-8040], Di Paola, Nicholas [0000-0002-9694-3913], Di Serio, Francesco [0000-0003-2822-704X], Dietzgen, Ralf G. [0000-0002-7772-2250], Digiaro, Michele [0009-0006-3089-3606], Dolja, Valerian V. [0000-0002-8148-4670], Dolnik, Olga [0000-0001-7739-4798], Drexler, J. Felix [0000-0002-3509-0232], Dürrwald, Ralf [0000-0002-3432-0438], Dufkova, Lucie [0000-0001-7302-2057], Dundon, William G. [0000-0002-2776-169X], Duprex, W. Paul [0000-0003-1716-6376], Dye, John M. [0000-0002-0883-5016], Easton, Andrew J. [0000-0002-2288-3882], Ebihara, Hideki [0000-0002-2576-9735], Elbeaino, Toufic [0000-0003-2211-7907], Ergünay, Koray [0000-0001-5422-1982], Fernandes, Jorlan [0000-0002-5039-0604], Fooks, Anthony R. [0000-0002-3243-6154], Formenty, Pierre B.H. [0000-0002-9482-5411], Forth, Leonie F [0000-0002-2708-2515], Fouchier, Ron A.M. [0000-0001-8095-2869], Freitas-Astúa, Juliana [0000-0002-0506-6880], Gago-Zachert, Selma [0000-0002-1084-2119], Gāo, George Fú [0000-0002-3869-615X], García, María Laura [0000-0001-6468-6943], García-Sastre, Adolfo [0000-0002-6551-1827], Garrison, Aura R. [0000-0003-3034-6400], Gbakima, Aiah [0000-0002-7642-0752], Goldstein, Tracey [0000-0002-1672-7410], Gonzalez, Jean-Paul J. [0000-0003-3063-1770], Griffiths, Anthony [0000-0001-5435-8364], Groschup, M. H. [0000-0003-0215-185X], Günther, Stephan [0000-0002-6562-0230], Guterres, Alexandro [0000-0001-8323-1477], Hall, Roy A. [0000-0001-5778-1387], Hammond, John [0000-0001-7593-747X], Hassan, Mohamed [0000-0002-1289-0878], Hepojoki, Jussi [0000-0001-5699-214X], Hepojoki, Satu [0000-0002-0696-1879], Hetzel, Udo [0000-0001-9142-560X], Hewson, Roger [0000-0003-2273-3152], Höper, Dirk [0000-0001-8408-2274], Horie, Masayuki [0000-0003-4682-7698], Hyndman, Timothy [0000-0002-7047-5023], Hughes, Holly R. [0000-0003-1380-8263], Hyndman, Timothy [0000-0003-4083-562X], Jambai, Amara [0000-0003-3754-2500], Jardim, Rodrigo [0000-0002-0943-5356], Jiāng, Dàohóng [0000-0002-3862-7461], Jonson, Gilda B. [0000-0003-0097-8634], Junglen, Sandra [0000-0002-3799-6011], Klempa, B. [0000-0002-6931-1224], Klingström, Jonas [0000-0001-9076-1441], Kobinger, Gary [0000-0003-0612-2298], Kondō, Hideki [0000-0001-9220-5350], Koonin, Eugene V. [0000-0003-3943-8299], Krupovic, Mart [0000-0001-5486-0098], Kurath, Gael [0000-0003-3294-560X], Laenen, Lies [0000-0001-9118-8608], Langevin, Stanley L. [0000-0002-6833-271X], Lee, Benhur [0000-0003-0760-1709], Lemos, Elba R.S. [0000-0003-3761-0200], Lukashevich, Igor S. [0000-0001-6523-5116], Maes, Piet [0000-0002-4571-5232], Marklewitz, Marco [0000-0003-1828-8770], Marzano, Shin-Yi L. [0000-0003-0548-3761], Mielke-Ehret, Nicole [0000-0003-0096-0696], Minafra, Angelantonio [0000-0002-0547-7129], Minutolo, Maria [0000-0001-7816-2657], Mühlberger, Elke [0000-0003-3547-9376], Naidu, Rayapati [0000-0002-7273-5116], Natsuaki, Tomohide [0000-0003-1823-7308], Navarro, José A. [0000-0002-0536-6074], Netesov, Sergey V. [0000-0002-7786-2464], Neumann, Gabriele [0000-0001-7054-1775], Nowotny, N. [0000-0002-3548-571X], Nunes, Márcio R.T. [0000-0003-0529-0230], Nylund, Are [0000-0002-1932-6604], Okland, Arnfinn Lodden [0000-0003-3062-4386], Oliveira, Renata C. [0000-0002-1904-7533], Pallás, Vicente [0000-0003-4954-989X], Pályi, Bernadett [0000-0003-1975-4198], Parrish, Colin R. [0000-0002-1836-6655], Pauvolid-Corrêa, Alex [0000-0002-6924-157X], Pawęska, Janusz T. [0000-0001-8776-7519], Radoshitzky, Sheli R. [0000-0001-8976-8056], Rahman, Aziz-Ul [0000-0002-3342-4462], Ramos-González, Pedro L. [0000-0002-9640-6587], Resende, Renato O. 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G., Vaira, Anna Maria, Van den Hoogen, Bernadette, Varsani, Arvind, Vasilakis, Nikos, Verbeek, Martin, Wahl, Victoria, Walker, Peter J., Wang, Hui, Wang, Jianwei, Wang, Xifeng, Wang, Lin-Fa, Wèi, Tàiyún, Wells, Heather, Whitfield, Anna E., Williams, John V., Wolf, Yuri I., Wú, Zhìqiáng, Yang, Xin, Yáng, Xīnglóu, Yu, Xuejie, Yutin, Natalya, Zerbini, F. Murilo, Zhang, Tong, Zhang, Yong-Zhen, Zhou, Guohui, and Zhou, Xueping

Abstract

In March 2020, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. At the genus rank, 20 new genera were added, two were deleted, one was moved, and three were renamed. At the species rank, 160 species were added, four were deleted, ten were moved and renamed, and 30 species were renamed. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.

Published
2020

29. Commodity risk assessment of grafted plants of Malus domestica from Moldova

Author

UCL - SST/ELI/ELIM - Applied Microbiology, Bragard, Claude, Baptista, Paula, Chatzivassiliou, Elisavet, Gonthier, Paolo, Jaques Miret, Josep Anton, Fejer Justesen, Annemarie, MacLeod, Alan, Magnusson, Christer Sven, Milonas, Panagiotis, Navas‐Cortes, Juan A, Parnell, Stephen, Potting, Roel, Reignault, Philippe Lucien, Stefani, Emilio, Thulke, Hans‐Hermann, Van der Werf, Wopke, Vicent Civera, Antonio, Zappalà, Lucia, Di Serio, Francesco, Gómez, Pedro, Urek, Gregor, Lucchi, Andrea, Carluccio, Anna Vittoria, Chiumenti, Michela, Fanelli, Elena, Bernardo, Umberto, Marzachì, Cristina, Bubici, Giovanni, de la Peña, Eduardo, Gardi, Ciro, Yuen, Jonathan, UCL - SST/ELI/ELIM - Applied Microbiology, Bragard, Claude, Baptista, Paula, Chatzivassiliou, Elisavet, Gonthier, Paolo, Jaques Miret, Josep Anton, Fejer Justesen, Annemarie, MacLeod, Alan, Magnusson, Christer Sven, Milonas, Panagiotis, Navas‐Cortes, Juan A, Parnell, Stephen, Potting, Roel, Reignault, Philippe Lucien, Stefani, Emilio, Thulke, Hans‐Hermann, Van der Werf, Wopke, Vicent Civera, Antonio, Zappalà, Lucia, Di Serio, Francesco, Gómez, Pedro, Urek, Gregor, Lucchi, Andrea, Carluccio, Anna Vittoria, Chiumenti, Michela, Fanelli, Elena, Bernardo, Umberto, Marzachì, Cristina, Bubici, Giovanni, de la Peña, Eduardo, Gardi, Ciro, and Yuen, Jonathan

Abstract

The European Commission requested the EFSA Panel on Plant Health to prepare and deliver risk assessments for commodities listed in Commission Implementing Regulation (EU) 2018/2019 as ‘High risk plants, plant products and other objects’. This Scientific Opinion covers plant health risks posed by defoliated and in dormant phase, grafted bare rooted plants for planting of Malus domestica imported from Moldova, taking into account the available scientific information, including the technical information provided by the applicant country. A list of 1,118 pests potentially associated with the commodity species was compiled. The relevance of these pests was assessed following defined criteria and based on evidence. The EU-quarantine pest Xiphinema rivesi non-EU populations fulfilled these criteria and was selected for further evaluation. For this pest, the risk mitigation measures proposed in the technical dossier from Moldova were evaluated taking into account the possible limiting factors. For this pest, an expert judgement is given on the likelihood of pest freedom taking into consideration the risk mitigation measures acting on it, including uncertainties associated with the assessment. The Expert Knowledge Elicitation indicated, with 95% certainty, that between 9,991 and 10,000 plants per 10,000 would be free of X. rivesi.

Published
2022

30. Commodity risk assessment of Prunus domestica plants from Ukraine

Author

UCL - SST/ELI/ELIM - Applied Microbiology, Bragard, Claude, Chatzivassiliou, Elisavet, Dehnen‐Schmutz, Katharina, Baptista, Paula, Gonthier, Paolo, Jacques, Marie‐Agnès, Jaques Miret, Josep Anton, Justesen, Annemarie Fejer, MacLeod, Alan, Magnusson, Christer Sven, Milonas, Panagiotis, Navas‐Cortes, Juan A, Parnell, Stephen, Potting, Roel, Reignault, Philippe L, Stefani, Emilio, Thulke, Hans‐Hermann, Van der Werf, Wopke, Vicent, Antonio, Zappalà, Lucia, Lucchi, Andrea, Gómez, Pedro, Urek, Gregor, Bernardo, Umberto, Bubici, Giovanni, Carluccio, Anna Vittoria, Chiumenti, Michela, Di Serio, Francesco, Fanelli, Elena, Marzachì, Cristina, Gardi, Ciro, Mosbach‐Schulz, Olaf, de la Peña, Eduardo, Yuen, Jonathan, UCL - SST/ELI/ELIM - Applied Microbiology, Bragard, Claude, Chatzivassiliou, Elisavet, Dehnen‐Schmutz, Katharina, Baptista, Paula, Gonthier, Paolo, Jacques, Marie‐Agnès, Jaques Miret, Josep Anton, Justesen, Annemarie Fejer, MacLeod, Alan, Magnusson, Christer Sven, Milonas, Panagiotis, Navas‐Cortes, Juan A, Parnell, Stephen, Potting, Roel, Reignault, Philippe L, Stefani, Emilio, Thulke, Hans‐Hermann, Van der Werf, Wopke, Vicent, Antonio, Zappalà, Lucia, Lucchi, Andrea, Gómez, Pedro, Urek, Gregor, Bernardo, Umberto, Bubici, Giovanni, Carluccio, Anna Vittoria, Chiumenti, Michela, Di Serio, Francesco, Fanelli, Elena, Marzachì, Cristina, Gardi, Ciro, Mosbach‐Schulz, Olaf, de la Peña, Eduardo, and Yuen, Jonathan

Abstract

The European Commission requested the EFSA Panel on Plant Health to prepare and deliver risk assessments for commodities listed in Commission Implementing Regulation (EU) 2018/2019 as ‘High risk plants, plant products and other objects’. This Scientific Opinion covers plant health risks posed by plants of Prunus domestica grafted on Prunus cerasifera imported from Ukraine, taking into account the available scientific information, including the technical information provided by Ukraine. All pests associated with the commodity were evaluated against specific criteria for their relevance for this opinion. One quarantine pest (Lopholeucaspis japonica), two protected zone quarantine pests (Erwinia amylovora and Xanthomonas arboricola pv. pruni) and one non-regulated pest (Eotetranychus prunicola) that fulfilled all relevant criteria were selected for further evaluation. For these four pests, the risk mitigation measures proposed in the technical dossier from Ukraine were evaluated taking into account the possible limiting factors. For the selected pests, an expert judgement is given on the likelihood of pest freedom taking into consideration the risk mitigation measures acting on the pest, including uncertainties associated with the assessment. The degree of pest freedom varies among the pests evaluated, with Xanthomonas arboricola pv. pruni being the pest most frequently expected on the imported plants. The Expert Knowledge Elicitation indicated with 95% certainty that between 9,870 and 10,000 bundles (consisting of 10 plants each) per 10,000 would be free from Xanthomonas arboricola pv. pruni.

Published
2022

31. Pest categorisation of Capsicum chlorosis virus

Author

UCL - SST/ELI/ELIM - Applied Microbiology, Bragard, Claude, Baptista, Paula, Chatzivassiliou, Elisavet, Gonthier, Paolo, Jaques Miret, Josep Anton, Justesen, Annemarie Fejer, MacLeod, Alan, Magnusson, Christer Sven, Milonas, Panagiotis, Navas‐Cortes, Juan A, Parnell, Stephen, Potting, Roel, Reignault, Philippe Lucien, Stefani, Emilio, Thulke, Hans‐Hermann, Van der Werf, Wopke, Vicent Civera, Antonio, Yuen, Jonathan, Zappalà, Lucia, Dehnen‐Schmutz, Katharina, Migheli, Quirico, Vloutoglou, Irene, Czwienczek, Ewelina, Streissl, Franz, Carluccio, Anna Vittoria, Chiumenti, Michela, Di Serio, Francesco, Rubino, Luisa, UCL - SST/ELI/ELIM - Applied Microbiology, Bragard, Claude, Baptista, Paula, Chatzivassiliou, Elisavet, Gonthier, Paolo, Jaques Miret, Josep Anton, Justesen, Annemarie Fejer, MacLeod, Alan, Magnusson, Christer Sven, Milonas, Panagiotis, Navas‐Cortes, Juan A, Parnell, Stephen, Potting, Roel, Reignault, Philippe Lucien, Stefani, Emilio, Thulke, Hans‐Hermann, Van der Werf, Wopke, Vicent Civera, Antonio, Yuen, Jonathan, Zappalà, Lucia, Dehnen‐Schmutz, Katharina, Migheli, Quirico, Vloutoglou, Irene, Czwienczek, Ewelina, Streissl, Franz, Carluccio, Anna Vittoria, Chiumenti, Michela, Di Serio, Francesco, and Rubino, Luisa

Abstract

The EFSA Panel on Plant Health conducted a pest categorisation of Capsicum chlorosis virus (CaCV) for the EU territory. The identity of CaCV, a member of the genus Orthotospovirus (family Tospoviridae), is established and reliable detection and identification methods are available. The pathogen is not included in the EU Commission Implementing Regulation 2019/2072. CaCV has been reported in Australia, China, India, Iran, Taiwan, Thailand and USA (Hawaii). In the EU, it has been reported once in Greece (Crete Island). The NPPO of Greece reported that CaCV is no longer present in Greece. CaCV infects plant species in the family Solanaceae (i.e. pepper, tomato) and several species of other families, including ornamentals. It may induce severe symptoms on its hosts, mainly on leaves and fruits, which may become unmarketable. The virus is transmitted in a persistent propagative mode by the thrips Ceratothripoides claratris, Frankliniella schultzei, Microcephalothrips abdominalis and Thrips palmi. C. claratris and T. palmi are EU quarantine pests. M. abdominalis is known to be present in several EU member states and it is not regulated in the EU. Plants for planting, parts of plants, fruits and cut flowers of CaCV hosts, and viruliferous thrips were identified as the most relevant pathways for the entry of CaCV into the EU. Cultivated and wild hosts of CaCV are distributed across the EU. Should the pest enter and establish in the EU territory, impact on the production of cultivated hosts is expected. Phytosanitary measures are available to prevent entry and spread of the virus in the EU. CaCV fulfils the criteria that are within the remit of EFSA to assess for it to be regarded as a potential Union quarantine pest.

Published
2022

32. Commodity risk assessment of Malus domestica plants from Turkey

Author

UCL - SST/ELI/ELIM - Applied Microbiology, Bragard, Claude, Baptista, Paula, Chatzivassiliou, Elisavet, Gonthier, Paolo, Jaques Miret, Josep Anton, Justesen, Annemarie Fejer, MacLeod, Alan, Magnusson, Christer Sven, Milonas, Panagiotis, Navas‐Cortes, Juan A, Parnell, Stephen, Potting, Roel, Reignault, Philippe Lucien, Stefani, Emilio, Thulke, Hans‐Hermann, Van der Werf, Wopke, Civera, Antonio Vicent, Zappalà, Lucia, Lucchi, Andrea, Gómez, Pedro, Urek, Gregor, Bernardo, Umberto, Bubici, Giovanni, Carluccio, Anna Vittoria, Chiumenti, Michela, Di Serio, Francesco, Fanelli, Elena, Gardi, Ciro, Marzachì, Cristina, Mosbach‐Schulz, Olaf, Yuen, Jonathan, UCL - SST/ELI/ELIM - Applied Microbiology, Bragard, Claude, Baptista, Paula, Chatzivassiliou, Elisavet, Gonthier, Paolo, Jaques Miret, Josep Anton, Justesen, Annemarie Fejer, MacLeod, Alan, Magnusson, Christer Sven, Milonas, Panagiotis, Navas‐Cortes, Juan A, Parnell, Stephen, Potting, Roel, Reignault, Philippe Lucien, Stefani, Emilio, Thulke, Hans‐Hermann, Van der Werf, Wopke, Civera, Antonio Vicent, Zappalà, Lucia, Lucchi, Andrea, Gómez, Pedro, Urek, Gregor, Bernardo, Umberto, Bubici, Giovanni, Carluccio, Anna Vittoria, Chiumenti, Michela, Di Serio, Francesco, Fanelli, Elena, Gardi, Ciro, Marzachì, Cristina, Mosbach‐Schulz, Olaf, and Yuen, Jonathan

Abstract

The European Commission requested the EFSA Panel on Plant Health to prepare and deliver risk assessments for commodities listed in Commission Implementing Regulation (EU) 2018/2019 as ‘High risk plants, plant products and other objects’. This Scientific Opinion covers plant health risks posed by dormant grafted plants, rootstocks, budwood and scions of Malus domestica imported from Turkey, taking into account the available scientific information, including the technical information provided by Turkey. All pests associated with the commodities were evaluated against specific criteria for their relevance for this opinion. Three quarantine pests (Anoplophora chinensis, Lopholeucaspis japonica and tomato ringspot virus), one protected zone quarantine pest (Erwinia amylovora) and eight non-regulated pests (Calepitrimerus baileyi, Cenopalpus irani, Cicadatra persica, Diplodia bulgarica, Hoplolaimus galeatus, Malacosoma parallela, Pratylenchus loosi and Pyrolachnus pyri) that fulfilled all relevant criteria were selected for further evaluation. For E. amylovora, special requirements are specified in Commission Implementing Regulation (EU) 2019/2072. Based on the information provided in the dossier, the specific requirements for E. amylovora were not met. For Anoplophora chinensis, special measures are specified in Commission Implementing Decision (EU) 2012/138. The exporting country does meet the requirement for a certificate regarding plants for planting that originate from Turkish provinces other than Istanbul. For the 10 remaining selected pests, the risk mitigation measures proposed in the technical dossier from Turkey were evaluated taking into account the possible limiting factors. For the selected pests an expert judgement is given on the likelihood of pest freedom taking into consideration the risk mitigation measures acting on the pest, including uncertainties associated with the assessment. The degree of pest freedom varies among the pests evaluated, with D. bulg

Published
2022

33. Pest categorisation of Apium virus Y

Author

UCL - SST/ELI/ELIM - Applied Microbiology, Bragard, Claude, Gonthier, Paolo, Jaques Miret, Josep Anton, Justesen, Annemarie Fejer, MacLeod, Alan, Magnusson, Christer Sven, Milonas, Panagiotis, Navas‐Cortes, Juan A, Parnell, Stephen, Potting, Roel, Thulke, Hans‐Hermann, Van der Werf, Wopke, Civera, Antonio Vicent, Yuen, Jonathan, Zappalà, Lucia, Dehnen‐Schmutz, Katharina, Migheli, Quirico, Stefani, Emilio, Vloutoglou, Irene, Czwienczek, Ewelina, Streissl, Franz, Chiumenti, Michela, Di Serio, Francesco, Rubino, Luisa, Reignault, Philippe Lucien, UCL - SST/ELI/ELIM - Applied Microbiology, Bragard, Claude, Gonthier, Paolo, Jaques Miret, Josep Anton, Justesen, Annemarie Fejer, MacLeod, Alan, Magnusson, Christer Sven, Milonas, Panagiotis, Navas‐Cortes, Juan A, Parnell, Stephen, Potting, Roel, Thulke, Hans‐Hermann, Van der Werf, Wopke, Civera, Antonio Vicent, Yuen, Jonathan, Zappalà, Lucia, Dehnen‐Schmutz, Katharina, Migheli, Quirico, Stefani, Emilio, Vloutoglou, Irene, Czwienczek, Ewelina, Streissl, Franz, Chiumenti, Michela, Di Serio, Francesco, Rubino, Luisa, and Reignault, Philippe Lucien

Abstract

Following a request from the EU Commission, the EFSA Panel on Plant Health conducted a pest categorisation of Apium virus Y (ApVY) for the EU territory. The identity of the ApVY, a member of the genus Potyvirus (family Potyviridae), is well established and reliable detection methods are available. The pathogen is not included in EU Commission Implementing Regulation 2019/2072. ApVY, considered endemic in Australia, was reported also in New Zealand and USA. In the EU, the virus was identified in Germany and Slovenia. No information on adoption of official control measures is available. In natural conditions, ApVY infects plant species of the family Apiaceae (i.e. celery, coriander, dill, parsley, bishop’s weed) in which it generally induces leaf symptoms and/or stunting. In some hosts (i.e. parsley and poison hemlock), ApVY may be asymptomatic. The virus is transmitted in a non-persistent manner by the aphid Myzus persicae which is widespread in the EU. Although ApVY transmission through seeds has been experimentally excluded for some hosts (i.e. poison hemlock and celery), uncertainty exists for the other hosts because seed transmission is not uncommon for potyvirids. Plants for planting, including seeds for sowing, were identified as potential pathways for entry of ApVY into the EU. Cultivated and wild hosts of ApVY are distributed across the EU. Economic impact on the production of the cultivated hosts is expected if further entry and spread in the EU occur. Phytosanitary measures are available to prevent further entry and spread of the virus. Currently, ApVY does not fulfil the criterion of being absent or present with restricted distribution and under official control to be regarded as a potential Union quarantine, unless official control is implemented. This conclusion is associated with high uncertainty regarding the current virus distribution in the EU.

Published
2022

34. Pest categorisation of High Plains wheat mosaic virus

Author

UCL - SST/ELI/ELIM - Applied Microbiology, Bragard, Claude, Baptista, Paula, Chatzivassiliou, Elisavet, Di Serio, Francesco, Gonthier, Paolo, Jaques Miret, Josep Anton, Justesen, Annemarie Fejer, MacLeod, Alan, Magnusson, Christer Sven, Milonas, Panagiotis, Navas‐Cortes, Juan A, Parnell, Stephen, Potting, Roel, Reignault, Philippe Lucien, Stefani, Emilio, Thulke, Hans‐Hermann, Van der Werf, Wopke, Vicent Civera, Antonio, Yuen, Jonathan, Zappalà, Lucia, Dehnen‐Schmutz, Katharina, Migheli, Quirico, Vloutoglou, Irene, Streissl, Franz, Chiumenti, Michela, Rubino, Luisa, UCL - SST/ELI/ELIM - Applied Microbiology, Bragard, Claude, Baptista, Paula, Chatzivassiliou, Elisavet, Di Serio, Francesco, Gonthier, Paolo, Jaques Miret, Josep Anton, Justesen, Annemarie Fejer, MacLeod, Alan, Magnusson, Christer Sven, Milonas, Panagiotis, Navas‐Cortes, Juan A, Parnell, Stephen, Potting, Roel, Reignault, Philippe Lucien, Stefani, Emilio, Thulke, Hans‐Hermann, Van der Werf, Wopke, Vicent Civera, Antonio, Yuen, Jonathan, Zappalà, Lucia, Dehnen‐Schmutz, Katharina, Migheli, Quirico, Vloutoglou, Irene, Streissl, Franz, Chiumenti, Michela, and Rubino, Luisa

Abstract

The EFSA Panel on Plant Health conducted a pest categorisation of High Plains wheat mosaic virus (HPWMoV) for the EU territory. The identity of HPWMoV, a member of the genus Emaravirus (family Fimoviridae), is well established and reliable identification methods are available. The pathogen is not included in the EU Commission Implementing Regulation 2019/2072. HPWMoV has been reported from Argentina, Australia, Canada, Ukraine and USA, and it is not known to be present in the EU. HPWMoV infects plant species of the family Poaceae (i.e. wheat, maize and several other cultivated or wild Poaceae species). It is the causal agent of High Plains disease of wheat and maize, inducing symptoms ranging from mild to severe mosaic, chlorosis and necrosis in wheat, and chlorotic streaks in maize plants. The virus is transmitted by the wheat curl mite Aceria tosichella, which is present in the EU. HPWMoV transmission via seeds was reported to occur in sweet corn. Sweet corn seeds for sowing were identified as the most relevant pathway for entry of HPWMoV into the EU. Seeds from other hosts and viruliferous wheat curl mites were identified as entry pathways associated with uncertainties. Machinery not appropriately cleaned may move infected seeds and/or parts of cereals infested by viruliferous mites. Cultivated and wild hosts of HPWMoV are distributed across the EU. Would the pest enter and establish in the EU territory, economic impact on the production of cultivated hosts is expected. Phytosanitary measures are available to prevent entry and spread of the virus in the EU. HPWMoV fulfils the criteria that are within the remit of EFSA to assess for it to be regarded as a potential Union quarantine pest.

Published
2022

35. Pest categorisation of coconut cadang‐cadang viroid.

Author

Bragard, Claude, Baptista, Paula, Chatzivassiliou, Elisavet, Gonthier, Paolo, Miret, Josep Anton Jaques, Justesen, Annemarie Fejer, MacLeod, Alan, Magnusson, Christer Sven, Milonas, Panagiotis, Navas‐Cortes, Juan A, Parnell, Stephen, Potting, Roel, Stefani, Emilio, Thulke, Hans‐Hermann, Van der Werf, Wopke, Vicent Civera, Antonio, Yuen, Jonathan, Zappalà, Lucia, Carluccio, Anna Vittoria, and Chiumenti, Michela

Subjects
COCONUT palm, COCONUT, PESTS, VEGETATIVE propagation, OIL palm
Abstract

The EFSA Panel on Plant Health updated its 2017 pest categorisation of coconut cadang cadang viroid (CCCVd) for the EU territory due to new data on its host range. The identity of CCCVd, a member of the genus Cocadviroid (family Pospiviroidae), is established and detection and identification methods are available. It is included as a quarantine pest for the EU in the Commission Implementing Regulation (EU) 2019/2072. CCCVd has been reported from the Philippines and Malaysia. It is not known to be present in the EU. The host range of CCCVd is restricted to Arecaceae species (palms), in particular, coconut palm (Cocos nucifera) to which it causes a lethal disease. Oil palm (Elaeis guineensis) and buri palm (Corypha utan) are other natural hosts of CCCVd. Palm species of several genera, including Phoenix spp. and other species grown and/or cultivated in the EU, have been identified as potential hosts. The viroid is naturally transmitted at low rate by seeds and pollen and possibly by additional not yet identified natural transmission means. It can be transmitted through vegetative propagation applied to some palm species. Plants for planting including seeds of its hosts have been identified as the main entry pathway of CCCVd. Potential hosts of CCCVd are present in the EU, therefore establishment is possible. Should the pest establish in the EU, an impact is expected, with uncertainty on its magnitude. The Panel identified the susceptibility of palm species grown in the EU as a key uncertainty potentially affecting the conclusion of this pest categorisation. Nevertheless, the pest satisfies the criteria that are within the remit of EFSA to assess for this viroid to be regarded as potential Union quarantine pest. [ABSTRACT FROM AUTHOR]

Published
2023
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36. Commodity risk assessment of Malus domestica plants from Turkey

Author

Bragard, Claude, Baptista, Paula, Chatzivassiliou, Elisavet, Gonthier, Paolo, Jaques Miret, Josep Anton, Justesen, Annemarie Fejer, MacLeod, Alan, Magnusson, Christer Sven, Milonas, Panagiotis, Navas‐Cortes, Juan A, Parnell, Stephen, Potting, Roel, Reignault, Philippe Lucien, Stefani, Emilio, Thulke, Hans‐Hermann, Van der Werf, Wopke, Civera, Antonio Vicent, Zappalà, Lucia, Lucchi, Andrea, Gómez, Pedro, Urek, Gregor, Bernardo, Umberto, Bubici, Giovanni, Carluccio, Anna Vittoria, Chiumenti, Michela, Di Serio, Francesco, Fanelli, Elena, Gardi, Ciro, Marzachì, Cristina, Mosbach‐Schulz, Olaf, Yuen, Jonathan, and UCL - SST/ELI/ELIM - Applied Microbiology

Subjects
Veterinary (miscellaneous), Apple, quarantine, Plant Science, Microbiology, pathway risk assessment, plant pest, Animal Science and Zoology, Parasitology, European Union, plant health, Food Science
Abstract

The European Commission requested the EFSA Panel on Plant Health to prepare and deliver risk assessments for commodities listed in Commission Implementing Regulation (EU) 2018/2019 as ‘High risk plants, plant products and other objects’. This Scientific Opinion covers plant health risks posed by dormant grafted plants, rootstocks, budwood and scions of Malus domestica imported from Turkey, taking into account the available scientific information, including the technical information provided by Turkey. All pests associated with the commodities were evaluated against specific criteria for their relevance for this opinion. Three quarantine pests (Anoplophora chinensis, Lopholeucaspis japonica and tomato ringspot virus), one protected zone quarantine pest (Erwinia amylovora) and eight non-regulated pests (Calepitrimerus baileyi, Cenopalpus irani, Cicadatra persica, Diplodia bulgarica, Hoplolaimus galeatus, Malacosoma parallela, Pratylenchus loosi and Pyrolachnus pyri) that fulfilled all relevant criteria were selected for further evaluation. For E. amylovora, special requirements are specified in Commission Implementing Regulation (EU) 2019/2072. Based on the information provided in the dossier, the specific requirements for E. amylovora were not met. For Anoplophora chinensis, special measures are specified in Commission Implementing Decision (EU) 2012/138. The exporting country does meet the requirement for a certificate regarding plants for planting that originate from Turkish provinces other than Istanbul. For the 10 remaining selected pests, the risk mitigation measures proposed in the technical dossier from Turkey were evaluated taking into account the possible limiting factors. For the selected pests an expert judgement is given on the likelihood of pest freedom taking into consideration the risk mitigation measures acting on the pest, including uncertainties associated with the assessment. The degree of pest freedom varies among the pests evaluated, with D. bulgarica being the pest most frequently expected on the imported plants. The expert knowledge elicitation indicated with 95% certainty that between 9,863 and 10,000 bundles (consisting of 10 or 25 plants each) per 10,000 would be free from D. bulgarica.

Published
2022

37. Pest categorisation of High Plains wheat mosaic virus

Author

Bragard, Claude, Baptista, Paula, Chatzivassiliou, Elisavet, Di Serio, Francesco, Gonthier, Paolo, Jaques Miret, Josep Anton, Justesen, Annemarie Fejer, Macleod, Alan, Magnusson, Christer Sven, Milonas, Panagiotis, Navas-Cortes, Juan A, Parnell, Stephen, Potting, Roel, Reignault, Philippe Lucien, Stefani, Emilio, Thulke, Hans-Hermann, Van der Werf, Wopke, Vicent Civera, Antonio, Yuen, Jonathan, Zappalà, Lucia, Dehnen-Schmutz, Katharina, Migheli, Quirico, Vloutoglou, Irene, Streissl, Franz, Chiumenti, Michela, Rubino, Luisa, and UCL - SST/ELI/ELIM - Applied Microbiology

Subjects
pest risk, Veterinary (miscellaneous), quarantine, food and beverages, Aceria tosichella, plant health, plant pest, sweet corn, wheat, Plant Science, Microbiology, Animal Science and Zoology, Parasitology, Food Science
Abstract

The EFSA Panel on Plant Health conducted a pest categorisation of High Plains wheat mosaic virus (HPWMoV) for the EU territory. The identity of HPWMoV, a member of the genus Emaravirus (family Fimoviridae), is well established and reliable identification methods are available. The pathogen is not included in the EU Commission Implementing Regulation 2019/2072. HPWMoV has been reported from Argentina, Australia, Canada, Ukraine and USA, and it is not known to be present in the EU. HPWMoV infects plant species of the family Poaceae (i.e. wheat, maize and several other cultivated or wild Poaceae species). It is the causal agent of High Plains disease of wheat and maize, inducing symptoms ranging from mild to severe mosaic, chlorosis and necrosis in wheat, and chlorotic streaks in maize plants. The virus is transmitted by the wheat curl mite Aceria tosichella, which is present in the EU. HPWMoV transmission via seeds was reported to occur in sweet corn. Sweet corn seeds for sowing were identified as the most relevant pathway for entry of HPWMoV into the EU. Seeds from other hosts and viruliferous wheat curl mites were identified as entry pathways associated with uncertainties. Machinery not appropriately cleaned may move infected seeds and/or parts of cereals infested by viruliferous mites. Cultivated and wild hosts of HPWMoV are distributed across the EU. Would the pest enter and establish in the EU territory, economic impact on the production of cultivated hosts is expected. Phytosanitary measures are available to prevent entry and spread of the virus in the EU. HPWMoV fulfils the criteria that are within the remit of EFSA to assess for it to be regarded as a potential Union quarantine pest.

Published
2022

40. Pest survey card on Beet curly top virus.

Author

Chiumenti, Michela, Delbianco, Alice, and Camilleri, Melanie

Subjects
*BEET curly top virus, *PLANT parasites
Abstract

This document provides the conclusions of the pest survey card that was prepared in the context of the EFSA mandate on plant pest surveillance (M‐2020‐0114) at the request of the European Commission. The full pest survey card for Beet curly top virus (BCTV) is published and available online in the EFSA Plant Pest Survey Cards Gallery at the following link and will be updated whenever new information becomes available: https://efsa.europa.eu/plants/planthealth/monitoring/surveillance/beet-curly-top-virus [ABSTRACT FROM AUTHOR]

Published
2023
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42. Sixty Years from the First Disease Description, a Novel Badnavirus Associated with Chestnut Mosaic Disease

Author

Marais, Armelle, primary, Murolo, Sergio, additional, Faure, Chantal, additional, Brans, Yoann, additional, Larue, Clément, additional, Maclot, François, additional, Massart, Sébastien, additional, Chiumenti, Michela, additional, Minafra, Angelantonio, additional, Romanazzi, Gianfranco, additional, Lefebvre, Marie, additional, Barreneche, Teresa, additional, Robin, Cécile, additional, Petit, Rémy J., additional, and Candresse, Thierry, additional

Published
2021
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43. Reassessing species demarcation criteria in viroid taxonomy by pairwise identity matrices

Author

Chiumenti, Michela, Navarro, Beatriz, Candresse, Thierry, Flores, Ricardo, Di Serio, Francesco, Serio, Francesco, Istituto per la Protezione Sostenibile delle Piante (CNR), Biologie du fruit et pathologie (BFP), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Bordeaux (UB), Instituto de Biologia Molecular y Celular de Plantas, Universitat de València (UV), and This project has been partially funded from the European Union’s Horizon 2020 Research and Innovation Program under the Marie Skłodowska-Curie grant agreement no.734736.

Subjects
Viroid, viruses, [SDV]Life Sciences [q-bio], Identity matrix, Virologie végétale, Pathologie végétale, Microbiology, Genome, 03 medical and health sciences, Reflections, Genus, Virology, Taxonomy (general), Identity score, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, AcademicSubjects/MED00860, pairwise identity threshold, 030304 developmental biology, 0303 health sciences, biology, 030306 microbiology, AcademicSubjects/SCI01130, AcademicSubjects/SCI02285, viroid species, biology.organism_classification, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, viroid classification, pairwise identity threshold, viroid species, Evolutionary biology, viroid classification, Identity (object-oriented programming), Pairwise comparison
Abstract

With a small, circular and non-protein coding RNA genome, viroids are the smallest infectious agents. They invade plants, which in turn may develop symptoms. Since their discovery about 50 years ago, more than thirty viroids have been reported and classified using as species demarcation less than 90 per cent sequence identity on the overall genome and evidence of biological divergence with respect to the closest related viroids. In the last few years, new viroids have been identified that infect latently their (frequently) woody hosts and have a narrow experimental hosts range, complicating and slowing down studies on their biology. As a consequence, several viroids are still waiting for classification. Moreover, the number of new viroids is expected to increase in the next years due to the use of high-throughput sequencing technologies with diagnostics purposes. Therefore, establishment of reliable species demarcation criteria mainly based on molecular features of viroids is needed. Here, viroid classification is reassessed and a scheme based on pairwise sequence identity matrices is developed. After identifying a threshold pairwise identity score (PWIS) for each viroid genus, to be used as a species demarcation criterion, we show that most of those yet unclassified viroids can be assigned to a known or to a new species, thus limiting the need for additional biological evidence to only a few more complex situations. The advantages of this PWIS-based method are that the proposed identity thresholds for species demarcations are not arbitrarily established and evidence for biological divergence is not mandatory. Importantly, the current classification is not essentially modified. A protocol for a tentative fast classification of new viroids according to the proposed approach is also provided.

Published
2021

44. Additional file 1 of High throughput sequencing from Angolan citrus accessions discloses the presence of emerging CTV strains

Author

Cunha, Aderito Tomàs Pais Da, Chiumenti, Michela, Ladeira, Laurindo Chambula, Kubaa, Raied Abou, Loconsole, Giuliana, Pantaleo, Vitantonio, and Minafra, Angelantonio

Subjects
food and beverages
Abstract

Additional file 1. Major CTV contigs with position on the mapping genome and coverage depth. The first BlastN hits are reported with the % of nucleotide identity and a relative strain attribution is presented.

Published
2021
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45. A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses

Author

Kutnjak, Denis, primary, Tamisier, Lucie, additional, Adams, Ian, additional, Boonham, Neil, additional, Candresse, Thierry, additional, Chiumenti, Michela, additional, De Jonghe, Kris, additional, Kreuze, Jan F., additional, Lefebvre, Marie, additional, Silva, Gonçalo, additional, Malapi-Wight, Martha, additional, Margaria, Paolo, additional, Mavrič Pleško, Irena, additional, McGreig, Sam, additional, Miozzi, Laura, additional, Remenant, Benoit, additional, Reynard, Jean-Sebastien, additional, Rollin, Johan, additional, Rott, Mike, additional, Schumpp, Olivier, additional, Massart, Sébastien, additional, and Haegeman, Annelies, additional

Published
2021
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48. 2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

Author

Kuhn, Jens H., Adkins, Scott, Alioto, Daniela, Alkhovsky, Sergey V., Amarasinghe, Gaya K., Anthony, Simon J., Avšič-Županc, Tatjana, Ayllón, María A., Bahl, Justin, Balkema-Buschmann, Anne, Ballinger, Matthew J., Bartonička, Tomáš, Basler, Christopher, Bavari, Sina, Beer, Martin, Bente, Dennis A., Bergeron, Éric, Bird, Brian H., Blair, Carol, Blasdell, Kim R., Bradfute, Steven B., Breyta, Rachel, Briese, Thomas, Brown, Paul A., Buchholz, Ursula J., Buchmeier, Michael J., Bukreyev, Alexander, Burt, Felicity, Buzkan, Nihal, Calisher, Charles H., Cao, Mengji, Casas, Inmaculada, Chamberlain, John, Chandran, Kartik, Charrel, Rémi N., Chen, Biao, Chiumenti, Michela, Choi, Il Ryong, Clegg, J. Christopher S., Crozier, Ian, da Graça, John V., Dal Bó, Elena, Dávila, Alberto M.R., de la Torre, Juan Carlos, de Lamballerie, Xavier, de Swart, Rik L., Di Bello, Patrick L., Di Paola, Nicholas, Di Serio, Francesco, Dietzgen, Ralf G., Digiaro, Michele, Dolja, Valerian V., Dolnik, Olga, Drebot, Michael A., Drexler, Jan Felix, Dürrwald, Ralf, Dufkova, Lucie, Dundon, William G., Duprex, W. Paul, Dye, John M., Easton, Andrew J., Ebihara, Hideki, Elbeaino, Toufic, Ergünay, Koray, Fernandes, Jorlan, Fooks, Anthony R., Formenty, Pierre B.H., Forth, Leonie F., Fouchier, Ron A.M., Freitas-Astúa, Juliana, Gago-Zachert, Selma, Gāo, George Fú, García, María Laura, García-Sastre, Adolfo, Garrison, Aura R., Gbakima, Aiah, Goldstein, Tracey, Gonzalez, Jean Paul J., Griffiths, Anthony, Groschup, Martin H., Günther, Stephan, Guterres, Alexandro, Hall, Roy A., Hammond, John, Hassan, Mohamed, Hepojoki, Jussi, Hepojoki, Satu, Hetzel, Udo, Hewson, Roger, Hoffmann, Bernd, Hongo, Seiji, Höper, Dirk, Horie, Masayuki, Hughes, Holly R., Hyndman, Timothy H., Jambai, Amara, Jardim, Rodrigo, Jiāng, Dàohóng, Jin, Qi, Jonson, Gilda B., Junglen, Sandra, Karadağ, Serpil, Keller, Karen E., Klempa, Boris, Klingström, Jonas, Kobinger, Gary, Kondō, Hideki, Koonin, Eugene V., Krupovic, Mart, Kurath, Gael, Kuzmin, Ivan V., Laenen, Lies, Lamb, Robert A., Lambert, Amy J., Langevin, Stanley L., Lee, Benhur, Lemos, Elba R.S., Leroy, Eric M., Li, Dexin, Lǐ, Jiànróng, Liang, Mifang, Liú, Wénwén, Liú, Yàn, Lukashevich, Igor S., Maes, Piet, Marciel de Souza, William, Marklewitz, Marco, Marshall, Sergio H., Martelli, Giovanni P., Martin, Robert R., Marzano, Shin Yi L., Massart, Sébastien, McCauley, John W., Mielke-Ehret, Nicole, Minafra, Angelantonio, Minutolo, Maria, Mirazimi, Ali, Mühlbach, Hans Peter, Mühlberger, Elke, Naidu, Rayapati, Natsuaki, Tomohide, Navarro, Beatriz, Navarro, José A., Netesov, Sergey V., Neumann, Gabriele, Nowotny, Norbert, Nunes, Márcio R.T., Nylund, Are, Økland, Arnfinn L., Oliveira, Renata C., Palacios, Gustavo, Pallas, Vicente, Pályi, Bernadett, Papa, Anna, Parrish, Colin R., Pauvolid-Corrêa, Alex, Pawęska, Janusz T., Payne, Susan, Pérez, Daniel R., Pfaff, Florian, Radoshitzky, Sheli R., Rahman, Aziz ul, Ramos-González, Pedro L., Resende, Renato O., Reyes, Carina A., Rima, Bertus K., Romanowski, Víctor, Robles Luna, Gabriel, Rota, Paul, Rubbenstroth, Dennis, Runstadler, Jonathan A., Ruzek, Daniel, Sabanadzovic, Sead, Salát, Jiří, Sall, Amadou Alpha, Salvato, Maria S., Sarpkaya, Kamil, Sasaya, Takahide, Schwemmle, Martin, Shabbir, Muhammad Z., Shí, Xiǎohóng, Shí, Zhènglì, Shirako, Yukio, Simmonds, Peter, Širmarová, Jana, Sironi, Manuela, Smither, Sophie, Smura, Teemu, Song, Jin Won, Spann, Kirsten M., Spengler, Jessica R., Stenglein, Mark D., Stone, David M., Straková, Petra, Takada, Ayato, Tesh, Robert B., Thornburg, Natalie J., Tomonaga, Keizō, Tordo, Noël, Towner, Jonathan S., Turina, Massimo, Tzanetakis, Ioannis, Ulrich, Rainer G., Vaira, Anna Maria, van den Hoogen, Bernadette, Varsani, Arvind, Vasilakis, Nikos, Verbeek, Martin, Wahl, Victoria, Walker, Peter J., Wang, Hui, Wang, Jianwei, Wang, Xifeng, Wang, Lin Fa, Wèi, Tàiyún, Wells, Heather, Whitfield, Anna E., Williams, John V., Wolf, Yuri I., Wú, Zhìqiáng, Yang, Xin, Yáng, Xīnglóu, Yu, Xuejie, Yutin, Natalya, Zerbini, F. Murilo, Zhang, Tong, Zhang, Yong Zhen, Zhou, Guohui, Zhou, Xueping, Kuhn, Jens H., Adkins, Scott, Alioto, Daniela, Alkhovsky, Sergey V., Amarasinghe, Gaya K., Anthony, Simon J., Avšič-Županc, Tatjana, Ayllón, María A., Bahl, Justin, Balkema-Buschmann, Anne, Ballinger, Matthew J., Bartonička, Tomáš, Basler, Christopher, Bavari, Sina, Beer, Martin, Bente, Dennis A., Bergeron, Éric, Bird, Brian H., Blair, Carol, Blasdell, Kim R., Bradfute, Steven B., Breyta, Rachel, Briese, Thomas, Brown, Paul A., Buchholz, Ursula J., Buchmeier, Michael J., Bukreyev, Alexander, Burt, Felicity, Buzkan, Nihal, Calisher, Charles H., Cao, Mengji, Casas, Inmaculada, Chamberlain, John, Chandran, Kartik, Charrel, Rémi N., Chen, Biao, Chiumenti, Michela, Choi, Il Ryong, Clegg, J. Christopher S., Crozier, Ian, da Graça, John V., Dal Bó, Elena, Dávila, Alberto M.R., de la Torre, Juan Carlos, de Lamballerie, Xavier, de Swart, Rik L., Di Bello, Patrick L., Di Paola, Nicholas, Di Serio, Francesco, Dietzgen, Ralf G., Digiaro, Michele, Dolja, Valerian V., Dolnik, Olga, Drebot, Michael A., Drexler, Jan Felix, Dürrwald, Ralf, Dufkova, Lucie, Dundon, William G., Duprex, W. Paul, Dye, John M., Easton, Andrew J., Ebihara, Hideki, Elbeaino, Toufic, Ergünay, Koray, Fernandes, Jorlan, Fooks, Anthony R., Formenty, Pierre B.H., Forth, Leonie F., Fouchier, Ron A.M., Freitas-Astúa, Juliana, Gago-Zachert, Selma, Gāo, George Fú, García, María Laura, García-Sastre, Adolfo, Garrison, Aura R., Gbakima, Aiah, Goldstein, Tracey, Gonzalez, Jean Paul J., Griffiths, Anthony, Groschup, Martin H., Günther, Stephan, Guterres, Alexandro, Hall, Roy A., Hammond, John, Hassan, Mohamed, Hepojoki, Jussi, Hepojoki, Satu, Hetzel, Udo, Hewson, Roger, Hoffmann, Bernd, Hongo, Seiji, Höper, Dirk, Horie, Masayuki, Hughes, Holly R., Hyndman, Timothy H., Jambai, Amara, Jardim, Rodrigo, Jiāng, Dàohóng, Jin, Qi, Jonson, Gilda B., Junglen, Sandra, Karadağ, Serpil, Keller, Karen E., Klempa, Boris, Klingström, Jonas, Kobinger, Gary, Kondō, Hideki, Koonin, Eugene V., Krupovic, Mart, Kurath, Gael, Kuzmin, Ivan V., Laenen, Lies, Lamb, Robert A., Lambert, Amy J., Langevin, Stanley L., Lee, Benhur, Lemos, Elba R.S., Leroy, Eric M., Li, Dexin, Lǐ, Jiànróng, Liang, Mifang, Liú, Wénwén, Liú, Yàn, Lukashevich, Igor S., Maes, Piet, Marciel de Souza, William, Marklewitz, Marco, Marshall, Sergio H., Martelli, Giovanni P., Martin, Robert R., Marzano, Shin Yi L., Massart, Sébastien, McCauley, John W., Mielke-Ehret, Nicole, Minafra, Angelantonio, Minutolo, Maria, Mirazimi, Ali, Mühlbach, Hans Peter, Mühlberger, Elke, Naidu, Rayapati, Natsuaki, Tomohide, Navarro, Beatriz, Navarro, José A., Netesov, Sergey V., Neumann, Gabriele, Nowotny, Norbert, Nunes, Márcio R.T., Nylund, Are, Økland, Arnfinn L., Oliveira, Renata C., Palacios, Gustavo, Pallas, Vicente, Pályi, Bernadett, Papa, Anna, Parrish, Colin R., Pauvolid-Corrêa, Alex, Pawęska, Janusz T., Payne, Susan, Pérez, Daniel R., Pfaff, Florian, Radoshitzky, Sheli R., Rahman, Aziz ul, Ramos-González, Pedro L., Resende, Renato O., Reyes, Carina A., Rima, Bertus K., Romanowski, Víctor, Robles Luna, Gabriel, Rota, Paul, Rubbenstroth, Dennis, Runstadler, Jonathan A., Ruzek, Daniel, Sabanadzovic, Sead, Salát, Jiří, Sall, Amadou Alpha, Salvato, Maria S., Sarpkaya, Kamil, Sasaya, Takahide, Schwemmle, Martin, Shabbir, Muhammad Z., Shí, Xiǎohóng, Shí, Zhènglì, Shirako, Yukio, Simmonds, Peter, Širmarová, Jana, Sironi, Manuela, Smither, Sophie, Smura, Teemu, Song, Jin Won, Spann, Kirsten M., Spengler, Jessica R., Stenglein, Mark D., Stone, David M., Straková, Petra, Takada, Ayato, Tesh, Robert B., Thornburg, Natalie J., Tomonaga, Keizō, Tordo, Noël, Towner, Jonathan S., Turina, Massimo, Tzanetakis, Ioannis, Ulrich, Rainer G., Vaira, Anna Maria, van den Hoogen, Bernadette, Varsani, Arvind, Vasilakis, Nikos, Verbeek, Martin, Wahl, Victoria, Walker, Peter J., Wang, Hui, Wang, Jianwei, Wang, Xifeng, Wang, Lin Fa, Wèi, Tàiyún, Wells, Heather, Whitfield, Anna E., Williams, John V., Wolf, Yuri I., Wú, Zhìqiáng, Yang, Xin, Yáng, Xīnglóu, Yu, Xuejie, Yutin, Natalya, Zerbini, F. Murilo, Zhang, Tong, Zhang, Yong Zhen, Zhou, Guohui, and Zhou, Xueping

Abstract

In March 2020, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. At the genus rank, 20 new genera were added, two were deleted, one was moved, and three were renamed. At the species rank, 160 species were added, four were deleted, ten were moved and renamed, and 30 species were renamed. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.

Published
2020

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