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Mahillon M, Brodard J, Schoen R, Botermans M, Dubuis N, Groux R, Pannell JR, Blouin AG, Schumpp O. Revisiting a pollen-transmitted ilarvirus previously associated with angular mosaic of grapevine. Virus Res 2024; 344:199362. [PMID: 38508402 PMCID: PMC10979282 DOI: 10.1016/j.virusres.2024.199362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 03/17/2024] [Accepted: 03/18/2024] [Indexed: 03/22/2024]
Abstract
We report the characterization of a novel tri-segmented RNA virus infecting Mercurialis annua, a common crop weed and model species in plant science. The virus, named "Mercurialis latent virus" (MeLaV) was first identified in a mixed infection with the recently described Mercurialis orthotospovirus 1 (MerV1) on symptomatic plants grown in glasshouses in Lausanne (Switzerland). Both viruses were found to be transmitted by Thrips tabaci, which presumably help the inoculation of infected pollen in the case of MeLaV. Complete genome sequencing of the latter revealed a typical ilarviral architecture and close phylogenetic relationship with members of the Ilarvirus subgroup 1. Surprisingly, a short portion of MeLaV replicase was found to be identical to the partial sequence of grapevine angular mosaic virus (GAMV) reported in Greece in the early 1990s. However, we have compiled data that challenge the involvement of GAMV in angular mosaic of grapevine, and we propose alternative causal agents for this disorder. In parallel, three highly-conserved MeLaV isolates were identified in symptomatic leaf samples in The Netherlands, including a herbarium sample collected in 1991. The virus was also traced in diverse RNA sequencing datasets from 2013 to 2020, corresponding to transcriptomic analyses of M. annua and other plant species from five European countries, as well as metaviromics analyses of bees in Belgium. Additional hosts are thus expected for MeLaV, yet we argue that infected pollen grains have likely contaminated several sequencing datasets and may have caused the initial characterization of MeLaV as GAMV.
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Affiliation(s)
- Mathieu Mahillon
- Research group Virology, Bacteriology and Phytoplasmology, Department of Plant protection, Agroscope, Nyon, Switzerland
| | - Justine Brodard
- Research group Virology, Bacteriology and Phytoplasmology, Department of Plant protection, Agroscope, Nyon, Switzerland
| | - Ruben Schoen
- Netherlands Institute for Vectors, Invasive plants and Plant health (NIVIP), Netherlands Food and Consumer Product Safety Authority, Wageningen, The Netherlands
| | - Marleen Botermans
- Netherlands Institute for Vectors, Invasive plants and Plant health (NIVIP), Netherlands Food and Consumer Product Safety Authority, Wageningen, The Netherlands
| | - Nathalie Dubuis
- Research group Virology, Bacteriology and Phytoplasmology, Department of Plant protection, Agroscope, Nyon, Switzerland
| | - Raphaël Groux
- Research group Virology, Bacteriology and Phytoplasmology, Department of Plant protection, Agroscope, Nyon, Switzerland
| | - John R Pannell
- Department of Ecology and Evolution, University of Lausanne (UNIL), Switzerland
| | - Arnaud G Blouin
- Research group Virology, Bacteriology and Phytoplasmology, Department of Plant protection, Agroscope, Nyon, Switzerland
| | - Olivier Schumpp
- Research group Virology, Bacteriology and Phytoplasmology, Department of Plant protection, Agroscope, Nyon, Switzerland.
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Temple C, Blouin AG, Boezen D, Botermans M, Durant L, De Jonghe K, de Koning P, Goedefroit T, Minet L, Steyer S, Verdin E, Zwart M, Massart S. Biological characterization of Physostegia chlorotic mottle virus, an emergent virus infecting vegetables in diversified production systems. Phytopathology 2024. [PMID: 38648112 DOI: 10.1094/phyto-06-23-0194-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
In 2014, Physostegia chlorotic mottle virus (PhCMoV) was discovered in Austria in Physostegia virginiana. Subsequent collaborative efforts established a link between the virus and severe fruit symptoms on important crops like tomato, eggplant, and cucumber across nine European countries. Thereafter, specific knowledge gaps, which are crucial to assess the risks PhCMoV can pose for the production and how to manage it, needed to be addressed. In this study, the transmission, prevalence, and disease severity of PhCMoV were examinated. This investigation led to the identification of PhCMoV presence in a new country, Switzerland. Furthermore, our research indicates that the virus was already present in Europe 30 years ago. Bioassays demonstrated PhCMoV can result in up to 100% tomato yield losses depending on the phenological stage of the plant at the time of infection. PhCMoV was found to naturally infect 12 new host plant species across eight families, extending its host range to 21 plant species across 15 plant families. The study also identified a polyphagous leafhopper (genus Anaceratagallia) as a natural vector of PhCMoV. Overall, PhCMoV was widespread in small-scale diversified vegetable farms in Belgium where tomato is grown in soil under tunnels, occurring in approximately one-third of such farms. However, outbreaks were sporadic, and were associated at least once with the cultivation in tomato tunnels of perennial plants that can serve as a reservoir host for the virus and its vector. To further explore this phenomenon and manage the virus, studying the ecology of the vector would be beneficial.
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Affiliation(s)
- Coline Temple
- Université de Liège Gembloux Agro-Bio Tech, 82209, Place du 20 Août, 7, Liege, Belgium, 4000;
| | - Arnaud G Blouin
- Université de Liège Gembloux Agro-Bio Tech, 82209, Agroscope, Route de Duillier 50, Case Postale 1012, Nyon, Vaud, Switzerland, 1260
- Nyon, Switzerland, 1260;
| | - Dieke Boezen
- Netherlands Institute of Ecology, 3886, Department of Microbial Ecology, Wageningen, Gelderland, Netherlands;
| | | | - Laurena Durant
- University of Liege Faculty of Gembloux Agro-Bio Tech, 82209, Gembloux, Belgium;
| | - Kris De Jonghe
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences, Burgemeester Van Gansberghelaan 96, Merelbeke, Belgium, 9820;
| | - Pier de Koning
- Netherlands Food and Product Safety Authority, Netherlands Institute for Vectors, Invasive plants and Plant health, Wageningen, Netherlands;
| | - Thomas Goedefroit
- ILVO, 74875, Plant Sciences Unit, Merelbeke, Oost-Vlaanderen, Belgium;
| | - Laurent Minet
- Centre Technique Horticole de Gembloux, Hortiforum asbl, Gembloux, Belgium;
| | - Stephan Steyer
- Walloon Agricultural Research Centre, 105048, Crops and Forest Health Unit, Gembloux, Belgium;
| | - Eric Verdin
- Institut National de Recherche pour l'Agriculture l'Alimentation et l'Environnement Departement AGROENV, 173475, Unité de Pathologie Végétale, Avignon, Provence-Alpes-Côte d'Azu, France;
| | - Mark Zwart
- Netherlands Institute of Ecology, 3886, Microbial Ecology, Postbus 50, Wageningen, Netherlands, 6700 AA;
| | - Sebastien Massart
- Université de Liège, Terra-Gembloux Agro-Bio Tech, Plant Pathology Laboratory, Passage des Déportés, 2, Gembloux, Belgium, 5030;
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3
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Chooi KM, Bell VA, Blouin AG, Sandanayaka M, Gough R, Chhagan A, MacDiarmid RM. The New Zealand perspective of an ecosystem biology response to grapevine leafroll disease. Adv Virus Res 2024; 118:213-272. [PMID: 38461030 DOI: 10.1016/bs.aivir.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2024]
Abstract
Grapevine leafroll-associated virus 3 (GLRaV-3) is a major pathogen of grapevines worldwide resulting in grapevine leafroll disease (GLD), reduced fruit yield, berry quality and vineyard profitability. Being graft transmissible, GLRaV-3 is also transmitted between grapevines by multiple hemipteran insects (mealybugs and soft scale insects). Over the past 20 years, New Zealand has developed and utilized integrated pest management (IPM) solutions that have slowly transitioned to an ecosystem-based biological response to GLD. These IPM solutions and combinations are based on a wealth of research within the temperate climates of New Zealand's nation-wide grape production. To provide context, the grapevine viruses present in the national vineyard estate and how these have been identified are described; the most pathogenic and destructive of these is GLRaV-3. We provide an overview of research on GLRaV-3 genotypes and biology within grapevines and describe the progressive development of GLRaV-3/GLD diagnostics based on molecular, serological, visual, and sensor-based technologies. Research on the ecology and control of the mealybugs Pseudococcus calceolariae and P. longispinus, the main insect vectors of GLRaV-3 in New Zealand, is described together with the implications of mealybug biological control agents and prospects to enhance their abundance and/or fitness in the vineyard. Virus transmission by mealybugs is described, with emphasis on understanding the interactions between GLRaV-3, vectors, and plants (grapevines, alternative hosts, or non-hosts of the virus). Disease management through grapevine removal and the economic influence of different removal strategies is detailed. Overall, the review summarizes research by an interdisciplinary team working in close association with the national industry body, New Zealand Winegrowers. Teamwork and communication across the whole industry has enabled implementation of research for the management of GLD.
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Affiliation(s)
- Kar Mun Chooi
- The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand
| | - Vaughn A Bell
- The New Zealand Institute for Plant and Food Research Limited, Havelock North, New Zealand.
| | | | | | - Rebecca Gough
- The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand
| | - Asha Chhagan
- The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand
| | - Robin M MacDiarmid
- The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand; The University of Auckland, Auckland, New Zealand
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4
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Mahillon M, Brodard J, Dubuis N, Gugerli P, Blouin AG, Schumpp O. Mixed infection of ITPase-encoding potyvirid and secovirid in Mercurialis perennis: evidences for a convergent euphorbia-specific viral counterstrike. Virol J 2024; 21:6. [PMID: 38178191 PMCID: PMC10768138 DOI: 10.1186/s12985-023-02257-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/04/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND In cellular organisms, inosine triphosphate pyrophosphatases (ITPases) prevent the incorporation of mutagenic deaminated purines into nucleic acids. These enzymes have also been detected in the genomes of several plant RNA viruses infecting two euphorbia species. In particular, two ipomoviruses produce replicase-associated ITPases to cope with high concentration of non-canonical nucleotides found in cassava tissues. METHOD Using high-throughput RNA sequencing on the wild euphorbia species Mercurialis perennis, two new members of the families Potyviridae and Secoviridae were identified. Both viruses encode for a putative ITPase, and were found in mixed infection with a new partitivirid. Following biological and genomic characterization of these viruses, the origin and function of the phytoviral ITPases were investigated. RESULTS While the potyvirid was shown to be pathogenic, the secovirid and partitivirid could not be transmitted. The secovirid was found belonging to a proposed new Comovirinae genus tentatively named "Mercomovirus", which also accommodates other viruses identified through transcriptome mining, and for which an asymptomatic pollen-associated lifestyle is suspected. Homology and phylogenetic analyses inferred that the ITPases encoded by the potyvirid and secovirid were likely acquired through independent horizontal gene transfer events, forming lineages distinct from the enzymes found in cassava ipomoviruses. Possible origins from cellular organisms are discussed for these proteins. In parallel, the endogenous ITPase of M. perennis was predicted to encode for a C-terminal nuclear localization signal, which appears to be conserved among the ITPases of euphorbias but absent in other plant families. This subcellular localization is in line with the idea that nucleic acids remain protected in the nucleus, while deaminated nucleotides accumulate in the cytoplasm where they act as antiviral molecules. CONCLUSION Three new RNA viruses infecting M. perennis are described, two of which encoding for ITPases. These enzymes have distinct origins, and are likely required by viruses to circumvent high level of cytoplasmic non-canonical nucleotides. This putative plant defense mechanism has emerged early in the evolution of euphorbias, and seems to specifically target certain groups of RNA viruses infecting perennial hosts.
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Affiliation(s)
- Mathieu Mahillon
- Research Group Virology, Bacteriology and Phytoplasmology, Plant Protection Department, Agroscope, Nyon, Switzerland
| | - Justine Brodard
- Research Group Virology, Bacteriology and Phytoplasmology, Plant Protection Department, Agroscope, Nyon, Switzerland
| | - Nathalie Dubuis
- Research Group Virology, Bacteriology and Phytoplasmology, Plant Protection Department, Agroscope, Nyon, Switzerland
| | - Paul Gugerli
- Research Group Virology, Bacteriology and Phytoplasmology, Plant Protection Department, Agroscope, Nyon, Switzerland
| | - Arnaud G Blouin
- Research Group Virology, Bacteriology and Phytoplasmology, Plant Protection Department, Agroscope, Nyon, Switzerland
| | - Olivier Schumpp
- Research Group Virology, Bacteriology and Phytoplasmology, Plant Protection Department, Agroscope, Nyon, Switzerland.
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5
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Kuhn JH, Abe J, Adkins S, Alkhovsky SV, Avšič-Županc T, Ayllón MA, Bahl J, Balkema-Buschmann A, Ballinger MJ, Kumar Baranwal V, Beer M, Bejerman N, Bergeron É, Biedenkopf N, Blair CD, Blasdell KR, Blouin AG, Bradfute SB, Briese T, Brown PA, Buchholz UJ, Buchmeier MJ, Bukreyev A, Burt F, Büttner C, Calisher CH, Cao M, Casas I, Chandran K, Charrel RN, Kumar Chaturvedi K, Chooi KM, Crane A, Dal Bó E, Carlos de la Torre J, de Souza WM, de Swart RL, Debat H, Dheilly NM, Di Paola N, Di Serio F, Dietzgen RG, Digiaro M, Drexler JF, Duprex WP, Dürrwald R, Easton AJ, Elbeaino T, Ergünay K, Feng G, Firth AE, Fooks AR, Formenty PBH, Freitas-Astúa J, Gago-Zachert S, Laura García M, García-Sastre A, Garrison AR, Gaskin TR, Gong W, Gonzalez JPJ, de Bellocq J, Griffiths A, Groschup MH, Günther I, Günther S, Hammond J, Hasegawa Y, Hayashi K, Hepojoki J, Higgins CM, Hongō S, Horie M, Hughes HR, Hume AJ, Hyndman TH, Ikeda K, Jiāng D, Jonson GB, Junglen S, Klempa B, Klingström J, Kondō H, Koonin EV, Krupovic M, Kubota K, Kurath G, Laenen L, Lambert AJ, Lǐ J, Li JM, Liu R, Lukashevich IS, MacDiarmid RM, Maes P, Marklewitz M, Marshall SH, Marzano SYL, McCauley JW, Mirazimi A, Mühlberger E, Nabeshima T, Naidu R, Natsuaki T, Navarro B, Navarro JA, Neriya Y, Netesov SV, Neumann G, Nowotny N, Nunes MRT, Ochoa-Corona FM, Okada T, Palacios G, Pallás V, Papa A, Paraskevopoulou S, Parrish CR, Pauvolid-Corrêa A, Pawęska JT, Pérez DR, Pfaff F, Plemper RK, Postler TS, Rabbidge LO, Radoshitzky SR, Ramos-González PL, Rehanek M, Resende RO, Reyes CA, Rodrigues TCS, Romanowski V, Rubbenstroth D, Rubino L, Runstadler JA, Sabanadzovic S, Sadiq S, Salvato MS, Sasaya T, Schwemmle M, Sharpe SR, Shi M, Shimomoto Y, Kavi Sidharthan V, Sironi M, Smither S, Song JW, Spann KM, Spengler JR, Stenglein MD, Takada A, Takeyama S, Tatara A, Tesh RB, Thornburg NJ, Tian X, Tischler ND, Tomitaka Y, Tomonaga K, Tordo N, Tu C, Turina M, Tzanetakis IE, Maria Vaira A, van den Hoogen B, Vanmechelen B, Vasilakis N, Verbeek M, von Bargen S, Wada J, Wahl V, Walker PJ, Waltzek TB, Whitfield AE, Wolf YI, Xia H, Xylogianni E, Yanagisawa H, Yano K, Ye G, Yuan Z, Zerbini FM, Zhang G, Zhang S, Zhang YZ, Zhao L, Økland AL. Annual (2023) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses (realm Riboviria: kingdom Orthornavirae: phylum Negarnaviricota). J Gen Virol 2023; 104:001864. [PMID: 37622664 PMCID: PMC10721048 DOI: 10.1099/jgv.0.001864] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 05/26/2023] [Indexed: 08/26/2023] Open
Abstract
In April 2023, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by one new family, 14 new genera, and 140 new species. Two genera and 538 species were renamed. One species was moved, and four were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.
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Affiliation(s)
- Jens H. Kuhn
- Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, Frederick, MD 21702, USA
| | - Junya Abe
- Ornamental Plants and Vegetables Research Center, Agricultural Research Department, Hokkaido Research Organization, Takikawa, Hokkaido, Japan
| | - Scott Adkins
- United States Department of Agriculture, Agricultural Research Service, US Horticultural Research Laboratory, Fort Pierce, FL, USA
| | - Sergey V. Alkhovsky
- D.I. Ivanovsky Institute of Virology of N.F. Gamaleya National Center on Epidemiology and Microbiology of Ministry of Health of Russian Federation, Moscow, Russia
| | - Tatjana Avšič-Županc
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - María A. Ayllón
- Centro de Biotecnología y Genómica de Plantas; Departamento de Biotecnología-Biología Vegetal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo, Pozuelo de Alarcón; Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Justin Bahl
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, Department of Epidemiology and Biostatistics, Insitute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Anne Balkema-Buschmann
- Friedrich-Loeffler-Institut, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Greifswald, Germany
| | - Matthew J. Ballinger
- Department of Biological Sciences, Mississippi State University, Starkville, MS,, Mississippi State, USA
| | | | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | | | - Éric Bergeron
- Division of High-Consequence Pathogens and Pathology, Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Nadine Biedenkopf
- Institute of Virology, Philipps-University Marburg, Marburg, Germany
| | - Carol D. Blair
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Kim R. Blasdell
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Arnaud G. Blouin
- Virology-Phytoplasmology Laboratory, Agroscope, 1260 Nyon, Switzerland
| | | | - Thomas Briese
- Center for Infection and Immunity, and Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, USA
| | - Paul A. Brown
- French Agency for Food, Environmental and Occupational Heath Safety ANSES, Laboratory of Ploufragan-Plouzané-Niort, Ploufragan, France
| | - Ursula J. Buchholz
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michael J. Buchmeier
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | | | - Felicity Burt
- Division of Virology, National Health Laboratory Service and Division of Virology, University of the Free State, Bloemfontein, Bloemfontein, South Africa
| | - Carmen Büttner
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Mengji Cao
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, PR China
| | - Inmaculada Casas
- Respiratory Virus and Influenza Unit, National Microbiology Center, Instituto de Salud Carlos III, Madrid, Spain
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rémi N. Charrel
- Unite des Virus Emergents (Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Krishna Kumar Chaturvedi
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Kar Mun Chooi
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Anya Crane
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Elena Dal Bó
- CIDEFI. Facultad de Ciencias Agrarias y Forestales, Universidad de La Plata, La Plata, Argentina
| | - Juan Carlos de la Torre
- Department of Immunology and Microbiology IMM-6, The Scripps Research Institute, La Jolla, CA, USA
| | - William M. de Souza
- World Reference Center for Emerging Viruses and Arboviruses and Department of Microbiology and Immunology, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Rik L. de Swart
- Department of Virology, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Humberto Debat
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Consejo Nacional de Investigaciones Científicas y Técnicas, Unidad de Fitopatología y Modelización Agrícola, Córdoba, Argentina
| | - Nolwenn M. Dheilly
- UMR 1161 Virology ANSES/INRAE/ENVA, ANSES Animal Health Laboratory, Maisons-Alfort, France
| | - Nicholas Di Paola
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Ralf G. Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Michele Digiaro
- CIHEAM, Istituto Agronomico Mediterraneo di Bari, Valenzano, Italy
| | - J. Felix Drexler
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - W. Paul Duprex
- School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | | | | | - Toufic Elbeaino
- CIHEAM, Istituto Agronomico Mediterraneo di Bari, Valenzano, Italy
| | - Koray Ergünay
- Department of Medical Microbiology, Virology Unit, Hacettepe University Faculty of Medicine, Ankara, Turkey
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution, Museum Support Center, Suitland, MD, USA
- One Health Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA
- Department of Entomology, Smithsonian Institution–National Museum of Natural History (NMNH), Washington, DC, USA
| | - Guozhong Feng
- China National Rice Research Institute, Hangzhou, PR China
| | - Andrew E. Firth
- Department of Pathology, University of Cambridge, Cambridge, UK
| | | | | | | | - Selma Gago-Zachert
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - María Laura García
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, CONICET UNLP, La Plata, Argentina
| | | | - Aura R. Garrison
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Thomas R. Gaskin
- Brandenburg State Office of Rural Development, Agriculture and Land Consolidation (LELF), Frankfurt, Germany
- Division Phytomedicine, Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität Zu Berlin, Berlin, Germany
| | - Wenjie Gong
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonoses Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, PR China
| | - Jean-Paul J. Gonzalez
- Department of Microbiology and Immunology, Division of Biomedical Graduate Research Organization, School of Medicine, Georgetown University, Washington, DC, USA
| | | | - Anthony Griffiths
- Department of Virology, Immunology and Microbiology, Chobanian and Avedisian School of Medicine; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Martin H. Groschup
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Ines Günther
- Division Phytomedicine, Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität Zu Berlin, Berlin, Germany
| | - Stephan Günther
- Department of Virology, WHO Collaborating Centre for Arboviruses and Hemorrhagic Fever Reference and Research, Bernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - John Hammond
- United States Department of Agriculture, Agricultural Research Service, USNA, Floral and Nursery Plants Research Unit, Beltsville, MD, USA
| | - Yusuke Hasegawa
- Department of Clinical Plant Science, Hosei University, Koganei, Tokyo, 184-8584, Japan
| | - Kazusa Hayashi
- Kochi Agricultural Research Center, Nankoku, Kochi, Japan
| | - Jussi Hepojoki
- Department of Virology, University of Helsinki, Medicum, Helsinki, Finland
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Colleen M. Higgins
- The School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Seiji Hongō
- Department of Infectious Diseases, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Masayuki Horie
- Graduate School of Veterinary Science, Osaka Metropolitan University; International Research Center for Infectious Diseases, Osaka Metropolitan University, Izumisano, Osaka, Japan
| | - Holly R. Hughes
- Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | - Adam J. Hume
- Department of Virology, Immunology and Microbiology, Chobanian and Avedisian School of Medicine; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Timothy H. Hyndman
- School of Veterinary Medicine, Murdoch University, Murdoch, WA, Australia
| | - Kenichi Ikeda
- Graduate School of Agricultural Science, Kobe University, Kobe, Hyogo, Japan
| | - Dàohóng Jiāng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, PR China
| | - Gilda B. Jonson
- International Rice Research Institute, College, Los Baños, 4032, Laguna, Philippines
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
| | - Boris Klempa
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jonas Klingström
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Hideki Kondō
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France
| | - Kenji Kubota
- Institute for Plant Protection, NARO, Tsukuba, Ibaraki, Japan
| | - Gael Kurath
- US Geological Survey Western Fisheries Research Center, Seattle, Washington, USA
| | - Lies Laenen
- KU Leuven, Rega Institute, Zoonotic Infectious Diseases unit; Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Amy J. Lambert
- Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | - Jiànróng Lǐ
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Jun-Min Li
- Institute of Plant Virology, Ningbo University, Ningbo, PR China
| | - Ran Liu
- Illumina (China), Beijing, PR China
| | - Igor S. Lukashevich
- Department of Pharmacology and Toxicology, School of Medicine, and the Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville, Louisville, KY, USA
| | - Robin M. MacDiarmid
- The New Zealand Institute for Plant and Food Research Limited; School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Piet Maes
- KU Leuven, Rega Institute, Zoonotic Infectious Diseases unit, Leuven, Belgium
| | | | - Sergio H. Marshall
- Instituto de Biología-Laboratorio de Genética Molecular-Pontificia Universidad Católica de ValparaísoCampus Curauma, Valparaíso, Chile
| | - Shin-Yi L. Marzano
- United States Department of Agriculture, Agricultural Research Service, Toledo, OH, USA
| | | | | | - Elke Mühlberger
- Department of Virology, Immunology and Microbiology, Chobanian and Avedisian School of Medicine; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | | | - Rayapati Naidu
- Department of Plant Pathology, Irrigated Agricultural Research and Extension Center, Washington State University, Prosser, WA, USA
| | | | - Beatriz Navarro
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - José A. Navarro
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Yutaro Neriya
- School of Agriculture, Utsunomiya University, Utsunomiya, Japan
| | | | - Gabriele Neumann
- Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, Madison, USA
| | - Norbert Nowotny
- Institute of Virology, University of Veterinary Medicine Vienna, Vienna, Austria
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | | | - Francisco M. Ochoa-Corona
- Institute for Biosecurity and Microbial Forensics. Stillwater, Oklahoma State University, Oklahoma, USA
| | - Tomoyuki Okada
- Kochi Agricultural Research Center, Nankoku, Kochi, Japan
| | - Gustavo Palacios
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vicente Pallás
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Cientificas-Universitat Politècnica de Valencia, Valencia, Spain
| | - Anna Papa
- National Reference Centre for Arboviruses and Haemorrhagic Fever viruses, Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | - Colin R. Parrish
- College of Veterinary Medicine, Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | | | - Janusz T. Pawęska
- Center for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham-Johannesburg, Gauteng, South Africa
| | - Daniel R. Pérez
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Florian Pfaff
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Richard K. Plemper
- Center for Translational Antiviral Research, Georgia State University Institute for Biomedical Sciences, Atlanta, GA, USA
| | - Thomas S. Postler
- Vaccine Design and Development Laboratory, International AIDS Vaccine Initiative, Brooklyn, NY, USA
| | - Lee O. Rabbidge
- The New Zealand Institute for Plant and Food Research Limited; The School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Sheli R. Radoshitzky
- Division of Antivirals, Office of Infectious Diseases, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | | | - Marius Rehanek
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Renato O. Resende
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | - Carina A. Reyes
- Instituto de Biotecnología y Biología Molecular, CONICET-UNLP, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Buenos Aires, Argentina
| | - Thaís C. S. Rodrigues
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
| | - Víctor Romanowski
- Instituto de Biotecnología y Biología Molecular, CONICET-UNLP, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Buenos Aires, Argentina
| | - Dennis Rubbenstroth
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Luisa Rubino
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Jonathan A. Runstadler
- Department of Infectious Disease & Global Health, Tufts University Cummings School of Veterinary Medicine, North Grafton, MA, USA
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi, Mississippi State, USA
| | - Sabrina Sadiq
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, Australia
| | - Maria S. Salvato
- Department of Veterinary Medicine, University of Maryland, College Park, MD 20742, USA
| | - Takahide Sasaya
- Institute for Plant Protection, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Martin Schwemmle
- Faculty of Medicine, University Medical Center-University Freiburg, Freiburg, Germany
| | - Stephen R. Sharpe
- Hawkesbury Institute for the Environment, Western Sydney University, Sydney, NSW, Australia
| | - Mang Shi
- Sun Yat-sen University, Shenzhen, PR China
| | | | | | - Manuela Sironi
- Bioinformatics Unit, Scientific Institute IRCCS “E. Medea”, Bosisio Parini, Italy
| | - Sophie Smither
- CBR Division, Dstl, Porton Down, Salisbury, Wiltshire, UK
| | - Jin-Won Song
- Department of Microbiology, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Kirsten M. Spann
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Jessica R. Spengler
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mark D. Stenglein
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Ayato Takada
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Sawana Takeyama
- Institute for Plant Protection, NARO, Tsukuba, Ibaraki, Japan
| | - Akio Tatara
- Faculty of Agricultural Production and Management, Shizuoka Professional University of Agriculture, Shizuoka, Japan
| | - Robert B. Tesh
- The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | | | - Xin Tian
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, PR China
| | - Nicole D. Tischler
- Laboratorio de Virología Molecular, Centro Ciencia & Vida, Fundación Ciencia & Vida and Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Yasuhiro Tomitaka
- Institute for Plant Protection, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Keizō Tomonaga
- Institute for Life and Medical Sciences (LiMe), Kyoto University, Kyoto, Japan
| | - Noël Tordo
- Institut Pasteur de Guinée, BP 4416, Conakry, Guinea
| | - Changchun Tu
- College of Veterinary Medicine, Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, PR China
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, PR China
| | - Massimo Turina
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Torino, Italy
| | - Ioannis E. Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR, USA
| | - Anna Maria Vaira
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Torino, Italy
| | | | - Bert Vanmechelen
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Nikos Vasilakis
- The University of Texas Medical Branch at Galveston, Galveston, TX,, USA
| | - Martin Verbeek
- Wageningen University and Research, Biointeractions and Plant Health, Wageningen, Netherlands
| | - Susanne von Bargen
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jiro Wada
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Victoria Wahl
- National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD, USA
| | - Peter J. Walker
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, QLD, Australia
| | - Thomas B. Waltzek
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, USA
| | - Anna E. Whitfield
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Han Xia
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, PR China
| | - Evanthia Xylogianni
- Plant Pathology Laboratory, Department of Crop Science, School of Agricultural Production, Infrastructure and Environment, Agricultural University of Athens, Votanikos, Athens, Greece
| | | | - Kazutaka Yano
- Kochi Agricultural Research Center, Nankoku, Kochi, Japan
| | - Gongyin Ye
- Institute of Insect Sciences, Zhejiang University, Hangzhou, PR China
| | - Zhiming Yuan
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, PR China
| | - F. Murilo Zerbini
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Guilin Zhang
- Center for Disease Control and Prevention of Xinjiang Military Command Area, Urumqi, Xinjiang, PR China
| | - Song Zhang
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, PR China
- Guangxi Academy of Specialty Crops, Guilin, Guangxi, PR China
| | - Yong-Zhen Zhang
- School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, PR China
| | - Lu Zhao
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
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Schoen R, de Koning PPM, de Krom C, Oplaat C, Westenberg M, Massart S, Temple C, De Jonghe K, Blouin AG, Botermans M. First report of lettuce ring necrosis virus in chili pepper and tomato in Belgium and The Netherlands. Plant Dis 2023. [PMID: 37093167 DOI: 10.1094/pdis-01-23-0036-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Lettuce ring necrosis virus (LRNV), genus Ophiovirus, was detected by the Netherlands Institute for Vectors, Invasive plants and Plant health (NIVIP) in June and November of 2021 in two samples of chili pepper fruits (Capsicum spp.), both in mixed infection with other viruses. The first sample originated from a production site in Belgium (Sample ID: 40009704) and the second from a production site in the Netherlands (Sample ID: 41115269). One of the fruits of 40009704 showed a light purple circular pattern, while fruits from 41115269 showed colored (ring)spots. The samples were analyzed using Illumina sequencing on a NovaSeq 6000 platform (PE 150) as described previously (Hammond et al., 2021), obtaining 39.9M and 22.8M total reads for 40009704 and 41115269. The corresponding sequence read archives (SRA) were deposited in the NCBI SRA database under BioProject accession number PRJNA917231. From both samples, the nearly complete genome of LRNV (RNA1-4) was obtained and deposited in GenBank (40009704, OQ160823- OQ160826 (7616, 1799, 1502, 1382 nt, mapped reads: 40K, 12K, 114K, 12K , average read coverage (ARC): 0.8K, 0.9K, 11.3K and 1.1K); 41115269, OQ160827- OQ160830 (7616, 1801, 1518, 1389 nt, mapped reads: 112K, 7K, 357K, 55K reads, ARC: 2.2K, 0.6K, 34K and 5.8K)). The shared sequence identities with the Genbank reference sequence of LRNV (NC_006051-NC_006051) were 99.2 and 99.2% (RNA1), 99.1 and 99.1% (RNA2), 98.3 and 98.8% (RNA3), 99.0 and 98.9% (RNA4) for 40009704 and 41115269 respectively. The shared sequence identities between 40009704 and 41115269 were 99.9 (RNA1), 99.0 (RNA2), 99.1 (RNA3) and 99.5% (RNA4). In addition to LRNV, the ophiovirus ranunculus white mottle virus (RWMV) was detected in both samples (OQ160831-OQ160834; OQ160835-OQ160838), while the tobamovirus pepper mild mottle virus (PMMoV) was present in the fruits of 41115269 (OQ160839). Since RWMV has been associated with leaf symptoms in pepper (Gambley et al., 2019; Rivarez et al., 2022) and the colored (ring)spots of 41115269 were very similar to reported symptoms of PMMoV-infected pepper fruits (Martínez-Ochoa et al., 2003), it remains unclear whether LRNV contributed to the observed symptoms. Additionally, LRNV was detected in tomato (Solanum lycopersicum) in Belgium in 2020. In the frame of a metagenomic survey using Virion-Associated Nucleic Acids (VANA)-based protocol (Maclot et al., 2021) on a Nextseq 500 platform (PE 150), partial genome sequences of LRNV were detected in two pools of tomato plants. One pool was made of 44 asymptomatic cultivars from a non-commercial grower (one sample per cultivar) yielding 118K total reads of which 84, 59, 335, and 18 reads mapped on RNA1, 2, 3, and 4, covering 35%, 69%, 100% and 55% of the genome, respectively. The other pool consisted of 15 plants from one cultivar from a production site yielding 3.1M total reads of which 6 and 5 reads mapped on RNA3 and 4, respectively. The detection of LRNV was confirmed for both pooled samples using the real-time RT-PCR method, targeting the CP gene, as described by Maachi et al. (2021). To our knowledge this is the first report of LRNV in pepper anywhere in the world. Additionally, although the disease lettuce ring necrosis in lettuce (Lactuca sativa) has been described in Belgium and the Netherlands before the causal agent was identified (Bos & Huijberts, 1996), this is the first official report of this virus in Belgium and the Netherlands. This publication resulted from pre-publication data sharing of sequences and biological data among plant virologists to provide more context to two independent findings (Hammond et al., 2021). Bos, L., & Huijberts, N. (1996). Lettuce ring necrosis, caused by a chytrid-borne agent distinct from lettuce big-vein 'virus'. European Journal of Plant Pathology, 102(9), 867-873. https://doi.org/10.1007/bf01877057 Gambley, C., Persley, D., & Thomas, J. E. (2019). First record of Ranunculus white mottle virus from Australia. New Disease Reports, 40(1), 13-13. https://doi.org/10.5197/j.2044-0588.2019.040.013 Hammond, J., Adams, I. P., Fowkes, A. R., McGreig, S., Botermans, M., Oorspronk, J. J. A., Westenberg, M., Verbeek, M., Dullemans, A. M., Stijger, C. C. M. M., Blouin, A. G., Massart, S., De Jonghe, K., Heyneman, M., Walsh, J. A., & Fox, A. (2021). Sequence analysis of 43-year old samples of Plantago lanceolata show that Plantain virus X is synonymous with Actinidia virus X and is widely distributed. Plant Pathology, 70, 249-258. https://doi.org/10.1111/ppa.13310 Maachi, A., Torre, C., Sempere, R. N., Hernando, Y., Aranda, M. A., & Donaire, L. (2021). Use of High-Throughput Sequencing and Two RNA Input Methods to Identify Viruses Infecting Tomato Crops. Microorganisms, 9(5). https://doi.org/10.3390/microorganisms9051043 Maclot, F. J., Debue, V., Blouin, A. G., Fontdevila Pareta, N., Tamisier, L., Filloux, D., & Massart, S. (2021). Identification, molecular and biological characterization of two novel secovirids in wild grass species in Belgium. Virus Res, 298, 198397. https://doi.org/10.1016/j.virusres.2021.198397 Martínez-Ochoa, N., Langston, D. B., Mullis, S. W., & Flanders, J. T. (2003). First Report of Pepper mild mottle virus in Jalapeno Pepper in Georgia. Plant Health Progress, 4(1). https://doi.org/10.1094/php-2003-1223-01-hn Rivarez, M. P. S., Kogej, Z., Jakos, N., Pecman, A., Seljak, G., Vucurovic, A., Ravnikar, M., Mehle, N., & Kutnjak, D. (2022). First Report of Ranunculus White Mottle Ophiovirus in Slovenia in Pepper with Yellow Leaf Curling Symptom and in Tomato. Plant Dis, PDIS08211624PDN. https://doi.org/10.1094/PDIS-08-21-1624-PDN.
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Affiliation(s)
- Ruben Schoen
- Dutch National Plant Protection Organization, Netherlands Institute for Vectors, Invasive plants and Plant health (NIVIP), Wageningen, Gelderland, Netherlands;
| | - Pier P M de Koning
- Dutch National Plant Protection Organization, Netherlands Institute for Vectors, Invasive plants and Plant health (NIVIP), Wageningen, Gelderland, Netherlands;
| | - Christel de Krom
- Dutch National Plant Protection Organization, Netherlands Institute for Vectors, Invasive plants and Plant health (NIVIP), Wageningen, Gelderland, Netherlands;
| | - Carla Oplaat
- Dutch National Plant Protection Organization, Netherlands Institute for Vectors, Invasive plants and Plant health (NIVIP), Wageningen, NL-GE, Netherlands;
| | - Marcel Westenberg
- Dutch National Plant Protection Organization, Netherlands Institute for Vectors, Invasive plants and Plant health (NIVIP), Wageningen, Netherlands;
| | - Sebastien Massart
- University of Liege Faculty of Gembloux Agro-Bio Tech, Integrated and Urban Plant Pathology Laboratory Av. Maréchal Juin 13, Bât 47, porte 4 Gembloux, BE 5030, Gembloux, Belgium;
| | - Coline Temple
- University of Liege Faculty of Gembloux Agro-Bio Tech, 82209, Integrated and Urban Plant Pathology Laboratory, Av. Maréchal Juin 13, Bât 47, porte 4, Gembloux, Belgium, 5030
- University of Liege Faculty of Gembloux Agro-Bio Tech, 82209, Integrated and Urban Plant Pathology Laboratory, Av. Maréchal Juin 13, Bât 47, porte 4, Gembloux, Belgium, 5030;
| | - Kris De Jonghe
- ILVO, 74875, Plant Sciences, Burgemeester Van Gansberghelaan 96, Merelbeke, Merelbeke, Belgium, 9820
- Burgemeester Van Gansberghelaan 96Burgemeester Van Gansberghelaan 96Belgium;
| | - Arnaud G Blouin
- Agroscope Location Changins, 54161, Virology-Phytoplasmology Laboratory, Nyon, Switzerland;
| | - Marleen Botermans
- Dutch National Plant Protection Organization, Netherlands Institute for Vectors, Invasive plants and Plant health (NIVIP), Geertjesweg 15, Wageningen, Gelderland, Netherlands, 6706EA;
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7
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Maclot F, Debue V, Malmstrom CM, Filloux D, Roumagnac P, Eck M, Tamisier L, Blouin AG, Candresse T, Massart S. Long-Term Anthropogenic Management and Associated Loss of Plant Diversity Deeply Impact Virome Richness and Composition of Poaceae Communities. Microbiol Spectr 2023; 11:e0485022. [PMID: 36916941 PMCID: PMC10100685 DOI: 10.1128/spectrum.04850-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 02/13/2023] [Indexed: 03/16/2023] Open
Abstract
Modern agriculture has influenced plant virus emergence through ecosystem simplification, introduction of new host species, and reduction in crop genetic diversity. Therefore, it is crucial to better understand virus distributions across cultivated and uncultivated communities in agro-ecological interfaces, as well as virus exchange among them. Here, we advance fundamental understanding in this area by characterizing the virome of three co-occurring replicated Poaceae community types that represent a gradient of grass species richness and management intensity, from highly managed crop monocultures to little-managed, species-rich grasslands. We performed a large-scale study on 950 wild and cultivated Poaceae over 2 years, combining untargeted virome analysis down to the virus species level with targeted detection of three plant viruses. Deep sequencing revealed (i) a diversified and largely unknown Poaceae virome (at least 51 virus species or taxa), with an abundance of so-called persistent viruses; (ii) an increase of virome richness with grass species richness within the community; (iii) stability of virome richness over time but a large viral intraspecific variability; and (iv) contrasting patterns of virus prevalence, coinfections, and spatial distribution among plant communities and species. Our findings highlight the complex structure of plant virus communities in nature and suggest the influence of anthropogenic management on viral distribution and prevalence. IMPORTANCE Because viruses have been mostly studied in cultivated plants, little is known about virus diversity and ecology in less-managed vegetation or about the influence of human management and agriculture on virome composition. Poaceae (grass family)-dominated communities provide invaluable opportunities to examine these ecological issues, as they are distributed worldwide across agro-ecological gradients, are essential for food security and conservation, and can be infected by numerous viruses. Here, we used multiple levels of analysis that considered plant communities, individual plants, virus species, and haplotypes to broaden understanding of the Poaceae virome and to evaluate host-parasite richness relationships within agro-ecological landscapes in our study area. We emphasized the influence of grass diversity and land use on the composition of viral communities and their life history strategies, and we demonstrated the complexity of plant-virus interactions in less-managed grass communities, such as the higher virus prevalence and overrepresentation of mixed virus infection compared to theoretical predictions.
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Affiliation(s)
- François Maclot
- Plant Pathology Laboratory, Terra-Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Virginie Debue
- Plant Pathology Laboratory, Terra-Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Carolyn M. Malmstrom
- Department of Plant Biology and Program in Ecology, Evolution, & Behavior, Michigan State University, East Lansing, Michigan, USA
| | - Denis Filloux
- CIRAD, UMR PHIM, Montpellier, France
- PHIM Plant Health Institute, CIRAD, INRAE, Institut Agro, IRD, University of Montpellier, Montpellier, France
| | - Philippe Roumagnac
- CIRAD, UMR PHIM, Montpellier, France
- PHIM Plant Health Institute, CIRAD, INRAE, Institut Agro, IRD, University of Montpellier, Montpellier, France
| | - Mathilde Eck
- Plant Pathology Laboratory, Terra-Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Lucie Tamisier
- Plant Pathology Laboratory, Terra-Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Arnaud G. Blouin
- Virology-Phytoplasmology Laboratory, Agroscope, Nyon, Switzerland
| | - Thierry Candresse
- University of Bordeaux, INRAE, UMR BFP, CS20032, Villenave d’Ornon, France
| | - Sébastien Massart
- Plant Pathology Laboratory, Terra-Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
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8
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Mahillon M, Brodard J, Kellenberger I, Blouin AG, Schumpp O. A novel weevil-transmitted tymovirus found in mixed infection on hollyhock. Virol J 2023; 20:17. [PMID: 36710353 PMCID: PMC9885571 DOI: 10.1186/s12985-023-01976-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/24/2023] [Indexed: 01/31/2023] Open
Abstract
Leaves of hollyhock (Alcea rosea) exhibiting vein chlorosis and yellow mosaic symptoms were collected at public sites in Lausanne and Nyon, two cities of western Switzerland. Diagnostic methods untangled in samples from both sites the mixed infections of a novel isometric virus, tentatively named "Alcea yellow mosaic virus" (AYMV) with the carlavirus Gaillardia latent virus. A new potyvirus was also identified in samples from Nyon. A combination of Illumina, Nanopore and Sanger sequencing was necessary to assemble the full-length genome of AYMV, revealing an exceptionally high cytidine content and other features typically associated with members of the genus Tymovirus. The host range of AYMV was found to be restricted to mallows, including ornamentals as well as economically important plants. Phylogenetic analyses further showed that AYMV belongs to a Tymovirus subclade that also gathers the other mallow-infecting members. The virus was readily transmitted by sap inoculation, and the weevil species Aspidapion radiolus was evidenced as a vector. Transmission assays using another weevil or other insect species did not succeed, and seed transmission was not observed.
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Affiliation(s)
- Mathieu Mahillon
- grid.417771.30000 0004 4681 910XResearch Group Virology, Bacteriology and Phytoplasmology, Agroscope, Nyon, Switzerland
| | - Justine Brodard
- grid.417771.30000 0004 4681 910XResearch Group Virology, Bacteriology and Phytoplasmology, Agroscope, Nyon, Switzerland
| | - Isabelle Kellenberger
- grid.417771.30000 0004 4681 910XResearch Group Virology, Bacteriology and Phytoplasmology, Agroscope, Nyon, Switzerland
| | - Arnaud G. Blouin
- grid.417771.30000 0004 4681 910XResearch Group Virology, Bacteriology and Phytoplasmology, Agroscope, Nyon, Switzerland
| | - Olivier Schumpp
- Research Group Virology, Bacteriology and Phytoplasmology, Agroscope, Nyon, Switzerland.
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9
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Silva JMF, Melo FL, Elena SF, Candresse T, Sabanadzovic S, Tzanetakis IE, Blouin AG, Villamor DEV, Mollov D, Constable F, Cao M, Saldarelli P, Cho WK, Nagata T. Virus classification based on in-depth sequence analyses and development of demarcation criteria using the Betaflexiviridae as a case study. J Gen Virol 2022; 103. [DOI: 10.1099/jgv.0.001806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Currently, many viruses are classified based on their genome organization and nucleotide/amino acid sequence identities of their capsid and replication-associated proteins. Although biological traits such as vector specificities and host range are also considered, this later information is scarce for the majority of recently identified viruses, characterized only from genomic sequences. Accordingly, genomic sequences and derived information are being frequently used as the major, if not only, criteria for virus classification and this calls for a full review of the process. Herein, we critically addressed current issues concerning classification of viruses in the family Betaflexiviridae in the era of high-throughput sequencing and propose an updated set of demarcation criteria based on a process involving pairwise identity analyses and phylogenetics. The proposed framework has been designed to solve the majority of current conundrums in taxonomy and to facilitate future virus classification. Finally, the analyses performed herein, alongside the proposed approaches, could be used as a blueprint for virus classification at-large.
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Affiliation(s)
- João Marcos Fagundes Silva
- Departamento de Biologia Celular, Instituto de Ciências Biológicas, University of Brasília, Brasília 70910-900, Brazil
| | - Fernando Lucas Melo
- Departamento de Fitopatologia, Instituto de Biología Integrativa de Sistemas, University of Brasília, Brasília 70910-900, Brazil
| | - Santiago F. Elena
- The Santa Fe Institute, Santa Fe, NM 87501, USA
- Instituto de Biología Integrativa de Sistemas (I2 13 SysBio), CSIC-Universitat de València, Paterna 14 46980 València, Spain
| | - Thierry Candresse
- Univ. Bordeaux, INRAE, UMR 1332 BFP, 33140 Villenave d’Ornon, France
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA
| | | | - Arnaud G. Blouin
- Virology-Phytoplasmology Laboratory, Agroscope, 1260 Nyon, Switzerland
| | | | - Dimitre Mollov
- USDA-ARS Horticultural Crops Disease and Pest Management Research Unit, Corvallis, OR, 97330, USA
| | - Fiona Constable
- Department of Jobs Precincts and Regions, Agriculture Victoria Research, Agribio, Bundoora, VIC 3083, Australia
| | - Mengji Cao
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing 400712, PR China
| | - Pasquale Saldarelli
- National Research Council of Italy (CNR), Institute for Sustainable Plant Protection (IPSP), Via Amendola 122/D, 70126 Bari, Italy
| | - Won Kyong Cho
- College of Biotechnology and Bioengineering, Sungkyunkwan University, Seoburo 2066, Suwon 16419, Gyeonggi, Republic of Korea
| | - Tatsuya Nagata
- Departamento de Biologia Celular, Instituto de Ciências Biológicas, University of Brasília, Brasília 70910-900, Brazil
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10
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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: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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11
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Temple C, Blouin AG, De Jonghe K, Foucart Y, Botermans M, Westenberg M, Schoen R, Gentit P, Visage M, Verdin E, Wipf-Scheibel C, Ziebell H, Gaafar YZA, Zia A, Yan XH, Richert-Pöggeler KR, Ulrich R, Rivarez MPS, Kutnjak D, Vučurović A, Massart S. Biological and Genetic Characterization of Physostegia Chlorotic Mottle Virus in Europe Based on Host Range, Location, and Time. Plant Dis 2022; 106:2797-2807. [PMID: 35394335 DOI: 10.1094/pdis-12-21-2800-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Application of high throughput sequencing (HTS) technologies enabled the first identification of Physostegia chlorotic mottle virus (PhCMoV) in 2018 in Austria. Subsequently, PhCMoV was detected in Germany and Serbia on tomatoes showing severe fruit mottling and ripening anomalies. We report here how prepublication data-sharing resulted in an international collaboration across eight laboratories in five countries, enabling an in-depth characterization of PhCMoV. The independent studies converged toward its recent identification in eight additional European countries and confirmed its presence in samples collected 20 years ago (2002). The natural plant host range was expanded from two to nine species across seven families, and we confirmed the association of PhCMoV presence with severe fruit symptoms on economically important crops such as tomato, eggplant, and cucumber. Mechanical inoculations of selected isolates in the greenhouse established the causality of the symptoms on a new indexing host range. In addition, phylogenetic analysis showed a low genomic variation across the 29 near-complete genome sequences available. Furthermore, a strong selection pressure within a specific ecosystem was suggested by nearly identical sequences recovered from different host plants through time. Overall, this study describes the European distribution of PhCMoV on multiple plant hosts, including economically important crops on which the virus can cause severe fruit symptoms. This work demonstrates how to efficiently improve knowledge on an emergent pathogen by sharing HTS data and provides a solid knowledge foundation for further studies on plant rhabdoviruses.[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)
- Coline Temple
- Plant Pathology Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège (ULIEGE), Gembloux 5030, Belgium
| | - Arnaud G Blouin
- Plant Pathology Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège (ULIEGE), Gembloux 5030, Belgium
- Plant Protection Department, Agroscope, 1260 Nyon, Switzerland
| | - Kris De Jonghe
- Plant Sciences Unit, Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke 9820, Belgium
| | - Yoika Foucart
- Plant Sciences Unit, Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke 9820, Belgium
| | - Marleen Botermans
- National Reference Centre of Plant Health, National Plant Protection Organization of the Netherlands, 6700 HC Wageningen, the Netherlands
| | - Marcel Westenberg
- National Reference Centre of Plant Health, National Plant Protection Organization of the Netherlands, 6700 HC Wageningen, the Netherlands
| | - Ruben Schoen
- National Reference Centre of Plant Health, National Plant Protection Organization of the Netherlands, 6700 HC Wageningen, the Netherlands
| | - Pascal Gentit
- Laboratoire de santé des végétaux, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Angers 49100, France
| | - Michèle Visage
- Laboratoire de santé des végétaux, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Angers 49100, France
| | - Eric Verdin
- Unité de Pathologie Végétale, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Avignon 84000, France
| | - Catherine Wipf-Scheibel
- Unité de Pathologie Végétale, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Avignon 84000, France
| | - Heiko Ziebell
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Braunschweig 38104, Germany
| | - Yahya Z A Gaafar
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Braunschweig 38104, Germany
| | - Amjad Zia
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Braunschweig 38104, Germany
| | - Xiao-Hua Yan
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Braunschweig 38104, Germany
| | - Katja R Richert-Pöggeler
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Braunschweig 38104, Germany
| | | | - Mark Paul S Rivarez
- Department of Biotechnology and Systems Biology, National Institute of Biology (NIB), Ljubljana 1000, Slovenia
| | - Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology (NIB), Ljubljana 1000, Slovenia
| | - Ana Vučurović
- Department of Biotechnology and Systems Biology, National Institute of Biology (NIB), Ljubljana 1000, Slovenia
| | - Sébastien Massart
- Plant Pathology Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège (ULIEGE), Gembloux 5030, Belgium
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12
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Fuentes S, Gibbs AJ, Adams IP, Hajizadeh M, Kreuze J, Fox A, Blouin AG, Jones RAC. Phylogenetics and Evolution of Potato Virus V: Another Potyvirus that Originated in the Andes. Plant Dis 2022; 106:691-700. [PMID: 34633236 DOI: 10.1094/pdis-09-21-1897-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Potato virus V (PVV) causes a disease of potato (Solanum tubersosum) in South and Central America, Europe, and the Middle East. We report here the complete genomic sequences of 42 new PVV isolates from the potato's Andean domestication center in Peru and of eight historical or recent isolates from Europe. When the principal open reading frames of these genomic sequences together with those of nine previously published genomic sequences were analyzed, only two from Peru and one from Iran were found to be recombinant. The phylogeny of the 56 nonrecombinant open reading frame sequences showed that the PVV population had two major phylogroups, one of which formed three minor phylogroups (A1 to A3) of isolates, all of which are found only in the Andean region of South America (Peru and Colombia), and the other formed two minor phylogroups, a basal one of Andean isolates (A4) that is paraphyletic to a crown cluster containing all the isolates found outside South America (World). This suggests that PVV originated in the Andean region, with only one minor phylogroup spreading elsewhere in the world. In minor phylogroups A1 and A3, there were two subclades on long branches containing isolates from S. phureja evolving more rapidly than the others, and these interfered with dating calculations. Although no temporal signal was directly detected among the dated nonrecombinant sequences, PVV and potato virus Y (PVY) are from the same potyvirus lineage and are ecologically similar, so "subtree dating" was done via a single maximum likelihood phylogeny of PVV and PVY sequences, and PVY's well-supported 157 ce "time to most common recent ancestor" was extrapolated to date that of PVV as 29 bce. Thus the independent historical coincidences supporting the datings of the PVV and PVY phylogenies are the same; PVV arose ≥2,000 years ago in the Andes and was taken to Europe during the Columbian Exchange, where it diversified around 1853 ce, soon after the European potato late blight pandemic. PVV is likely to be more widespread than currently realized and is of biosecurity relevance for world regions that have not yet recorded its presence.[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)
- Segundo Fuentes
- Crop and System Sciences Division, International Potato Center, La Molina, Lima 15023, Peru
| | - Adrian J Gibbs
- Emeritus Faculty, Australian National University, Canberra, ACT 2600, Australia
| | - Ian P Adams
- Fera Science Ltd, Sand Hutton, York YO41 1LZ, UK
| | - Mohammad Hajizadeh
- Plant Protection Department, Faculty of Agriculture, University of Kurdistan, Sanandaj 6617715175, Iran
| | - Jan Kreuze
- Crop and System Sciences Division, International Potato Center, La Molina, Lima 15023, Peru
| | - Adrian Fox
- Fera Science Ltd, Sand Hutton, York YO41 1LZ, UK
| | - Arnaud G Blouin
- Plant Pathology Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège, Gembloux 5031, Belgium
| | - Roger A C Jones
- University of Western Australia Institute of Agriculture, University of Western Australia, Crawley, WA 6009, Australia
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13
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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14
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Gaafar YZA, Herz K, Hartrick J, Fletcher J, Blouin AG, MacDiarmid R, Ziebell H. Investigating the Pea Virome in Germany-Old Friends and New Players in the Field(s). Front Microbiol 2020; 11:583242. [PMID: 33281777 PMCID: PMC7691430 DOI: 10.3389/fmicb.2020.583242] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/28/2020] [Indexed: 12/21/2022] Open
Abstract
Peas are an important legume for human and animal consumption and are also being used as green manure or intermediate crops to sustain and improve soil condition. Pea production faces constraints from fungal, bacterial, and viral diseases. We investigated the virome of German pea crops over the course of three successive seasons in different regions of pea production to gain an overview of the existing viruses. Pools from 540 plants, randomly selected from symptomatic and asymptomatic peas, and non-crop plants surrounding the pea fields were used for ribosomal RNA-depleted total RNA extraction followed by high-throughput sequencing (HTS) and RT-PCR confirmation. Thirty-five different viruses were detected in addition to nine associated nucleic acids. From these viruses, 25 are classified as either new viruses, novel strains or viruses that have not been reported previously from Germany. Pea enation mosaic virus 1 and 2 were the most prevalent viruses detected in the pea crops, followed by pea necrotic yellow dwarf virus (PNYDV) and turnip yellows virus which was also found also in the surrounding non-legume weeds. Moreover, a new emaravirus was detected in symptomatic peas in one region for two successive seasons. Most of the identified viruses are known to be aphid transmissible. The results revealed a high virodiversity in the German pea fields that poses new challenges to diagnosticians, researchers, risk assessors and policy makers, as the impact of the new findings are currently unknown.
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Affiliation(s)
- Yahya Z A Gaafar
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Kerstin Herz
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Jonas Hartrick
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - John Fletcher
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Arnaud G Blouin
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand.,School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Robin MacDiarmid
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand.,School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Heiko Ziebell
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
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15
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Maree HJ, Blouin AG, Diaz-Lara A, Mostert I, Al Rwahnih M, Candresse T. Status of the current vitivirus taxonomy. Arch Virol 2019; 165:451-458. [PMID: 31845154 DOI: 10.1007/s00705-019-04500-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 11/12/2019] [Indexed: 11/25/2022]
Abstract
Since the establishment of the genus Vitivirus, several additional viruses have been sequenced and proposed to represent new species of this genus. Currently, the International Committee on Taxonomy of Viruses recognizes 15 vitivirus species. The report of new vitiviruses that fail to completely adhere to the species demarcation criteria, the incorporation of non-vitivirus grapevine viruses in the unofficial "naming system", and the existence of non-grapevine vitiviruses lead to inconsistencies in classification. In this report, we give a brief overview of vitiviruses and use currently available information to clarify the present status of the vitivirus taxonomy.
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Affiliation(s)
- H J Maree
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa.
- Citrus Research International, P.O. Box 2201, Matieland, 7602, South Africa.
| | - A G Blouin
- Integrated and Urban Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, 5030, Gembloux, Belgium
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - A Diaz-Lara
- Department of Plant Pathology, University of California-Davis, Davis, CA, 95616, USA
| | - I Mostert
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - M Al Rwahnih
- Department of Plant Pathology, University of California-Davis, Davis, CA, 95616, USA
| | - T Candresse
- INRAE, Univ. Bordeaux, UMR BFP, 33882, Villenave d'Ornon Cedex, France
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Diaz-Lara A, Klaassen V, Stevens K, Sudarshana MR, Rowhani A, Maree HJ, Chooi KM, Blouin AG, Habili N, Song Y, Aram K, Arnold K, Cooper ML, Wunderlich L, Battany MC, Bettiga LJ, Smith RJ, Bester R, Xiao H, Meng B, Preece JE, Golino D, Al Rwahnih M. Characterization of grapevine leafroll-associated virus 3 genetic variants and application towards RT-qPCR assay design. PLoS One 2018; 13:e0208862. [PMID: 30540844 PMCID: PMC6291115 DOI: 10.1371/journal.pone.0208862] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 11/24/2018] [Indexed: 11/18/2022] Open
Abstract
Grapevine leafroll-associated virus 3 (GLRaV-3) is the most widely prevalent and economically important of the complex of RNA viruses associated with grapevine leafroll disease (GLD). Phylogenetic studies have grouped GLRaV-3 isolates into nine different monophyletic groups and four supergroups, making GLRaV-3 a genetically highly diverse virus species. In addition, new divergent variants have been discovered recently around the world. Accurate identification of the virus is an essential component in the management and control of GLRaV-3; however, the diversity of GLRaV-3, coupled with the limited sequence information, have complicated the development of a reliable detection assay. In this study, GLRaV-3 sequence data available in GenBank and those generated at Foundation Plant Services, University of California-Davis, was used to develop a new RT-qPCR assay with the capacity to detect all known GLRaV-3 variants. The new assay, referred to as FPST, was challenged against samples that included plants infected with different GLRaV-3 variants and originating from 46 countries. The FPST assay detected all known GLRaV-3 variants, including the highly divergent variants, by amplifying a small highly conserved region in the 3' untranslated terminal region (UTR) of the virus genome. The reliability of the new RT-qPCR assay was confirmed by an enzyme linked immunosorbent assay (ELISA) that can detect all known GLRaV-3 variants characterized to date. Additionally, three new GLRaV-3 divergent variants, represented by four isolates, were identified using a hierarchical testing process involving the FPST assay, GLRaV-3 variant-specific assays and high-throughput sequencing analysis. These variants were distantly related to groups I, II, III, V, VI, VII and IX, but much similar to GLRaV-3 variants with no assigned group; thus, they may represent new clades. Finally, based on the phylogenetic analysis, a new GLRaV-3 subclade is proposed and named as group X.
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Affiliation(s)
- Alfredo Diaz-Lara
- Department of Plant Pathology, University of California-Davis, Davis, California, United States of America
| | - Vicki Klaassen
- Foundation Plant Services, University of California-Davis, Davis, California, United States of America
| | - Kristian Stevens
- Department of Evolution and Ecology, University of California-Davis, Davis, California, United States of America
| | - Mysore R. Sudarshana
- United States Department of Agriculture, Agriculture Research Service, University of California-Davis, Davis, California, United States of America
| | - Adib Rowhani
- Department of Plant Pathology, University of California-Davis, Davis, California, United States of America
| | - Hans J. Maree
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | - Kar Mun Chooi
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Arnaud G. Blouin
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Nuredin Habili
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, Australia
| | - Yashu Song
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Kamyar Aram
- Department of Plant Pathology, University of California-Davis, Davis, California, United States of America
| | - Kari Arnold
- University of California, Cooperative Extension-Stanislaus County, Modesto, California, United States of America
| | - Monica L. Cooper
- University of California, Cooperative Extension-Napa County, Napa, California, United States of America
| | - Lynn Wunderlich
- University of California, Cooperative Extension-Central Sierra, Placerville, California, United States of America
| | - Mark C. Battany
- University of California, Cooperative Extension-San Luis Obispo County, San Luis Obispo, California, United States of America
| | - Larry J. Bettiga
- University of California, Cooperative Extension-Monterey County, Monterey, California, United States of America
| | - Rhonda J. Smith
- University of California, Cooperative Extension-Sonoma County, Sonoma, California, United States of America
| | - Rachelle Bester
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | - Huogen Xiao
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Baozhong Meng
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - John E. Preece
- National Clonal Germplasm Repository, United States Department of Agriculture, Agricultural Research Service, Davis, California, United States of America
| | - Deborah Golino
- Department of Plant Pathology, University of California-Davis, Davis, California, United States of America
| | - Maher Al Rwahnih
- Department of Plant Pathology, University of California-Davis, Davis, California, United States of America
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17
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Blouin AG, Chooi KM, Warren B, Napier KR, Barrero RA, MacDiarmid RM. Grapevine virus I, a putative new vitivirus detected in co-infection with grapevine virus G in New Zealand. Arch Virol 2018; 163:1371-1374. [DOI: 10.1007/s00705-018-3738-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 12/23/2017] [Indexed: 02/06/2023]
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18
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Blouin AG, Ross HA, Hobson-Peters J, O'Brien CA, Warren B, MacDiarmid R. A new virus discovered by immunocapture of double-stranded RNA, a rapid method for virus enrichment in metagenomic studies. Mol Ecol Resour 2016; 16:1255-63. [PMID: 26990372 DOI: 10.1111/1755-0998.12525] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 02/24/2016] [Accepted: 02/26/2016] [Indexed: 11/30/2022]
Abstract
Next-generation sequencing technologies enable the rapid identification of viral infection of diseased organisms. However, despite a consistent decrease in sequencing costs, it is difficult to justify their use in large-scale surveys without a virus sequence enrichment technique. As the majority of plant viruses have an RNA genome, a common approach is to extract the double-stranded RNA (dsRNA) replicative form, to enrich the replicating virus genetic material over the host background. The traditional dsRNA extraction is time-consuming and labour-intensive. We present an alternative method to enrich dsRNA from plant extracts using anti-dsRNA monoclonal antibodies in a pull-down assay. The extracted dsRNA can be amplified by reverse transcriptase-polymerase chain reaction and sequenced by next-generation sequencing. In our study, we have selected three distinct plant hosts: Māori potato (Solanum tuberosum), rengarenga (Arthropodium cirratum) and broadleaved dock (Rumex obtusifolius) representing a cultivated crop, a New Zealand-native ornamental plant and a weed, respectively. Of the sequence data obtained, 31-74% of the reads were of viral origin, and we identified five viruses including Potato virus Y and Potato virus S in potato; Turnip mosaic virus in rengarenga (a new host record); and in the dock sample Cherry leaf roll virus and a novel virus belonging to the genus Macluravirus. We believe that this new assay represents a significant opportunity to upscale virus ecology studies from environmental, primary industry and/or medical samples.
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Affiliation(s)
- Arnaud G Blouin
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand.,School of Biological Sciences, University of Auckland, P.O. Box 92019, Auckland, New Zealand
| | - Howard A Ross
- School of Biological Sciences, University of Auckland, P.O. Box 92019, Auckland, New Zealand
| | - Jody Hobson-Peters
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Qld, 4072, Australia
| | - Caitlin A O'Brien
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Qld, 4072, Australia
| | - Ben Warren
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - Robin MacDiarmid
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand.,School of Biological Sciences, University of Auckland, P.O. Box 92019, Auckland, New Zealand
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19
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Chavan RR, Blouin AG, Cohen D, Pearson MN. Characterization of the complete genome of a novel citrivirus infecting Actinidia chinensis. Arch Virol 2013; 158:1679-86. [PMID: 23494225 DOI: 10.1007/s00705-013-1654-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 02/01/2013] [Indexed: 11/28/2022]
Abstract
A ssRNA virus from kiwifruit (Actinidia spp.) was identified as a member of the family Betaflexiviridae. It was mechanically transmitted to the herbaceous indicators Nicotiana benthamiana, N. clevelandii, N. glutinosa and N. occidentalis. The complete genome was comprised of three ORFs and a 3'poly (A) tail. Phylogenetic analysis of the entire genome indicated it was a novel member of the genus Citrivirus (family Betaflexiviridae). The complete nucleotide sequence differed from that of citrus leaf blotch virus (CLBV) by ~ 26 %. The movement protein (ORF2) and coat protein (ORF3) shared 95-96 % and 90-92 % amino acid sequence identity, respectively, with CLBV. The replicase polyprotein (ORF1) was distinctly different from published CLBV sequences, with 78-79 % amino acid sequence identity, while the 5' UTR and 3' UTR differed from CLBV by 28 % and 29 %, respectively. The sequence differences indicate that the citrivirus from Actinidia is either a divergent strain of CLBV or a member of a new citrivirus species.
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Affiliation(s)
- Ramesh R Chavan
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand
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20
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Blouin AG, Chavan RR, Pearson MN, MacDiarmid RM, Cohen D. Detection and characterisation of two novel vitiviruses infecting Actinidia. Arch Virol 2012; 157:713-22. [PMID: 22274622 DOI: 10.1007/s00705-011-1219-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Accepted: 11/30/2011] [Indexed: 10/14/2022]
Abstract
Two co-infecting novel vitiviruses from Actinidia chinensis were identified from mechanically inoculated Nicotiana occidentalis. Both virus genomes were sequenced and share 64% nucleotide identity. Their overall structure is typical of vitiviruses, with five open reading frames (ORFs) and a polyadenylated 3' end. Open reading frame 4 (ORF4) encodes the coat protein, the most conserved gene of the vitiviruses, in which they share 75% amino acid identity, 61-68% with grapevine virus B, 55-59% with grapevine virus A, and 37-42% with grapevine virus E. Based on the molecular criteria for species demarcation in the family Betaflexiviridae, these are two novel viruses, tentatively named Actinidia virus A and Actinidia virus B.
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Affiliation(s)
- Arnaud G Blouin
- The New Zealand Institute for Plant and Food Research Ltd., Auckland, New Zealand.
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21
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Blouin AG, Greenwood DR, Chavan RR, Pearson MN, Clover GRG, MacDiarmid RM, Cohen D. A generic method to identify plant viruses by high-resolution tandem mass spectrometry of their coat proteins. J Virol Methods 2010; 163:49-56. [PMID: 19712699 DOI: 10.1016/j.jviromet.2009.08.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2009] [Revised: 08/12/2009] [Accepted: 08/17/2009] [Indexed: 10/20/2022]
Abstract
Although a number of protocols have been developed for detection of viruses at the genus or family level, universal approaches to detect and identify unknown viruses are still required. High-resolution tandem mass spectrometry was used to identify accurately peptide masses and their constituent sequences from partially purified plant virus preparations. Analysis of the peptide fragment masses against a virus database using pattern-matching algorithms identified sequences with homology to known virus peptides and also predicted peptides using de novo sequence analysis. This method provided sufficient information to confirm the identity of two known viruses that were included as controls (Cucumber mosaic virus and Tomato spotted wilt virus) and to identify unknown viruses in six viral isolates. The unknown viruses have been identified as four common viruses (Alfalfa mosaic virus, Tobacco streak virus, Citrus leaf blotch virus and Ribgrass mosaic virus), and two novel viruses (a potexvirus and a vitivirus). The identification of viruses from five distinct families by the tandem mass spectrometric determination of their coat protein demonstrates that this is a useful method for initial virus identification. This method, complemented with molecular or immunological procedures, provides a rapid and convenient way to identify both known and novel plant viruses.
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Affiliation(s)
- Arnaud G Blouin
- The New Zealand Institute for Plant and Food Research Ltd., Auckland, New Zealand
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22
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Abstract
Although male courtship songs have been repeatedly implicated in sexual isolation between numerous Drosophila species, no genetic studies have evaluated the genetic basis of differences between species beyond using quantitative genetic analyses of hybrids or surveying associations of song characters to five or fewer genetic markers. Here, we dissect the genetic basis of the difference between D. pseudoobscura and D. persimilis in two courtship song elements (interpulse interval and intrapulse frequency) using 15 molecular markers. We also evaluate the association between song elements and sexual isolation in these backcross hybrid males of these species. We find that song differences between these species are associated with at least two or three genomic regions, and the species difference in interpulse interval may be oligogenic. Courtship song differences are especially strongly associated with two inversions that differentiate these species. Further, we found that interpulse interval is strongly associated with mating success to D. pseudoobscura females, while intrapulse frequency is associated with mating success to D. persimilis females. Implications of these findings are discussed.
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Affiliation(s)
- M A Williams
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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23
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Abstract
The effects of light therapy on food intake and affective symptoms of bulimia nervosa (BN) were examined in a double-blind study. Eighteen women who met DSM-III-R criteria for BN were randomly assigned to receive either 2500 lux of bright light (experimental condition) or < 500 lux of dim light (placebo condition) daily in the early evening for a 1-week period. The Structured Interview Guide for the Hamilton Depression Rating Scale-Seasonal Affective Disorder Version (SIGH-SAD), the Beck Depression Inventory (BDI), and the Bulimic Symptoms Checklist were administered to subjects before light exposure, after 1 week of light exposure, and after 7 days of withdrawal of light exposure. Throughout the study, the Profile of Mood States and the Daily Binge Record were completed daily. Compared with subjects in the dim light condition, subjects in the bright light condition showed a significant improvement in depressed mood during light exposure, as measured by both the BDI and the SIGH-SAD. There was a return to pretreatment levels of depression after withdrawal of light exposure. No changes in depression were noted in the placebo group. No effect of light therapy was found on the frequency, size, or content of binge-eating episodes. The results are discussed in terms of the physiological processes associated with light therapy and seasonal affective disorder that may underlie the affective and food intake symptoms of BN.
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Affiliation(s)
- A G Blouin
- Department of Psychiatry, Ottawa Civic Hospital, ON, Canada
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24
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Abstract
This study was designed to examine the association between body image and eating-related attitudes among male bodybuilders in relation to two athletic comparison groups, runners and martial artists. It was also of interest to examine whether steroid use may be associated with body image disturbances in athletes. The volunteer sample of 139 male athletes recruited from fitness centers comprised 43 bodybuilders, 48 runners, and 48 martial artists (tae kwon do practitioners). Standardized measures of body dissatisfaction, drive for thinness, drive for bulk, bulimia, self-esteem, depression, maturity fears, and perfectionism as well as questionnaires designed to measure attitudes toward steroids, and rates of steroid use were administered in a manner that encouraged disclosure. Bodybuilders reported significantly greater body dissatisfaction, with a high drive for bulk, high drive for thinness, and increased bulimic tendencies than either of the other athletic groups. In addition bodybuilders reported significant elevations on measures of perfectionism, ineffectiveness, and lower self-esteem. They also reported the greatest use of anabolic steroids and most liberal attitudes towards using steroids. Steroid users reported that the most significant reason for using steroids was to improve looks. Steroid users reported an elevated drive to put on muscle mass in the form of bulk, greater maturity fears, and enhanced bulimic tendencies than nonusers. The results suggest that male bodybuilders are at risk for body image disturbance and the associated psychological characteristics that have been commonly reported among eating disorder patients. These psychological characteristics also appear to predict steroid use in this group of males.
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Affiliation(s)
- A G Blouin
- Department of Psychiatry, Ottawa Civic Hospital, Ontario, Canada
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25
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Abstract
Prognostic indicators of short-term outcome were identified in 69 women with the DSM-III-R diagnosis of bulimia nervosa who participated in a weekly 10-session structured cognitive-behavioral outpatient group program. Prior to treatment, all subjects completed the computerized Diagnostic Interview Schedule (DIS), the Moos Family Environment Scale (FES), the Diagnostic Survey for Eating Disorders (DSED), the Beck Depression Inventory (BDI), the Hopkins Symptom Checklist, Revised (SCL-90-R), the Bulimic Cognitive Distortions Scale (BCDS), the Eating Disorders Inventory (EDI), and the Bulimic Symptoms Checklist (BSCL). The latter three scales were readministered on completion of the 10-week group. Symptom improvement was assessed by examining percentage reduction in binge frequency, purge frequency, and summed scores for the EDI subscales Bulimia, Drive for Thinness, and Body Dissatisfaction. The only significant predictor of improvement in binge frequency and bulimic cognitions was family environment. Conflicted, controlling, and over-organized family environments appear to impede both reductions in binge frequency and changes in bulimic cognitions. Reduction in vomit frequency was associated with weight history and with laxative or diuretic use. The implications for planning psychotherapeutic interventions in bulimia nervosa are discussed.
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Affiliation(s)
- J H Blouin
- Department of Psychiatry, Ottawa Civic Hospital, Ontario, Canada
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26
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Abstract
Nineteen bulimic women and 22 age-matched controls were randomly assigned to receive 25 g of glucose or a placebo injection under double-blind conditions. Blood samples of glucose, insulin, and glucagon, and psychometric assessments of mood and food cravings were obtained 10 min before, and 0, 5, 10, 20, 30, 45, and 60 min after injection. Blood levels of the large neutral amino acids (LNAAs) tryptophan, tyrosine, leucine, valine, phenylalanine, and leucine were determined at 10 min before and 60 min after the injection. Bulimic subjects were found to report more symptoms of distressed mood throughout the entire monitoring period than controls. Five minutes following glucose ingestion the self-reports of depression, fatigue, anxiety, and bewilderment rose to a level among the bulimic subjects that was above that at baseline, and was higher than that of bulimia nervosa (BN) subjects receiving placebo. No comparable change in mood was observed among controls. Blood glucose levels were correlated with mood in the bulimic group, but not in controls. In addition, the glucose injection induced a heightened urge to binge in the bulimic group (compared to placebo at 10 and 60 min), whereas reducing food cravings (for sweets) in the controls (at 5 min). When collapsed across time and injection condition, the blood glucose level of bulimics was lower than that of controls. There were no differences in insulin response between the groups. The bulimic group was found to have lower baseline levels of blood tryptophan, whereas no differences in the tryptophan/LNAA ratio were observed either at baseline or following glucose.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- A G Blouin
- Department of Psychiatry, Ottawa Civic Hospital, Ontario, Canada
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Levitan RD, Blouin AG, Navarro JR, Hill J. Validity of the computerized DIS for diagnosing psychiatric inpatients. Can J Psychiatry 1991; 36:728-31. [PMID: 1790517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The validity of a self-administered, computerized version of the National Institute of Mental Health Diagnostic Interview Schedule (DIS) was evaluated with a group of 41 psychiatric inpatients. Each patient was administered the computerized DIS (C-DIS) and a semi-structured clinical interview using the symptom checklist developed by Helzer et al. The concordance between the C-DIS and symptom checklist was comparable to that found in earlier studies of the original DIS. The overall distribution of kappas was also similar to those of previous studies. Overall, the results suggest that computerized administration may be a feasible alternative to face-to-face administration of the DIS.
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Blouin AG, Conners CK, Seidel WT, Blouin J. The independence of hyperactivity from conduct disorder: methodological considerations. Can J Psychiatry 1989; 34:279-82. [PMID: 2736472 DOI: 10.1177/070674378903400403] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
It has been claimed that the childhood behavioural factors "hyperactivity" and "conduct disorder" are highly correlated. The fact that hyperactive symptoms load heavily on the conduct disorder factor has also been used to support the notion that hyperactivity is not an independent behavioural dimension. The present study employs a large sample of combined clinic and normal children to demonstrate that both of these observations are artifacts of methodological technique. When factor score coefficients are used to interpret factors, the hyperactive symptoms do not load on the conduct disorder factor. If factor scores are defined by the use of unit weights, as in previous studies, then the intercorrelation between the hyperactive and conduct disorder factors is high. The use of factor score coefficients to define factors, on the other hand, produces uncorrelated factors. The results support the idea that hyperactivity and conduct disorder are independent behavioural dimensions.
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Affiliation(s)
- A G Blouin
- Department of Psychiatry, Ottawa Civic Hospital, Ont
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Blouin AG, Blouin JH, Perez EL, Bushnik T, Zuro C, Mulder E. Treatment of bulimia with fenfluramine and desipramine. J Clin Psychopharmacol 1988; 8:261-9. [PMID: 3062043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Desipramine and fenfluramine were administered to bulimic patients in a 15-week study of double-blind, placebo-controlled, crossover design. The 22 patients in the study met DSM-III criteria for bulimia and were of normal weight. Twelve subjects were randomly allocated to the fenfluramine group, and 10 subjects received desipramine. Half the subjects in each group received the active drug in the first 6 weeks and half received placebo. There was a 3-week washout period, after which subjects were crossed over for the remaining 6 weeks. The Eating Disorder Inventory, profile of Mood States, bulimia symptom checklists, and Hopkins Symptom Checklist were administered at weeks 0, 2, 4, 6, 9, 11, 13, and 15. Subjects maintained a daily record of bingeing, vomiting, and laxative/diuretic abuse. Results indicated that both drugs had beneficial effects on bingeing and vomiting frequency, although a greater proportion of patients were identified who responded to fenfluramine than to desipramine. Fenfluramine and desipramine were also effective in reducing the psychological symptoms of bulimia, such as the urge to binge, and feelings of depression. Results suggest that direct alteration of central food intake regulatory centers can effectively control bulimia.
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Affiliation(s)
- A G Blouin
- Department of Psychiatry, Ottawa Civic Hospital, Ontario, Canada
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Abstract
The National Institute of Mental Health (NIMH) Diagnostic Interview Schedule (DIS) is a highly structured interview designed to be administered by lay interviewers and to yield psychiatric diagnoses. While the DIS has been used widely in large research centers, its use has been limited due to its complexity and need for extensive training to administer. In the present study 100 volunteers consisting of 80 psychiatric patients and 20 normal controls completed a self-administering computerized version of the DIS on two occasions. A standardized Computer Attitude Scale (CAS) was administered to each volunteer before the first and after the second computerized DIS (C-DIS). The C-DIS yielded acceptable test-retest reliability. Certain diagnoses were found to yield high test-retest reliability while reliability was lower for others. This general pattern was similar to the results of previous procedural validity studies. Patients found the C-DIS generally easy to use and operate, and after using the C-DIS, felt that their level of expertise in using computers had improved. Generally, the results support the use of computerized administration of the DIS.
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Affiliation(s)
- A G Blouin
- Department of Psychiatry, Ottawa Civic Hospital, Ontario, Canada
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Abstract
The effect of piracetam on visual event-related potentials (ERP) was investigated in a double-blind placebo-controlled study. Eight- to 12-year-old dyslexic males were randomly assigned to 3.3 g/day of piracetam or matching placebo in two divided doses over a 12-week period. Children performed a vigilance task in which they pressed a key when two alphabetic letters or shapes occurred in sequence. ERPs to letters and shapes, for active and passive responses, were recorded at the vertex and left and right parietal areas of the scalp. Performance measures included letter- and form-hits, misses, commission errors and reaction times. Piracetam increased the amplitude of a late positive component (believed to correspond to P300) at the vertex for letter-hits. Piracetam also increased the latency of this component in both hemispheres, but only for active responses (letter-hits) in the left hemisphere and passive responses (correct rejections and misses) in the right hemisphere. Although piracetam did not significantly affect performance, reaction time to letter-hits was significantly correlated with the latency of the P300 component, suggesting that letters created increased effort or attentional demand on the subjects compared with forms. An early ERP component (P225) also showed increased amplitude to piracetam in both hemispheres and effects were limited to form-hits. These effects were thought to possibly reflect slow negative potentials arising from stimulus anticipation in the CNV-like paradigm. In view of the small sample size, the results were cautiously interpreted as indicating a facilitation of verbal processing mechanisms responsible for analyzing the verbal significance of visual stimuli.
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Feinstein C, Blouin AG, Egan J, Conners CK. Depressive symptomatology in a child psychiatric outpatient population: correlations with diagnosis. Compr Psychiatry 1984; 25:379-91. [PMID: 6467918 DOI: 10.1016/0010-440x(84)90073-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
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Trites RL, Blouin AG, Laprade K. Factor analysis of the Conners Teacher Rating Scale based on a large normative sample. J Consult Clin Psychol 1983. [PMID: 7142537 DOI: 10.1037//0022-006x.50.5.615] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Abstract
Studies of nutritional effects on behavior of children present many of the same methodological problems as studies of drugs on behavior of children. Dependent measures must be made across several classes of response at different time scales and levels of precision. A schema is presented for an integrated series of nutritional studies. The effects of missing breakfast and of simple sugars are used to illustrate several applications from this schema, including autonomic (evoked cardiac response), central (event-related potentials), and behavioral measures. Each class of measures is found to be sensitive to these nutritional manipulations. Attention and motor behavior appear to be quite sensitive to subtle nutritional effects.
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