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Minutolo M, Nicoloso V, Cinque M, Chiumenti M, Simeone GDR, Serio FD, Alioto D, Navarro B. A Polyvalent Tool for Detecting Coguviruses in Multiple Hosts Allowed the Identification of a Novel Seed-Transmitted Coguvirus Infecting Brassicaceae. PHYTOPATHOLOGY 2024; 114:823-831. [PMID: 38079350 DOI: 10.1094/phyto-10-23-0362-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2024]
Abstract
The genus Coguvirus, a recently established genus in the family Phenuiviridae, includes several species whose members infect both woody and herbaceous hosts, suggesting a broader host range and wider distribution than previously. To gain insights into the epidemiology and biology of coguviruses, a polyvalent reverse transcription-PCR assay using degenerate primers was developed. The specificity of the assay for coguviruses was confirmed by testing citrus and apple plants infected by previously reported coguviruses and/or several unrelated viruses. The expected 236-bp amplicon was obtained from citrus, apple, pear, watermelon, and several species of the family Brassicaceae. Sequencing of the PCR amplicons allowed the identification, for the first time in Italy and/or Europe, of several coguviruses in multiple hosts, confirming the effectiveness of the assay. Moreover, a new virus, tentatively named Brassica oleracea Torzella virus 1 (BoTV1), was detected in several plants of Torzella cabbage. The complete +genome of BoTV1, determined by high-throughput sequencing and 5' rapid amplification of cDNA ends, revealed that it has the typical molecular features of coguviruses and fulfils the current criteria to be classified as a member of a new species, for which the tentative name Coguvirus torzellae is proposed. The same polyvalent assay was also used to investigate and confirm that BoTV1 is transmitted through seeds in black cabbage, thus providing the first evidence on the relevance of this natural transmission mode in the epidemiology of coguviruses. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Maria Minutolo
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II, 80055, Portici, Italy
| | - Vittorio Nicoloso
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, 70126, Bari, Italy
| | - Maria Cinque
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II, 80055, Portici, Italy
| | - Michela Chiumenti
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, 70126, Bari, Italy
| | | | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, 70126, Bari, Italy
| | - Daniela Alioto
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II, 80055, Portici, Italy
| | - Beatriz Navarro
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, 70126, Bari, Italy
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Dai R, Yang S, Pang T, Tian M, Wang H, Zhang D, Wu Y, Kondo H, Andika IB, Kang Z, Sun L. Identification of a negative-strand RNA virus with natural plant and fungal hosts. Proc Natl Acad Sci U S A 2024; 121:e2319582121. [PMID: 38483998 PMCID: PMC10962957 DOI: 10.1073/pnas.2319582121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/29/2024] [Indexed: 03/19/2024] Open
Abstract
The presence of viruses that spread to both plant and fungal populations in nature has posed intriguingly scientific question. We found a negative-strand RNA virus related to members of the family Phenuiviridae, named Valsa mali negative-strand RNA virus 1 (VmNSRV1), which induced strong hypovirulence and was prevalent in a population of the phytopathogenic fungus of apple Valsa canker (Valsa mali) infecting apple orchards in the Shaanxi Province of China. Intriguingly, VmNSRV1 encodes a protein with a viral cell-to-cell movement function in plant tissue. Mechanical leaf inoculation showed that VmNSRV1 could systemically infect plants. Moreover, VmNSRV1 was detected in 24 out of 139 apple trees tested in orchards in Shaanxi Province. Fungal inoculation experiments showed that VmNSRV1 could be bidirectionally transmitted between apple plants and V. mali, and VmNSRV1 infection in plants reduced the development of fungal lesions on leaves. Additionally, the nucleocapsid protein encoded by VmNSRV1 is associated with and rearranged lipid droplets in both fungal and plant cells. VmNSRV1 represents a virus that has adapted and spread to both plant and fungal hosts and shuttles between these two organisms in nature (phyto-mycovirus) and is potential to be utilized for the biocontrol method against plant fungal diseases. This finding presents further insights into the virus evolution and adaptation encompassing both plant and fungal hosts.
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Affiliation(s)
- Ruoyin Dai
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production and College of Plant Protection, Northwest A&F University, Yangling712100, China
| | - Shian Yang
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production and College of Plant Protection, Northwest A&F University, Yangling712100, China
| | - Tianxing Pang
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production and College of Plant Protection, Northwest A&F University, Yangling712100, China
| | - Mengyuan Tian
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production and College of Plant Protection, Northwest A&F University, Yangling712100, China
| | - Hao Wang
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production and College of Plant Protection, Northwest A&F University, Yangling712100, China
| | - Dong Zhang
- Yangling Sub-Center of National Center for Apple Improvement and College of Horticulture, Northwest A&F University, Yangling712100, China
| | - Yunfeng Wu
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production and College of Plant Protection, Northwest A&F University, Yangling712100, China
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki710-0046, Japan
| | - Ida Bagus Andika
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao266109, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production and College of Plant Protection, Northwest A&F University, Yangling712100, China
| | - Liying Sun
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production and College of Plant Protection, Northwest A&F University, Yangling712100, China
- Institute of Plant Science and Resources, Okayama University, Kurashiki710-0046, Japan
- Institute of Future Agriculture, Northwest A&F University, Yangling712100, China
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Li P, Bhattacharjee P, Gagkaeva T, Wang S, Guo L. A novel bipartite negative-stranded RNA mycovirus of the order Bunyavirales isolated from the phytopathogenic fungus Fusarium sibiricum. Arch Virol 2023; 169:13. [PMID: 38155262 DOI: 10.1007/s00705-023-05942-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 11/20/2023] [Indexed: 12/30/2023]
Abstract
A novel negative-stranded RNA mycovirus was isolated from the phytopathogenic fungus Fusarium sibiricum strain AH32. This virus, tentatively named "Fusarium sibiricum coguvirus 1" (FsCV1), has a bipartite genome consisting of two RNA segments (RNA1 and RNA2). The negative-sense RNA1 is 6711 nt in length, encoding the RNA-dependent RNA polymerase (RdRp, p251) in the viral complementary (vc) strand. The ambisense RNA2 (1204 nt long) encodes two proteins from overlapping genes: the nucleocapsid protein (NP, p38) in the vc strand and a protein of unknown function (UFP, p36) in the viral (v) strand. In contrast to other Bunyavirales members, in FsCV1, the two open reading frames are separated by a long AU-rich intergenic region (IR). Sequence comparisons and phylogenetic analysis based on RdRp and NP sequences demonstrated that FsCV1 is a novel bipartite negative-stranded RNA mycovirus of the genus Coguvirus, family Phenuiviridae, order Bunyavirales.
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Affiliation(s)
- Pengfei Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Pallab Bhattacharjee
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tatiana Gagkaeva
- All-Russian Institute of Plant Protection, Pushkin, St. Petersburg, Russian Federation
| | - Shuangchao Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lihua Guo
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
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4
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Devendran R, Kavalappara SR, Simmons AM, Bag S. Whitefly-Transmitted Viruses of Cucurbits in the Southern United States. Viruses 2023; 15:2278. [PMID: 38005954 PMCID: PMC10675411 DOI: 10.3390/v15112278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023] Open
Abstract
Cucurbits are economically important crops that are widely cultivated in many parts of the world, including the southern US. In recent years, higher temperatures have favored the rapid build-up of whiteflies in the fall-grown cucurbits in this region. As a result, whitefly-transmitted viruses (WTVs) have severely impacted the marketable yield of cucurbits. In this review, we discuss three major groups of WTVs negatively impacting cucurbit cultivation in the southern US, including begomoviruses, criniviruses, and ipomoviruses. Here, we discuss the available information on the biology, epidemiology and advances made toward detecting and managing these viruses, including sources of resistance and cultural practices.
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Affiliation(s)
| | | | - Alvin M. Simmons
- U.S. Vegetable Laboratory, Agricultural Research Service, United States Department of Agriculture, Charleston, SC 29414, USA
| | - Sudeep Bag
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA
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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: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [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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6
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Togoobat B, Wu N, Wang X, Cao M, Xu Z. Viromic approach reveals differences in the composition, diversity and relative abundance of pumpkin viruses across main growing regions of China. Virology 2023; 585:61-71. [PMID: 37295338 DOI: 10.1016/j.virol.2023.05.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 05/11/2023] [Accepted: 05/17/2023] [Indexed: 06/12/2023]
Abstract
China is the leading country for pumpkin production in the world. As other cucurbits, diseases caused by viruses are among the serious threats to pumpkin production, but our knowledge on the virus species infecting pumpkin plants is fragmentary. To understand the occurrence of viral diseases on pumpkin, we determined the geographical distribution characteristics, relative abundance and evolutionary relationship of pumpkin infected viruses by meta-transcriptome sequencing (RNA-seq) and viromic analysis of 159 samples exhibited typical viral symptoms collected across China in this study. Totally, 11 known and 3 new viruses were identified. Interestingly, 3 new viruses identified in this study should be positive-sense single-stranded RNA virus whose hosts are prokaryotes. The viruses identified in different sampling locations exhibit significant variations in term of virus species and relative abundance. Here, the results provide valuable information for understanding the virus species and their diversity in cultivated pumpkin across major growing regions of China.
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Affiliation(s)
- Batchimeg Togoobat
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; Laboratory for Plant Pathology, Institute of Plant Protection, Ulaanbaatar, Mongolia
| | - Nan Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Xifeng Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mengji Cao
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Chongqing, China
| | - Zhongtian Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China.
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7
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Wang X, Liao R, Yang X, Liu Q, Zhang S, Cao M. Complete genome sequence of Edgeworthia chrysantha mosaic-associated virus, a tentative new member of the genus Coguvirus (family Phenuiviridae). Arch Virol 2022; 167:2827-2831. [PMID: 36175794 DOI: 10.1007/s00705-022-05608-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/17/2022] [Indexed: 12/14/2022]
Abstract
A new negative-strand RNA (nsRNA) virus genome was discovered in Edgeworthia chrysantha Lindl. This virus, tentatively named "Edgeworthia chrysantha mosaic-associated virus" (ECMaV), has a bipartite genome that comprises (i) a nsRNA1, encoding the viral RNA-dependent RNA polymerase (RdRp), and (ii) an ambisense RNA2, coding for the putative movement protein (MP) and nucleocapsid protein (NP), with the open reading frames separated by a long AU-rich intergenic region (IR). Sequence comparisons and phylogenetic analysis showed that the RdRp is closely related to those of other recently discovered plant-infecting nsRNA viruses in the new genus Coguvirus and that ECMaV can be classified as a member of a novel species.
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Affiliation(s)
- Xiaoru Wang
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China.,Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Ruiling Liao
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China.,Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Xinying Yang
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China.,Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Qiyan Liu
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China.,Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Song Zhang
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China.,Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Mengji Cao
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China. .,Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China.
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8
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Gilford CJ, Ali A. First report of Watermelon crinkle leaf-associated virus 2 infecting watermelon (Citrullus lanatus) in Oklahoma. PLANT DISEASE 2022; 107:973. [PMID: 35961015 DOI: 10.1094/pdis-05-22-1238-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Watermelon (Citrullus lanatus) is one of the major cucurbit crops in Oklahoma, which is grown on >1,200 acres. It contributes $16 million to the state's economy (Shrefler et al., 2017; NASS, 2022). During the 2021 growing season, virus-like symptoms on watermelon plants were observed in a grower's field in Blaine County, Oklahoma. These symptoms included mottling, crinkled leaf edges, and a unique yellow mosaic pattern (Fig. 1). Leaf tissue samples were randomly collected from nine plants and total RNA was extracted using Spectrum Plant Total RNA Kit (Sigma-Aldrich). Total RNA from one sample (named BL13) was subjected to high-throughput sequencing (HTS) on the NextSeq 500/550 High-Output kit v2.5 (Illumina, USA) at the genomic facility of Oklahoma State University. A total of 21,52,786 trimmed pair-end reads were assembled using CLC Genomics Workbench (v12.0.3) (Qiagen, Inc.) and subjected to BLASTn analysis. Of these, three contigs of 6,626 bp, 1,383 bp and 1,233 bp (average coverage 20,658X) showed 99% nucleotide (nt) sequence identity with RNA1 of a watermelon crinkle leaf-associated virus (WCLaV-2) isolate from Brazil (LC636073). The HTS data for BL13 samples also revealed three contigs of 263 pb, 567 bp and 1,066 bp that matched with cucumis melo crytpic virus isolate CmCV-HLI but was not confirmed by RT-PCR. The presence of WCLaV-2 in the BL13 sample was confirmed by RT-PCR using primers (RNA1-F: 5'-CAAAACGCCCATAAG AATAG-3'and RNA1-R: 5'- CTCCATTAATGAGAACTAGGAG-3') which amplified a 1.2 kb segment of the RNA1. The PCR product was confirmed on 1% agarose gel, cloned and three independent recombinant clones Sanger sequenced (Eurofins Genomics LLC, Louisville, KY, USA). The resulting consensus sequence (1.2 Kb) (ON453838) was subjected to a BLASTn search against the Genbank databases, resulting in 99.76% nt identity with WCLaV-2 RNA1 (Accession no. LC636073). Screening of the remaining eight symptomatic samples by RT-PCR revealed another positive sample (named BL7) for WCLaV-2. Consensus nt sequence (1.2 Kb) analysis for the virus isolate from the BL7 sample (Accession no. ON453839) shared 99.84% nt identities with WCLaV-2 RNA1 (LC636073). Total RNA from BL13 and BL7 samples, as well as the remaining seven samples, were tested against three major potyviruses (PRSV-W, WMV, and ZYMV) by multiplex RT-PCR (Rajbanshi & Ali, 2019). Both BL13 and BL7 samples were negative to all three potyviruses but the other eight samples were positive to one or two of the potyviruses. WCLaV-2 is a negative-sense ssRNA virus (family Phenuiviridae) and has been recently reported from watermelon in China (Xin et al., 2017) and Brazil (Maeda et al. 2022). In the United States, it has been reported from Florida (Hendrick et al., 2021), Georgia (Adeleke et al., 2022), and Texas (Hernandez et al., 2021). The mode of transmission of WCLaV-2 and its direct effect on watermelon fruit is not known (Xin et al., 2017; Maeda et al., 2022). Our results report for the first time the occurrence of WCLaV-2 infecting watermelon naturally in Oklahoma and show a further potential threat to watermelon production in the State. Further studies are needed to determine the incidence of WCLaV-2 in other counties of Oklahoma.
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Affiliation(s)
- Clark J Gilford
- The University of Tulsa, Biological Science, Tulsa, Oklahoma, United States;
| | - Akhtar Ali
- University of Tulsa, Biological Science, 800 S Tucker Dr, Tulsa, Oklahoma, United States, 74104-9700;
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Park JW, da Graça JV, Gonzalez M, Louzada ES, Alabi OJ, Kunta M. First Report of Citrus Virus A in Texas Associated with Oak Leaf Patterns in Citrus sinensis. PLANT DISEASE 2022; 106:PDIS03210628PDN. [PMID: 34962411 DOI: 10.1094/pdis-03-21-0628-pdn] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Jong-Won Park
- Texas A&M University-Kingsville Citrus Center, Weslaco, TX 78599
| | - John V da Graça
- Texas A&M University-Kingsville Citrus Center, Weslaco, TX 78599
| | - Marissa Gonzalez
- Texas A&M University-Kingsville Citrus Center, Weslaco, TX 78599
| | | | - Olufemi J Alabi
- Texas A&M University-Kingsville Citrus Center, Weslaco, TX 78599
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Maeda MHK, Koyama LHH, Campos RNS, Kauffmann CM, Souza JO, Gilbertson R, Inoue-Nagata AK, Freitas DMS, Nogueira DRS, Melo FL, Nagata T. First Report of Watermelon Crinkle Leaf-Associated Virus 1 and 2 Infecting Watermelon ( Citrullus lanatus) Plants in Brazil. PLANT DISEASE 2022; 106:773. [PMID: 34455800 DOI: 10.1094/pdis-06-21-1325-pdn] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Affiliation(s)
- M H K Maeda
- Laboratório de Virologia Geral, Instituto de Ciências Biológicas, Universidade de Brasília, DF, Brazil
| | - L H H Koyama
- Laboratório de Virologia Geral, Instituto de Ciências Biológicas, Universidade de Brasília, DF, Brazil
| | - R N S Campos
- Laboratório de Virologia Geral, Instituto de Ciências Biológicas, Universidade de Brasília, DF, Brazil
| | - C M Kauffmann
- Pós-graduação em Fitopatologia, Universidade de Brasília, DF, Brazil
| | - J O Souza
- Embrapa-Hortaliças, Brasília, DF, Brazil
| | - R Gilbertson
- Department of Plant Pathology, University of California Davis, CA, U.S.A
| | | | | | | | - F L Melo
- Laboratório de Virologia Geral, Instituto de Ciências Biológicas, Universidade de Brasília, DF, Brazil
| | - T Nagata
- Laboratório de Virologia Geral, Instituto de Ciências Biológicas, Universidade de Brasília, DF, Brazil
- Pós-graduação em Fitopatologia, Universidade de Brasília, DF, Brazil
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11
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Adeleke IA, Kavalappara SR, Torrance T, Bennett JE, McGregor C, Srinivasan R, Bag S. First report of watermelon crinkle leaf-associated virus 1 naturally infecting watermelon (Citrullus lanatus) in Georgia, USA. PLANT DISEASE 2022; 106:2273. [PMID: 35100033 DOI: 10.1094/pdis-11-21-2521-pdn] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Watermelon (Citrullus lanatus) is one of the major vegetable crops grown in Georgia during the spring and summer seasons, contributing $180 million of farmgate value to the state's economy (Georgia Farm Gate Value Report 2019). During the summer of 2021, watermelon plants with foliar symptoms such as yellow mottling, chlorosis, and wrinkling with thickened, bunchy, and upward curling were observed on commercial fields of Georgia, USA. A disease incidence of 15-20% in ~56 ac in Tift county and 10-15% in ~60 ac in Wilcox county was observed. The symptoms observed were similar to those described for watermelon crinkle leaf-associated viruses (WCLaV-1 and WCLaV-2) from Florida (Hendrick et al., 2021) and Texas (Hernandez et al., 2021). Symptomatic leaves from Tift (n=40) and Wilcox (n=20) counties were collected, surface sterilized with 0.1% bleach and used for total nucleic acid extractions using MagMAX 96 Viral RNA isolation kit (ThermoFisher Scientific, Waltham, MA, USA) following the manufacturer's instruction without DNase treatment. The potential introduction of WCLaV-1 and WCLaV-2 into Georgia was tested by reverse-transcription-polymerase chain reaction (RT-PCR) assay using specific primers targeting RNA-dependent-RNA polymerase (RdRp) and movement protein (MP) genes of both viruses (Hernandez et al., 2021). The expected amplicon sizes for RdRp (~900 nt) and MP (~500 nt) genes of WCLaV-1 located on RNA 1 and RNA 2 segements, respectively, were observed in 39 of 40 (97.5%) samples from Tift and seven of 20 (35%) samples from Wilcox. However, WCLaV-2 was not detected in any of the tested samples. All 60 samples also tested negative for the whitefly-transmitted viruses prevalent in the region, including cucurbit chlorotic yellows virus, cucurbit yellow stunting disorder virus, and cucurbit leaf crumple virus using virus-specific primers (Kavalappara et al., 2021). A subset of the samples analyzed by RT-PCR were also tested by SYBR green-based real-time RT-PCR assay targeting MP gene of WCLaV-1 using primers WCLaV-1FP (5'TCCACAAGCTTGATGGA- GGG3') and WCLaV-1RP (5'TCCCGAGTGAGGAAGCTAGT3'). The virus was detected in samples from both counties and the results matched with those obtained by the conventional RT-PCR assays (Suppl. Table 1). The presence of WCLaV-1 was further confirmed by sequencing (Genewiz, South Plainfield, NJ, USA) coupled with BLASTn analysis of amplicons resulted from the conventional RT-PCR from three randomly selected samples . The partial RdRp sequences (OL469153 to OL469155) were 99.3% and 99.9% identical to the corresponding sequences of WCLaV-1 isolates from China (KY781184) and Texas (MW559074) respectively. The partial MP sequences (OL469150 to OL469152) were 100% identical to those from China (KY781185) and Texas (MW559077). WCLaV-1 and WCLaV-2 were first discovered in Asia (Xin et al., 2017). Both viruses were subsequently reported from North and South Americas (Hendrick et al., 2021; Hernandez et al., 2021; Maeda et al., 2021), indicating their geographical expansion. Biological information, including vector relations, is unknown for both viruses and other members of the genus Coguvirus (family Phenuiviridae), to which they are provisionally assigned (Zhang et al., 2021). Further studies are also required to understand the biology and impact of both viruses on watermelon production and other crops, if any.
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Affiliation(s)
- Ismaila Adeyemi Adeleke
- University of Georgia College of Agricultural and Environmental Sciences - Tifton Campus, 117299, Department of Plant Pathology, Tifton, Georgia, United States;
| | - Saritha Raman Kavalappara
- University of Georgia College of Agricultural and Environmental Sciences - Tifton Campus, 117299, Department of Plant Pathology, Tifton, Georgia, United States;
| | - Ty Torrance
- University of Georgia College of Agricultural and Environmental Sciences, 96665, Agriculture & Natural Resources, Tifton, Georgia, United States;
| | - John Elec Bennett
- University of Georgia College of Agricultural and Environmental Sciences, 96665, Agriculture & Natural Resources, Rochelle, Georgia, United States;
| | - Cecilia McGregor
- University of Georgia College of Agricultural and Environmental Sciences, 96665, Department of Horticulture, Athens, Georgia, United States;
| | - Rajagopalbabu Srinivasan
- University of Georgia College of Agricultural and Environmental Sciences, 96665, Department of Entomology, Griffin , Georgia, United States;
| | - Sudeep Bag
- University of Georgia College of Agricultural and Environmental Sciences - Tifton Campus, 117299, Department of Plant Pathology, Tifton, Georgia, United States;
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12
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Hendricks KEM, Hernandez RN, Roberts PD, Isakeit T, Alabi OJ. First Report of watermelon crinkle leaf-associated virus 1 (WCLaV-1) and WCLaV-2 in Watermelon ( Citrullus lanatus) Plants Coinfected with Cucurbit chlorotic yellows virus in Florida. PLANT DISEASE 2022; 106:PDIS06211141PDN. [PMID: 34191533 DOI: 10.1094/pdis-06-21-1141-pdn] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Affiliation(s)
- Katherine E M Hendricks
- Department of Plant Pathology, University of Florida, Southwest Florida Research and Education Center, Immokalee, FL 34142
| | - Regina N Hernandez
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843
| | - Pamela D Roberts
- Department of Plant Pathology, University of Florida, Southwest Florida Research and Education Center, Immokalee, FL 34142
| | - Thomas Isakeit
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843
| | - Olufemi J Alabi
- Department of Plant Pathology and Microbiology, Texas A&M AgriLife Research and Extension Center, Weslaco, TX 78596
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13
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Duarte MA, Campos FS, Araújo Neto OF, Silva LA, Silva AB, Aguiar TC, Santos RN, Souza UJB, Alves GB, Melo FL, Ardisson-Araujo DMP, Aguiar RWS, Ribeiro BM. Identification of potential new mosquito-associated viruses of adult Aedes aegypti mosquitoes from Tocantins state, Brazil. Braz J Microbiol 2021; 53:51-62. [PMID: 34727360 DOI: 10.1007/s42770-021-00632-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 10/07/2021] [Indexed: 11/29/2022] Open
Abstract
Medically important arboviruses such as dengue virus (DENV), Zika virus (ZIKV), and chikungunya virus (CHIKV) are primarily transmitted by the globally distributed mosquito Aedes aegypti. Increasing evidence suggests that the transmission of some viruses can be influenced by mosquito-specific and mosquito-borne viruses. Advancements in high-throughput sequencing (HTS) and bioinformatics have expanded our knowledge on the richness of viruses harbored by mosquitoes. HTS was used to characterize the presence of virus sequences in wild-caught adult Ae. aegypti from Tocantins (TO) state, Brazil. Samples of mosquitoes were collected in four cities of Tocantins state and submitted to RNA isolation, followed by sequencing at an Illumina HiSeq platform. Our results showed initially by Krona the presence of 3% of the sequenced reads belonging to the viral database. After further analysis, the virus sequences were found to have homology to two viral families found in insects Phenuiviridae and Metaviridae. Three possible viral strains including putative new viruses were detected and named Phasi Charoen-like phasivirus isolate To-1 (PCLV To-1), Aedes aegypti To virus 1 (AAToV1), and Aedes aegypti To virus 2 (AAToV2). The results presented in this work contribute to the growing knowledge about the diversity of viruses in mosquitoes and might be useful for future studies on the interaction between insect-specific viruses and arboviruses.
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Affiliation(s)
- Matheus A Duarte
- Faculdade de Agronomia E Veterinária, Universidade de Brasília, Brasília, DF, 70.910-900, Brazil
| | - Fabrício S Campos
- Laboratório de Bioinformática E Biotecnologia, Universidade Federal Do Tocantins, Campus de Gurupi, Gurupi, TO, 77.402-970, Brazil.
| | - Osvaldo F Araújo Neto
- Laboratório de Bioinformática E Biotecnologia, Universidade Federal Do Tocantins, Campus de Gurupi, Gurupi, TO, 77.402-970, Brazil
| | - Leonardo A Silva
- Departamento de Biologia Celular, Instituto de Biologia, Universidade de Brasília, Brasília, DF, 70.910-900, Brazil
| | - Arthur B Silva
- Laboratório de Bioinformática E Biotecnologia, Universidade Federal Do Tocantins, Campus de Gurupi, Gurupi, TO, 77.402-970, Brazil
| | - Thalita C Aguiar
- Laboratório de Bioinformática E Biotecnologia, Universidade Federal Do Tocantins, Campus de Gurupi, Gurupi, TO, 77.402-970, Brazil
| | - Raissa N Santos
- Laboratório de Bioinformática E Biotecnologia, Universidade Federal Do Tocantins, Campus de Gurupi, Gurupi, TO, 77.402-970, Brazil
| | - Ueric J B Souza
- Laboratório de Bioinformática E Biotecnologia, Universidade Federal Do Tocantins, Campus de Gurupi, Gurupi, TO, 77.402-970, Brazil
| | - Giselly B Alves
- Laboratório de Biologia Molecular, Universidade Federal Do Tocantins, Campus de Gurupi, Gurupi, TO, 77.402-970, Brazil
| | - Fernando L Melo
- Departamento de Fitopatologia, Instituto de Biologia, Universidade de Brasília, Brasília, DF, 70.910-900, Brazil
| | - Daniel M P Ardisson-Araujo
- Laboratório de Virologia de Insetos, Universidade Federal de Santa Maria, Santa Maria, RS, 97.105-900, Brazil
| | - Raimundo W S Aguiar
- Laboratório de Biologia Molecular, Universidade Federal Do Tocantins, Campus de Gurupi, Gurupi, TO, 77.402-970, Brazil
| | - Bergmann M Ribeiro
- Departamento de Biologia Celular, Instituto de Biologia, Universidade de Brasília, Brasília, DF, 70.910-900, Brazil
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14
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Liu Z, Dong Z, Zhan B, Li S. Characterization of an Isolate of Citrus Concave Gum-Associated Virus from Apples in China and Development of an RT-RPA Assay for the Rapid Detection of the Virus. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112239. [PMID: 34834603 PMCID: PMC8621397 DOI: 10.3390/plants10112239] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/07/2021] [Accepted: 10/12/2021] [Indexed: 05/17/2023]
Abstract
Apple (Malus domestica) fruits exhibiting bright stripe symptoms were identified in Weihai City, Shandong Province, China. To investigate the virome in the apple samples, the method of high throughput sequencing (HTS) was used to identify the viruses. It was found that the sequence of citrus concave gum-associated virus (CCGaV) was involved in the apple transcriptome dataset. The full-length genome of the CCGaV-Weihai isolate contained two segments, the RNA1 was 6674 nt in size containing a conserved RNA-dependent RNA polymerase (RdRp), and the RNA2 was ambisense, 2706 nt in length, encoding a movement protein (MP) and a coat protein (CP). Sequence alignment and phylogenetic analyses indicated that CCGaV-Weihai was more closely related to CCGaV-H2799 isolated from the apple host in the United States and distantly related to CCGaV-CGW2 from Citrus sinensis in Italy, indicating a possibly geographical and host differentiation of CCGaV isolates. This was the first identification and characterization of CCGaV infecting apples in China. Additionally, a rapid and sensitive reverse transcription recombinase polymerase amplification (RT-RPA) assay technique was established for CCGaV detection in apple plants. The RT-RPA of CCGaV was not affected by other common viruses in apple plants and is about 10-fold more sensitive than the conventional reverse transcription polymerase chain reaction method, which can be used in large-scale testing.
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Affiliation(s)
- Zhen Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.L.); (Z.D.)
| | - Zhenfei Dong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.L.); (Z.D.)
- Department of Fruit Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Binhui Zhan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.L.); (Z.D.)
- Correspondence: (B.Z.); (S.L.)
| | - Shifang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.L.); (Z.D.)
- Correspondence: (B.Z.); (S.L.)
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15
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Zhang S, Tian X, Navarro B, Di Serio F, Cao M. Watermelon crinkle leaf-associated virus 1 and watermelon crinkle leaf-associated virus 2 have a bipartite genome with molecular signatures typical of the members of the genus Coguvirus (family Phenuiviridae). Arch Virol 2021; 166:2829-2834. [PMID: 34319452 DOI: 10.1007/s00705-021-05181-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 05/10/2021] [Indexed: 11/25/2022]
Abstract
Watermelon crinkle leaf-associated virus 1 and watermelon crinkle leaf-associated virus 2 (WCLaV-1 and WCLaV-2), two unclassified members of the order Bunyavirales, are phylogenetically related to members of the genus Coguvirus (family Phenuiviridae). The genome of both viruses was reported previously to be composed of three RNA segments. However, the terminal sequences of two genomic RNA segments, namely those encoding the putative movement protein (MP) and the nucleocapsid (NP) protein, remained undetermined. High-throughput sequencing of total RNA and small RNA preparations, combined with reverse transcription PCR amplification followed by sequencing, revealed that the WCLaV-1 and WCLaV-2 possess a bipartite genome consisting of a negative-sense RNA1, encoding the RNA-dependent RNA polymerase, and an ambisense RNA2, encoding the putative movement (MP) and nucleocapsid (NP) proteins. The two open reading frames of RNA2 are in opposite orientations and are separated by a long AU-rich intergenic region (IR) that may assume a hairpin conformation. RNA1 and RNA2 of both viruses share almost identical 5' and 3' termini, which are complementary to each other up to 20 nt. This genome organization is typical of members of the genus Coguvirus, with which WCLaV-1 and WCLaV-2 also share similar terminal 5' and 3' sequences of RNA1 and RNA2. These molecular features, together with phylogenetic reconstructions support the classification of WCLaV-1 and WCLaV2 as members of two new species in the genus Coguvirus.
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Affiliation(s)
- Song Zhang
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, 400712, China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, 400715, China
| | - Xin Tian
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, 400712, China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, 400715, China
| | - Beatriz Navarro
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, 70126, Bari, Italy
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, 70126, Bari, Italy.
| | - Mengji Cao
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, 400712, China.
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, 400715, China.
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16
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Neriya Y, Morikawa T, Hamamoto K, Noguchi K, Kobayashi T, Suzuki T, Nishigawa H, Natsuaki T. Characterization of tulip streak virus, a novel virus associated with the family Phenuiviridae. J Gen Virol 2021; 102. [PMID: 33226319 DOI: 10.1099/jgv.0.001525] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In Japan, tulip-growing areas have been plagued by viral diseases for decades, but the viruses causing the damage remain undescribed. In this study, Nicotiana benthamiana and Chenopodium quinoa plants mechanically inoculated with crude sap from a symptomatic tulip flower exhibited necrosis symptoms. Additionally, flexuous and filamentous virus particles were detected by electron microscopy analysis. Moreover, we determined the complete sequences of two genomic segments of the tulip streak virus (TuSV), which is a new virus associated with streaking symptoms, on the basis of a next-generation sequencing analysis. Homology analyses of the amino acid sequence of RNA-dependent RNA polymerase and the terminal sequence of the genomic RNA indicated that TuSV is associated with viruses in the family Phenuiviridae, but differs substantially from other reported viruses.
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Affiliation(s)
- Yutaro Neriya
- School of Agriculture, Utsunomiya University, Mine-machi 350, Utsunomiya, Tochigi 321-8505, Japan
| | - Toshiyuki Morikawa
- Toyama Prefectural Agricultural, Forestry and Fisheries Research Center, Yoshioka 1124-1, Toyama, Toyama 939-8153, Japan
| | - Kakeru Hamamoto
- School of Agriculture, Utsunomiya University, Mine-machi 350, Utsunomiya, Tochigi 321-8505, Japan
| | - Kengo Noguchi
- School of Agriculture, Utsunomiya University, Mine-machi 350, Utsunomiya, Tochigi 321-8505, Japan
| | - Tominari Kobayashi
- School of Agriculture, Utsunomiya University, Mine-machi 350, Utsunomiya, Tochigi 321-8505, Japan
| | - Tomohiro Suzuki
- Center for Bioscience Research and Education, Utsunomiya University, Mine-machi 350, Utsunomiya, Tochigi 321-8505, Japan
| | - Hisashi Nishigawa
- School of Agriculture, Utsunomiya University, Mine-machi 350, Utsunomiya, Tochigi 321-8505, Japan
| | - Tomohide Natsuaki
- School of Agriculture, Utsunomiya University, Mine-machi 350, Utsunomiya, Tochigi 321-8505, Japan
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17
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Abstract
Botrytis cinerea is one of the most important plant-pathogenic fungus. Products based on microorganisms can be used in biocontrol strategies alternative to chemical control, and mycoviruses have been explored as putative biological agents in such approaches. Here, we have explored the mycovirome of B. cinerea isolates from grapevine of Italy and Spain to increase the knowledge about mycoviral diversity and evolution, and to search for new widely distributed mycoviruses that could be active ingredients in biological products to control this hazardous fungus. A total of 248 B. cinerea field isolates were used for our metatranscriptomic study. Ninety-two mycoviruses were identified: 62 new mycoviral species constituting putative novel viral genera and families. Of these mycoviruses, 57 had a positive-sense single-stranded RNA (ssRNA) genome, 19 contained a double-stranded RNA (dsRNA) genome, 15 had a negative-sense ssRNA genome, and 1 contained a single-stranded DNA (ssDNA) genome. In general, ssRNA mycoviruses were widely distributed in all sampled regions, the ssDNA mycovirus was more frequently found in Spain, and dsRNA mycoviruses were scattered in some pools of both countries. Some of the identified mycoviruses belong to clades that have never been found associated with Botrytis species: Botrytis-infecting narnaviruses; alpha-like, umbra-like, and tymo-like ssRNA+ mycoviruses; trisegmented ssRNA- mycovirus; bisegmented and tetrasegmented dsRNA mycoviruses; and finally, an ssDNA mycovirus. Among the results obtained in this massive mycovirus screening, the discovery of novel bisegmented viruses, phylogenetically related to narnaviruses, is remarkable.IMPORTANCE The results obtained here have expanded our knowledge of mycoviral diversity, horizontal transfers, and putative cross-kingdom events. To date, this study presents the most extensive and wide diversity collection of mycoviruses infecting the necrotrophic fungus B. cinerea The collection included all types of mycoviruses, with dsRNA, ssRNA+, ssRNA-, and ssDNA genomes, most of which were discovered here, and some of which were previously reported as infecting B. cinerea or other plant-pathogenic fungi. Some of these mycoviruses are reported for the first time here associated with B. cinerea, as a trisegmented ssRNA- mycovirus and as an ssDNA mycovirus, but even more remarkablly, we also describe here four novel bisegmented viruses (binarnaviruses) not previously described in nature. The present findings significantly contribute to general knowledge in virology and more particularly in the field of mycovirology.
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18
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Chen Z, Anane RF, Wang Z, Gao L, Chen L, Li S, Wen G, Zhao M. Complete genome sequence analysis of a novel coguvirus isolated from Paris polyphylla var. yunnanensis. Arch Virol 2021; 166:2045-2050. [PMID: 33944994 DOI: 10.1007/s00705-021-05087-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/21/2021] [Indexed: 10/21/2022]
Abstract
A novel negative-stranded (ns) RNA virus tentatively named "Yunnan paris negative-stranded virus" (YPNSV), was isolated from Paris polyphylla var. yunnanensis plants exhibiting leaf chlorosis and mosaic symptoms in Yunnan. Its complete genome sequence was determined using Illumina and Sanger sequencing. YPNSV has a bipartite genome that consists of a negative-stranded (ns) RNA1 encoding the viral RNA-dependent RNA polymerase (RdRp, p251), an ambisense RNA2 coding for the putative movement protein (MP, p46) and nucleocapsid protein (NP, p39), with the two open reading frames separated by a long intergenic region that is rich in A and U. Sequence comparisons showed that the RdRp, MP, and NP of YPNSV are most similar to those of watermelon crinkle leaf-associated virus 2 (WCLaV-2), with 69.1%, 50.4%, and 60.9% amino acid sequence identity, respectively. Phylogenetic analysis based on deduced amino acid sequences of RdRp and NP showed that YPNSV clustered in a clade with coguviruses and that its closest known relative is WCLaV-2. Based on the above results, YPNSV should be regarded as a new member of genus Coguvirus, family Phenuiviridae.
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Affiliation(s)
- Zeli Chen
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China.,College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China.,Research and Development Center for Heath Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
| | - Rex Frimpong Anane
- CAS Center for Excellence in Animal Evolution and Genetics, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming, 650223, Yunnan, China.,State Key Laboratory for Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming, 650223, Yunnan, China
| | - Zhe Wang
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China.,Research and Development Center for Heath Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
| | - Like Gao
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China.,Research and Development Center for Heath Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
| | - Lu Chen
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China.,Research and Development Center for Heath Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
| | - Shangyun Li
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China.,College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China.,Research and Development Center for Heath Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
| | - Guosong Wen
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China.,College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China.,Research and Development Center for Heath Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China
| | - Mingfu Zhao
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China. .,Research and Development Center for Heath Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, 650201, Yunnan, China.
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19
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Tang L, Song L, Ye Z, Lin C, Wang B, Lin J, Gao C, Wang A. A novel negative-stranded RNA virus of the order Bunyavirales identified in Brassica campestris L. ssp. chinensis. Arch Virol 2021; 166:1525-1528. [PMID: 33721097 DOI: 10.1007/s00705-021-05031-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 01/24/2021] [Indexed: 02/07/2023]
Abstract
Here, we report the full-length genome sequence of a novel cogu-like virus identified in Brassica campestris L. ssp. Chinensis (B. campestris), an economically important vegetable in China. This virus, tentatively named "Brassica campestris chinensis coguvirus 1" (BCCoV1), has a bipartite genome that consists of two RNA molecules (RNA1 and RNA2). The negative-stranded (ns) RNA1 is 6757 nt in length, encoding the putative RNA-dependent RNA polymerase (RdRp), and the ambisense RNA2 is 3061 nt long, encoding the putative movement protein (MP) and nucleocapsid protein (NP). A homology search of the RdRp, MP, and NP showed that they are closely related to five other recently discovered negative-stranded RNA (nsRNA) viruses infecting plants, belonging to the new genus Coguvirus. Phylogenetic analysis of the 252-kDa RdRp confirmed the classification of this virus, showing that BCCoV1 possibly belongs to the genus Coguvirus, family Phenuiviridae, order Bunyavirales. The present study improves our understanding of the viral diversity in B. campestris and the evolution of nsRNA viruses.
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Affiliation(s)
- Liguang Tang
- Wuhan Vegetable Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei Province, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Liping Song
- Wuhan Vegetable Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei Province, China
| | - Zhibiao Ye
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Chufa Lin
- Wuhan Vegetable Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei Province, China
| | - Bincai Wang
- Wuhan Vegetable Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei Province, China
| | - Jiazao Lin
- Wuhan Vegetable Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei Province, China
| | - Changbin Gao
- Wuhan Vegetable Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei Province, China
| | - Aihua Wang
- Wuhan Vegetable Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei Province, China.
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20
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Hernandez RN, Isakeit T, Al Rwahnih M, Villegas C, Alabi OJ. First report of watermelon crinkle leaf-associated virus 1 (WCLaV-1) and WCLaV-2 infecting watermelon ( Citrullus lanatus) in the United States. PLANT DISEASE 2021; 105:2025. [PMID: 33630684 DOI: 10.1094/pdis-02-21-0249-pdn] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Watermelon (Citrullus lanatus) and other cucurbits are cultivated globally, and Texas ranks among its top 5 producers in the U.S. In July 2020, plants with virus-like disease symptoms consisting of mild leaf crinkling and yellow mosaic patterns were observed in a 174-ha watermelon field in Burleson Co., TX; disease incidence was visually estimated at 5%. Total nucleic acids were extracted from leaf tissues of 5 randomly sampled plants (Dellaporta 1983) and their equimolar amounts were made into a composite sample that was used for cDNA library construction with TruSeq Stranded Total RNA with Ribo-Zero Plant Kit (Illumina). The cDNA library was sequenced on the Illumina NextSeq 500 platform, generating ~37M single-end reads (each 75 nt), which were analyzed as per Al Rwahnih et al. (2018). Of these, 58,200 and 27,500 reads mapped to the genomes of watermelon crinkle leaf-associated virus 1 (WCLaV-1) and WCLaV-2 (Xin et al. 2017), respectively, along with 4 other virus-specific reads (data not shown). The near complete RNA1-RNA3 segments of WCLaV-1 (354-652X) and WCLaV-2 (144-258X) were generated from the mapped reads and they shared ≥96% nt identities with published RNA segments of both viruses. The results were verified by RT-PCR using newly designed primers WCLaV-1vRP: 5'-GGTGAGTTAGTGTGTCTGAAGG/WCLaV-1cRP: 5'-GAGGTTGCCTGAGGTGATAAG to target 881 bp of the RNA1-encoded RNA-dependent RNA polymerase (RdRP), WCLaV-1vMP: 5'-GAAGGTTTGCTCCCTTGAAATG/WCLaV-1cMP: 5'-GACTGTGGCTGAAGAGTCTATG target 538 bp of the RNA2-encoded movement protein (MP), and WCLaV-1vNP: 5'-CGAATAGACTCTGGAGGGTAGA/WCLaV-1cMP: 5'-GAAAGCAAGAAAGCTGGCTAAA target 786 bp of the RNA3-encoded nucleoprotein (NP). Similarly, the WWCLaV-2-specific primers WCLaV-2vRP: 5'-GTCTCACATTCCTGCACTAACT/WCLaV-2cRP: 5'-ATCGGTCCTGGGTTATTTGTATC target 968 bp of the RdRP, WCLaV-2vMP: 5'-GACTTCAGAACCTCAACATCCA/WCLaV-2cMP: 5'-CAAGGGAGAGTGCTGACAAA target 562 bp of the MP, and WCLaV-2vNP: 5'-ATTCCCAGTGAGAGCAACAA/WCLaV-2cMP: 5'-GAGGTGGAGGTAGGAAAGAAAG target 449 bp of the NP. Fresh cDNA synthesized from the 5 samples with PrimeScript First Strand cDNA synthesis kit (Takara Bio) were tested by PCR with all 6 primer pairs using the PrimeSTAR GXL DNA Polymerase kit (Takara Bio). Three of the 5 samples were positive for both viruses and one sample was positive for each virus. The obtained products from 4 samples were cloned individually into pJET1.2/Blunt vector (Thermo Scientific, USA), followed by bidirectional Sanger-sequencing of the plasmids with the GenElute Five-Minute Plasmid Miniprep kit (Sigma-Aldrich). In pairwise comparisons, the partial RNA1-RNA3 sequences of WCLaV-1 (GenBank accession nos. MW559074-82) shared 100% nt/aa identities with each other and with corresponding sequences of WCLaV-1 isolate KF-1 from China (KY781184-86). The partial RNA1-RNA3 sequences of WCLaV-2 (MW559083-91) shared 97-100% nt/96-100% aa identities with each other and with corresponding sequences of WCLaV-2 isolate KF-15 from China (KY781187-89). This is the first report of WCLaV-1 and WCLaV-2 in Texas and the first record of both viruses in the U.S. and elsewhere outside of China. Both negative-sense, single-stranded RNA viruses represent a novel taxon in the family Phenuiviridae (order Bunyavirales) (Xin et al. 2017). While aspects of the biology of both viruses are yet to be elucidated, our results expand their geographical range. The detection primers developed here will be useful for screening cucurbits germplasm to avert their spread.
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Affiliation(s)
- Regina Nicole Hernandez
- Texas A&M University College Station, 14736, Department of Plant Pathology & Microbiology, College Station, Texas, United States;
| | - Thomas Isakeit
- 2132 TAMUCollege Station, Texas, United States, 77843-2132;
| | - Maher Al Rwahnih
- University of California, Dept. of Plant Pathology, One Shields Avenue, Davis, California, United States, 95616;
| | - Cecilia Villegas
- Texas A&M AgriLife Research and Extension Center, Department of Plant Pathology & Microbiology, Weslaco, Texas, United States;
| | - Olufemi Joseph Alabi
- Texas A&M University, Department of Plant Pathology & Microbiology, 2401 E. Bus. Hwy. 83, Weslaco, Texas, United States, 78596
- United States;
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21
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Zhang S, Huang A, Zhou X, Li Z, Dietzgen RG, Zhou C, Cao M. Natural Defect of a Plant Rhabdovirus Glycoprotein Gene: A Case Study of Virus-Plant Coevolution. PHYTOPATHOLOGY 2021; 111:227-236. [PMID: 32648524 DOI: 10.1094/phyto-05-20-0191-fi] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Seven isolates of a putative cytorhabdovirus (family Rhabdoviridae, order Mononegavirales) designated as citrus-associated rhabdovirus (CiaRV) were identified in citrus, passion fruit, and paper bush from the same geographical area in China. CiaRV, bean-associated cytorhabdovirus (Brazil), and papaya virus E (Ecuador) should be taxonomically classified in the species Papaya cytorhabdovirus. Due to natural mutations, the glycoprotein (G) and P4 genes were impaired in citrus-infecting isolates of CiaRV, resulting in an atypical rhabdovirus genome organization of 3' leader-N-P-P3-M-L-5' trailer. The P3 protein of CiaRV shared a common origin with begomoviral movement proteins (family Geminiviridae). Secondary structure analysis and trans-complementation of movement-deficient tomato mosaic virus and potato virus X mutants by CiaRV P3 supported its function in viral cell-to-cell trafficking. The wide geographical dispersal of CiaRV and related viruses suggests an efficient transmission mechanism, as well as an underlying risk to global agriculture. Both the natural phenomenon and experimental analyses demonstrated presence of the "degraded" type of CiaRV in citrus, in parallel to "undegraded" types in other host plant species. This case study shows a plant virus losing the function of an important but nonessential gene, likely due to host shift and adaption, which deepened our understanding of course of natural viral diversification.
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Affiliation(s)
- Song Zhang
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing 400712, China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Aijun Huang
- National Navel Orange Research Center, College of Life Science, Gannan Normal University, Ganzhou, China
| | - Xin Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhenghe Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Changyong Zhou
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing 400712, China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Mengji Cao
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing 400712, China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
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22
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Liu H, Wang G, Yang Z, Wang Y, Zhang Z, Li L, Waqas M, Hong N, Liu H, Wang G, Hong N, Hong J, Zhang J, Xu L, Qi L. Identification and Characterization of a Pear Chlorotic Leaf Spot-Associated Virus, a Novel Emaravirus Associated with a Severe Disease of Pear Trees in China. PLANT DISEASE 2020; 104:2786-2798. [PMID: 32997610 DOI: 10.1094/pdis-01-20-0040-re] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Pear chlorotic leaf spot (PCLS) is a recently emerged disease of commercially cultivated sandy pear (Pyrus pyrifolia) trees in central and southern China. By integrating high-throughput sequencing and conventional Sanger sequencing of reverse-transcription (RT)-PCR products, a novel emaravirus infecting pear trees was identified and molecularly characterized. The virus was provisionally named pear chlorotic leaf spot-associated virus (PCLSaV). PCLSaV shows the typical molecular features of members of the genus Emaravirus in the family Fimoviridae. It has a genome composed of at least five negative-sense RNA segments, with each containing a single open reading frame and two complementary 13-nucleotide stretches at the 5' and 3' termini. PCLSaV shows a close phylogenetic relationship with recognized emaraviruses but forms a separate clade. Moreover, double-membrane-bound bodies were observed in PCLSaV-infected tissues and in extracts of PCLSaV-infected leaves. For the first time, our study revealed the profile distribution of viral RNA reads from the RNA-seq libraries of three samples along the RNA1 to RNA5 of an emaravirus. Field surveys combined with specific RT-PCR assays revealed the presence of PCLSaV in almost all PCLS-diseased pear samples, strongly supporting the association of the virus with the PCLS disease. This study revealed the first emaravirus infecting pear trees and its association with a severe pear chlorotic leaf disease.
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Affiliation(s)
- Huazhen Liu
- Key Lab of Crop Disease Monitoring and Safety Control in Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Guoping Wang
- Key Lab of Crop Disease Monitoring and Safety Control in Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Zuokun Yang
- Key Lab of Crop Disease Monitoring and Safety Control in Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yanxiang Wang
- Key Lab of Crop Disease Monitoring and Safety Control in Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Zhe Zhang
- Key Lab of Crop Disease Monitoring and Safety Control in Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Longhui Li
- Key Lab of Crop Disease Monitoring and Safety Control in Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Muhammad Waqas
- Key Lab of Crop Disease Monitoring and Safety Control in Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Ni Hong
- Key Lab of Crop Disease Monitoring and Safety Control in Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Huazhen Liu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Guoping Wang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Ni Hong
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Jian Hong
- Analysis Center of Agrobiology and Environmental Sciences, Zhejiang University, Hangzhou, Zhejiang 317502, China
| | - Jinguo Zhang
- National Sand Pear Germplasm Repository in Wuchang, Research Institute of Fruit and Tea, Hubei Academy of Agricultural Science, Wuhan, Hubei 430064, China
| | - Lei Xu
- Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi 330200, China
| | - Liying Qi
- Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi 330200, China
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23
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Bejerman N, Debat H, Dietzgen RG. The Plant Negative-Sense RNA Virosphere: Virus Discovery Through New Eyes. Front Microbiol 2020; 11:588427. [PMID: 33042103 PMCID: PMC7524893 DOI: 10.3389/fmicb.2020.588427] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 08/27/2020] [Indexed: 12/21/2022] Open
Abstract
The use of high-throughput sequencing (HTS) for virus diagnostics, as well as the importance of this technology as a valuable tool for discovery of novel viruses has been extensively investigated. In this review, we consider the application of HTS approaches to uncover novel plant viruses with a focus on the negative-sense, single-stranded RNA virosphere. Plant viruses with negative-sense and ambisense RNA (NSR) genomes belong to several taxonomic families, including Rhabdoviridae, Aspiviridae, Fimoviridae, Tospoviridae, and Phenuiviridae. They include both emergent pathogens that infect a wide range of plant species, and potential endophytes which appear not to induce any visible symptoms. As a consequence of biased sampling based on a narrow focus on crops with disease symptoms, the number of NSR plant viruses identified so far represents only a fraction of this type of viruses present in the virosphere. Detection and molecular characterization of NSR viruses has often been challenging, but the widespread implementation of HTS has facilitated not only the identification but also the characterization of the genomic sequences of at least 70 NSR plant viruses in the last 7 years. Moreover, continuing advances in HTS technologies and bioinformatic pipelines, concomitant with a significant cost reduction has led to its use as a routine method of choice, supporting the foundations of a diverse array of novel applications such as quarantine analysis of traded plant materials and genetic resources, virus detection in insect vectors, analysis of virus communities in individual plants, and assessment of virus evolution through ecogenomics, among others. The insights from these advancements are shedding new light on the extensive diversity of NSR plant viruses and their complex evolution, and provide an essential framework for improved taxonomic classification of plant NSR viruses as part of the realm Riboviria. Thus, HTS-based methods for virus discovery, our ‘new eyes,’ are unraveling in real time the richness and magnitude of the plant RNA virosphere.
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Affiliation(s)
- Nicolás Bejerman
- Instituto de Patología Vegetal - Centro de Investigaciones Agropecuarias - Instituto Nacional de Tecnología Agropecuaria, Córdoba, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Unidad de Fitopatología y Modelización Agrícola, Buenos Aires, Argentina
| | - Humberto Debat
- Instituto de Patología Vegetal - Centro de Investigaciones Agropecuarias - Instituto Nacional de Tecnología Agropecuaria, Córdoba, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Unidad de Fitopatología y Modelización Agrícola, Buenos Aires, Argentina
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
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24
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Herath V, Romay G, Urrutia CD, Verchot J. Family Level Phylogenies Reveal Relationships of Plant Viruses within the Order Bunyavirales. Viruses 2020; 12:v12091010. [PMID: 32927652 PMCID: PMC7551631 DOI: 10.3390/v12091010] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/03/2020] [Accepted: 09/08/2020] [Indexed: 12/14/2022] Open
Abstract
Bunyavirales are negative-sense segmented RNA viruses infecting arthropods, protozoans, plants, and animals. This study examines the phylogenetic relationships of plant viruses within this order, many of which are recently classified species. Comprehensive phylogenetic analyses of the viral RNA dependent RNA polymerase (RdRp), precursor glycoprotein (preGP), the nucleocapsid (N) proteins point toward common progenitor viruses. The RdRp of Fimoviridae and Tospoviridae show a close evolutional relationship while the preGP of Fimoviridae and Phenuiviridae show a closed relationship. The N proteins of Fimoviridae were closer to the Phasmaviridae, the Tospoviridae were close to some Phenuiviridae members and the Peribunyaviridae. The plant viral movement proteins of species within the Tospoviridae and Phenuiviridae were more closely related to each other than to members of the Fimoviridae. Interestingly, distal ends of 3′ and 5′ untranslated regions of species within the Fimoviridae shared similarity to arthropod and vertebrate infecting members of the Cruliviridae and Peribunyaviridae compared to other plant virus families. Co-phylogeny analysis of the plant infecting viruses indicates that duplication and host switching were more common than co-divergence with a host species.
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Affiliation(s)
- Venura Herath
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX 77802, USA; (V.H.); (G.R.); (C.D.U.)
- Department of Agriculture Biology, Faculty of Agriculture, University of Peradeniya, Peradeniya 20400, Sri Lanka
| | - Gustavo Romay
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX 77802, USA; (V.H.); (G.R.); (C.D.U.)
| | - Cesar D. Urrutia
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX 77802, USA; (V.H.); (G.R.); (C.D.U.)
| | - Jeanmarie Verchot
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX 77802, USA; (V.H.); (G.R.); (C.D.U.)
- Correspondence: ; Tel.: +1-979-845-1788
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25
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Two New Putative Plant Viruses from Wood Metagenomics Analysis of an Esca Diseased Vineyard. PLANTS 2020; 9:plants9070835. [PMID: 32635154 PMCID: PMC7412230 DOI: 10.3390/plants9070835] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/02/2020] [Accepted: 07/02/2020] [Indexed: 12/19/2022]
Abstract
The concept of plant as a holobiont is now spreading among the scientific community and the importance to study plant-associated microorganisms is becoming more and more necessary. Along with bacteria and fungi, also viruses can play important roles during the holobiont-environment interactions. In grapevine, viruses are studied mainly as pathological agents, and many species (more than 80) are known to be able to replicate inside its tissues. In this study two new viral species associated with grape wood tissues are presented, one belongs to the Potyviridae family and one to the Bunyavirales order. Due to the ability of potyviruses to enhance heterologous virus replication, it will be important to assess the presence of such a virus in the grapevine population to understand its ecological role. Furthermore, the association of the cogu-like virus with esca symptomatic samples opens new questions and the necessity of a more detailed characterization of this virus.
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26
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Cao M, Zhang S, Li M, Liu Y, Dong P, Li S, Kuang M, Li R, Zhou Y. Discovery of Four Novel Viruses Associated with Flower Yellowing Disease of Green Sichuan Pepper ( Zanthoxylum Armatum) by Virome Analysis. Viruses 2019; 11:v11080696. [PMID: 31370205 PMCID: PMC6723833 DOI: 10.3390/v11080696] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 07/28/2019] [Accepted: 07/28/2019] [Indexed: 01/21/2023] Open
Abstract
An emerging virus-like flower yellowing disease (FYD) of green Sichuan pepper (Zanthoxylum armatum v. novemfolius) has been recently reported. Four new RNA viruses were discovered in the FYD-affected plant by the virome analysis using high-throughput sequencing of transcriptome and small RNAs. The complete genomes were determined, and based on the sequence and phylogenetic analysis, they are considered to be new members of the genera Nepovirus (Secoviridae), Idaeovirus (unassigned), Enamovirus (Luteoviridae), and Nucleorhabdovirus (Rhabdoviridae), respectively. Therefore, the tentative names corresponding to these viruses are green Sichuan pepper-nepovirus (GSPNeV), -idaeovirus (GSPIV), -enamovirus (GSPEV), and -nucleorhabdovirus (GSPNuV). The viral population analysis showed that GSPNeV and GSPIV were dominant in the virome. The small RNA profiles of these viruses are in accordance with the typical virus-plant interaction model for Arabidopsis thaliana. Rapid and sensitive RT-PCR assays were developed for viral detection, and used to access the geographical distributions. The results revealed a correlation between GSPNeV and the FYD. The viruses pose potential threats to the normal production of green Sichuan pepper in the affected areas due to their natural transmission and wide spread in fields. Collectively, our results provide useful information regarding taxonomy, transmission and pathogenicity of the viruses as well as management of the FYD.
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Affiliation(s)
- Mengji Cao
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China.
| | - Song Zhang
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Min Li
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Yingjie Liu
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Peng Dong
- Chongqing Agricultural Technology Extension Station, Chongqing 401121, China
| | - Shanrong Li
- Chongqing Agricultural Technology Extension Station, Chongqing 401121, China
| | - Mi Kuang
- Chongqing Agricultural Technology Extension Station, Chongqing 401121, China
| | - Ruhui Li
- USDA-ARS, National Germplasm Resources Laboratory, Beltsville, MD 20705, USA
| | - Yan Zhou
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China.
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27
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Two Novel Negative-Sense RNA Viruses Infecting Grapevine Are Members of a Newly Proposed Genus within the Family Phenuiviridae. Viruses 2019; 11:v11080685. [PMID: 31357479 PMCID: PMC6724010 DOI: 10.3390/v11080685] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 07/23/2019] [Accepted: 07/24/2019] [Indexed: 11/17/2022] Open
Abstract
Two novel negative-stranded (ns)RNA viruses were identified by high throughput sequencing in grapevine. The genomes of both viruses, named grapevine Muscat rose virus (GMRV) and grapevine Garan dmak virus (GGDV), comprise three segments with each containing a unique gene. Based on sequence identity and presence of typical domains/motifs, the proteins encoded by the two viruses were predicted to be: RNA-dependent RNA polymerase (RdRp), nucleocapsid protein (NP), and putative movement protein (MP). These proteins showed the highest identities with orthologs in the recently discovered apple rubbery wood viruses 1 and 2, members of a tentative genus (Rubodvirus) within the family Phenuiviridae. The three segments of GMRV and GGDV share almost identical sequences at their 5' and 3' termini, which are also complementary to each other and may form a panhandle structure. Phylogenetics based on RdRp, NP and MP placed GMRV and GGDV in the same cluster with rubodviruses. Grapevine collections were screened for the presence of both novel viruses via RT-PCR, identifying infected plants. GMRV and GGDV were successfully graft-transmitted, thus, they are the first nsRNA viruses identified and transmitted in grapevine. Lastly, different evolutionary scenarios of nsRNA viruses are discussed.
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28
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Grandjean F, Gilbert C, Razafimafondy F, Vucić M, Delaunay C, Gindre P, Bouchard J, Raimond M, Moumen B. A new bunya-like virus associated with mass mortality of white-clawed crayfish in the wild. Virology 2019; 533:115-124. [DOI: 10.1016/j.virol.2019.05.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 05/12/2019] [Accepted: 05/23/2019] [Indexed: 01/22/2023]
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29
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Wylie SJ, Tran TT, Nguyen DQ, Koh SH, Chakraborty A, Xu W, Jones MGK, Li H. A virome from ornamental flowers in an Australian rural town. Arch Virol 2019; 164:2255-2263. [PMID: 31183556 DOI: 10.1007/s00705-019-04317-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 05/18/2019] [Indexed: 11/25/2022]
Abstract
Samples of leaves exhibiting symptoms resembling those caused by virus infection were collected from ornamental street flowers in a rural town in Western Australia. Thirty-seven leaf samples were collected from plants of iris, tulip, lily, daffodil, stock and grape hyacinth. Shotgun sequencing of cDNA derived from leaf samples was done, and analysis showed that about 6% of the sequences obtained were of viral origin. Assembly of virus-like sequences revealed complete or partial genome sequences of 13 virus isolates representing 11 virus species. Eight of the isolates were of potyviruses, one was of a macluravirus, three were of potexviruses, and one was of a bunya-like virus. The complete genome of an isolate originally classified as ornithogalum mosaic virus was genetically divergent and differed in polyprotein cleavage motifs, and we propose that this isolate represents a distinct species. The implications of importing to Australia live plant propagules infected with viruses are discussed.
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Affiliation(s)
- S J Wylie
- Plant Biotechnology Research Group-Virology, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, 6150, Australia.
| | - T T Tran
- Plant Biotechnology Research Group-Virology, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, 6150, Australia
| | - D Q Nguyen
- Plant Biotechnology Research Group-Virology, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, 6150, Australia
| | - S-H Koh
- Plant Biotechnology Research Group-Virology, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, 6150, Australia
| | - A Chakraborty
- Plant Biotechnology Research Group-Virology, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, 6150, Australia
| | - W Xu
- Plant Biotechnology Research Group-Virology, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, 6150, Australia
- Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - M G K Jones
- Plant Biotechnology Research Group-Virology, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, 6150, Australia
| | - H Li
- Plant Biotechnology Research Group-Virology, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, 6150, Australia
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30
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Lin YH, Fujita M, Chiba S, Hyodo K, Andika IB, Suzuki N, Kondo H. Two novel fungal negative-strand RNA viruses related to mymonaviruses and phenuiviruses in the shiitake mushroom (Lentinula edodes). Virology 2019; 533:125-136. [PMID: 31153047 DOI: 10.1016/j.virol.2019.05.008] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/21/2019] [Accepted: 05/19/2019] [Indexed: 02/04/2023]
Abstract
There is still limited information on the diversity of (-)ssRNA viruses that infect fungi. Here, we have discovered two novel (-)ssRNA mycoviruses in the shiitake mushroom (Lentinula edodes). The first virus has a monopartite RNA genome and relates to that of mymonaviruses (Mononegavirales), especially to Hubei rhabdo-like virus 4 from arthropods and thus designated as Lentinula edodes negative-strand RNA virus 1. The second virus has a putative bipartite RNA genome and is related to the recently discovered bipartite or tripartite phenui-like viruses (Bunyavirales) associated with plants and ticks, and designated as Lentinula edodes negative-strand RNA virus 2 (LeNSRV2). LeNSRV2 is likely the first segmented (-)ssRNA virus known to infect fungi. Its smaller RNA segment encodes a putative nucleocapsid and a plant MP-like protein using a potential ambisense coding strategy. These findings enhance our understanding of the diversity, evolution and spread of (-)ssRNA viruses in fungi.
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Affiliation(s)
- Yu-Hsin Lin
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan
| | - Miki Fujita
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan
| | - Sotaro Chiba
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan; Asian Satellite Campuses Institute, Nagoya University, Nagoya 464-8601, Japan
| | - Kiwamu Hyodo
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan
| | - Ida Bagus Andika
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan
| | - Hideki Kondo
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan.
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31
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Velasco L, Arjona-Girona I, Cretazzo E, López-Herrera C. Viromes in Xylariaceae fungi infecting avocado in Spain. Virology 2019; 532:11-21. [PMID: 30986551 DOI: 10.1016/j.virol.2019.03.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 03/29/2019] [Accepted: 03/29/2019] [Indexed: 12/25/2022]
Abstract
Four isolates of Entoleuca sp., family Xylariaceae, Ascomycota, recovered from avocado rhizosphere in Spain were analyzed for mycoviruses presence. For that, the dsRNAs from the mycelia were extracted and subjected to metagenomics analysis that revealed the presence of eleven viruses putatively belonging to families Partitiviridae, Hypoviridae, Megabirnaviridae, and orders Tymovirales and Bunyavirales, in addition to one ourmia-like virus plus other two unclassified virus species. Moreover, a sequence with 98% nucleotide identity to plant endornavirus Phaseolus vulgaris alphaendornavirus 1 has been identified in the Entoleuca sp. isolates. Concerning the virome composition, the four isolates only differed in the presence of the bunyavirus and the ourmia-like virus, while all other viruses showed common patterns. Specific primers allowed the detection by RT-PCR of these viruses in a collection of Entoleuca sp. and Rosellinia necatrix isolates obtained from roots of avocado trees. Results indicate that intra- and interspecies horizontal virus transmission occur frequently in this pathosystem.
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Affiliation(s)
- Leonardo Velasco
- Instituto Andaluz de Investigación y Formación Agraria (IFAPA), 29140, Churriana, Málaga, Spain.
| | - Isabel Arjona-Girona
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, C.S.I.C, Córdoba, Spain
| | - Enrico Cretazzo
- Instituto Andaluz de Investigación y Formación Agraria (IFAPA), 29140, Churriana, Málaga, Spain
| | - Carlos López-Herrera
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, C.S.I.C, Córdoba, Spain
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32
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Navarro B, Zicca S, Minutolo M, Saponari M, Alioto D, Di Serio F. A Negative-Stranded RNA Virus Infecting Citrus Trees: The Second Member of a New Genus Within the Order Bunyavirales. Front Microbiol 2018; 9:2340. [PMID: 30333811 PMCID: PMC6176071 DOI: 10.3389/fmicb.2018.02340] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 09/12/2018] [Indexed: 11/13/2022] Open
Abstract
A new RNA virus has been identified from a sweet orange tree in southern Italy. This virus, tentatively named citrus virus A (CiVA), has a bipartite genome composed of (i) a negative-stranded (ns) RNA1, encoding the viral RNA-dependent RNA polymerase (RdRp), and (ii) an ambisense RNA2, coding for the putative movement protein (MP) and nucleocapsid protein (NP), with the two open reading frames separated by a long AU-rich intergenic region (IR) adopting a hairpin conformation. CiVA genomic RNAs and the encoded proteins resemble those of the recently discovered citrus concave gum-associated virus (CCGaV). This CCGaV, a nsRNA virus associated with the ancient citrus concave gum disease, has been proposed as the representative member of a new genus tentatively named Coguvirus. Molecular and phylogenetic analyses presented here support the classification of CiVA, and likely of other two recently described nsRNA viruses infecting plants, in this new genus. By showing that the evolutionary origin of the MP of all the putative coguviruses likely differs from that of their respective RdRp and NP, this study also provides evidence of a likely modular genome evolution for these viruses. Moreover, phylogenetic data support the proposal that, during the evolutionary history of nsRNA viruses, the plant-infecting viruses most likely emerged from an invertebrate-infecting ancestor several times as independent events. CiVA was identified in a field sweet orange tree not showing any obvious symptom and was graft-transmitted to sweet orange, grapefruit, rough lemon and Dweet tangor indicator plants that did not developed symptoms. The capacity of infecting citrus hosts of several species was also confirmed by a preliminary survey that identified orange, mandarin, clementine and lemon trees as natural hosts of CiVA in several fields of southern Italy, again without any obvious association with specific symptoms.
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Affiliation(s)
- Beatriz Navarro
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Stefania Zicca
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Maria Minutolo
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II, Portici, Italy
| | - Maria Saponari
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Daniela Alioto
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II, Portici, Italy
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
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Wright AA, Szostek SA, Beaver-Kanuya E, Harper SJ. Diversity of three bunya-like viruses infecting apple. Arch Virol 2018; 163:3339-3343. [PMID: 30132135 DOI: 10.1007/s00705-018-3999-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 08/01/2018] [Indexed: 11/29/2022]
Abstract
High-throughput sequencing of two trees with apple decline revealed the presence of three bunya-like viruses: apple rubbery wood-associated viruses 1 and 2 (ARWaV-1, ARWaV-2) and citrus concave gum-associated virus (CCGaV), which previously had only been observed in citrus trees. The apple and citrus CCGaV isolates shared over 97% sequence identity. A global collection of apple trees was screened by RT-PCR for these viruses. Twenty-seven of 30 trees were infected with one or more bunya-like virus. Sequence data revealed some diversity among isolates but no geographic grouping. Additional work will be needed to determine if any of these viruses contribute to apple decline.
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Affiliation(s)
- A A Wright
- Department of Plant Pathology, Washington State University, Prosser, WA, USA.
| | - S A Szostek
- Department of Plant Pathology, Washington State University, Prosser, WA, USA
| | - E Beaver-Kanuya
- Department of Plant Pathology, Washington State University, Prosser, WA, USA
| | - S J Harper
- Department of Plant Pathology, Washington State University, Prosser, WA, USA
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Sogatella furcifera hepe-like virus: First member of a novel Hepeviridae clade identified in an insect. Virus Res 2018; 250:81-86. [PMID: 29605729 DOI: 10.1016/j.virusres.2018.03.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 03/27/2018] [Accepted: 03/28/2018] [Indexed: 11/22/2022]
Abstract
A novel virus was identified in the white-backed planthopper (Sogatella furcifera, Hemiptera: Delphacidae) and tentatively named Sogatella furcifera hepe-like virus (SfHeV). Its genome is a linear, single-stranded monopartite RNA, 7,312 nucleotides (nt) long with a 66-nt 5' UTR, 54-nt 3' UTR, and 28-nt polyA, showing typical genomic features of viruses in the family Hepeviridae, but highly divergent from known members in the family, with amino acid sequence identities of only 18.9-23% (ORF1), 13.1-18.8% (ORF2) and 1.9-11% (ORF3). Phylogenetic analysis revealed that SfHeV was closer to cutthroat trout virus (CTV), but did not cluster with any members of the family. SfHeV is the first hepe-like virus identified in a hemipteran insect and was detected in all developmental stages suggesting the presence of some level of vertical transmission. On the basis of these data, we propose that SfHeV represents a novel clade in the family Hepeviridae and tentatively name the genus Insecthepevirus.
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Zhang P, Liu W, Cao M, Massart S, Wang X. Two novel totiviruses in the white-backed planthopper, Sogatella furcifera. J Gen Virol 2018; 99:710-716. [PMID: 29580322 DOI: 10.1099/jgv.0.001052] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
There is little information about commensal viruses in the white-backed planthopper, Sogatella furcifera, although it is an important agricultural insect. Here, two novel double-stranded RNA viruses related to the viruses in the family Totiviridae were identified using next-generation sequencing and tentatively named Sogatella furcifera totivirus 1 and 2 (SfTV1 and SfTV2). Their complete genomes consist of 6310 and 6303 nt, respectively, showing typical genomic features with viruses in the family Totiviridae. Identity, phylogenetic and conserved sequence analyses showed that SfTV1, SfTV2 and three other insect viruses may form a proposed novel genus of the family Totiviridae. Vertical transmission of the two viruses was highly efficient, and they were detected in all insect tissues and developmental stages, with the highest titres in the adult and in the haemolymph and reproductive organs. To our knowledge, this is the first report of viruses in the family Totiviridae found in a hemipteran insect.
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Affiliation(s)
- Peipei Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China.,Laboratory of Phytopathology, University of Liège, Gembloux Agro-BioTech, Passage des déportés, 2, 5030 Gembloux, Belgium
| | - Wenwen Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Mengji Cao
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, PR China
| | - Sebastien Massart
- Laboratory of Phytopathology, University of Liège, Gembloux Agro-BioTech, Passage des déportés, 2, 5030 Gembloux, Belgium
| | - Xifeng Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
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Identification of Novel Viruses in Amblyomma americanum, Dermacentor variabilis, and Ixodes scapularis Ticks. mSphere 2018; 3:mSphere00614-17. [PMID: 29564401 PMCID: PMC5853492 DOI: 10.1128/msphere.00614-17] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 01/29/2018] [Indexed: 12/21/2022] Open
Abstract
Ticks carry a wide range of known human and animal pathogens and are postulated to carry others with the potential to cause disease. Here we report a discovery effort wherein unbiased high-throughput sequencing was used to characterize the virome of 2,021 ticks, including Ixodes scapularis (n = 1,138), Amblyomma americanum (n = 720), and Dermacentor variabilis (n = 163), collected in New York, Connecticut, and Virginia in 2015 and 2016. We identified 33 viruses, including 24 putative novel viral species. The most frequently detected viruses were phylogenetically related to members of the Bunyaviridae and Rhabdoviridae families, as well as the recently proposed Chuviridae. Our work expands our understanding of tick viromes and underscores the high viral diversity that is present in ticks. IMPORTANCE The incidence of tick-borne disease is increasing, driven by rapid geographical expansion of ticks and the discovery of new tick-associated pathogens. The examination of the tick microbiome is essential in order to understand the relationship between microbes and their tick hosts and to facilitate the identification of new tick-borne pathogens. Genomic analyses using unbiased high-throughput sequencing platforms have proven valuable for investigations of tick bacterial diversity, but the examination of tick viromes has historically not been well explored. By performing a comprehensive virome analysis of the three primary tick species associated with human disease in the United States, we gained substantial insight into tick virome diversity and can begin to assess a potential role of these viruses in the tick life cycle.
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Zhang P, Liu Y, Liu W, Cao M, Massart S, Wang X. Identification, Characterization and Full-Length Sequence Analysis of a Novel Polerovirus Associated with Wheat Leaf Yellowing Disease. Front Microbiol 2017; 8:1689. [PMID: 28932215 PMCID: PMC5592212 DOI: 10.3389/fmicb.2017.01689] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/21/2017] [Indexed: 11/13/2022] Open
Abstract
To identify the pathogens responsible for leaf yellowing symptoms on wheat samples collected from Jinan, China, we tested for the presence of three known barley/wheat yellow dwarf viruses (BYDV-GAV, -PAV, WYDV-GPV) (most likely pathogens) using RT-PCR. A sample that tested negative for the three viruses was selected for small RNA sequencing. Twenty-five million sequences were generated, among which 5% were of viral origin. A novel polerovirus was discovered and temporarily named wheat leaf yellowing-associated virus (WLYaV). The full genome of WLYaV corresponds to 5,772 nucleotides (nt), with six AUG-initiated open reading frames, one non-AUG-initiated open reading frame, and three untranslated regions, showing typical features of the family Luteoviridae. Sequence comparison and phylogenetic analyses suggested that WLYaV had the closest relationship with sugarcane yellow leaf virus (ScYLV), but the identities of full genomic nucleotides and deduced amino acid sequence of coat protein (CP) were 64.9 and 86.2%, respectively, below the species demarcation thresholds (90%) in the family Luteoviridae. Furthermore, agroinoculation of Nicotiana benthamiana leaves with a cDNA clone of WLYaV caused yellowing symptoms on the plant. Our study adds a new polerovirus that is associated with wheat leaf yellowing disease, which would help to identify and control pathogens of wheat.
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Affiliation(s)
- Peipei Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesBeijing, China
- Laboratory of Phytopathology, University of Liège, Gembloux Agro-Bio TechGembloux, Belgium
| | - Yan Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesBeijing, China
| | - Wenwen Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesBeijing, China
| | - Mengji Cao
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest UniversityChongqing, China
| | - Sebastien Massart
- Laboratory of Phytopathology, University of Liège, Gembloux Agro-Bio TechGembloux, Belgium
| | - Xifeng Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesBeijing, China
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