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A framework for the evaluation of biosecurity, commercial, regulatory, and scientific impacts of plant viruses and viroids identified by NGS technologies
Title A framework for the evaluation of biosecurity, commercial, regulatory, and scientific impacts of plant viruses and viroids identified by NGS technologies Author Massart Sebastien Co-authors Candresse Thierry Gil José Lacomme Christophe Predajňa Lukáš 1985 SAVBIOMED ; SAVVIR - Biomedicínske centrum SAV SCOPUS ORCID Ravnikar Maja Reynard J.S. Rumbou Artemis Saldarelli Pasquale Škoric Dijana Vainio Eeva J. Valkonen Jari P.T. Vanderschuren Hervé Varveri Christina Wetzel T. Source document Frontiers in Microbiology. Vol. 8 (2017), art. no. 45, p. 1-7 Language eng - English Country CH - Switzerland Document kind rozpis článkov z periodík (rbx) Citations JONES, Susan - BAIZAN-EDGE, Amanda - MACFARLANE, Stuart - TORRANCE, Lesley. Viral Diagnostics in Plants Using Next Generation Sequencing: Computational Analysis in Practice. In FRONTIERS IN PLANT SCIENCE. ISSN 1664-462X, 2017, vol. 8, no., pp. XIN, Min - CAO, Mengji - LIU, Wenwen - REN, Yingdang - ZHOU, Xueping - WANG, Xifeng. Two Negative-Strand RNA Viruses Identified in Watermelon Represent a Novel Clade in the Order Bunyavirales. In FRONTIERS IN MICROBIOLOGY. ISSN 1664-302X, 2017, vol. 8, no., pp. FAGUNDES SILVA, Joao Marcos - AL RWAHNIH, Maher - BLAWID, Rosana - NAGATA, Tatsuya - MARTINS FAJARDO, Thor Vinicius. Discovery and molecular characterization of a novel enamovirus, Grapevine enamovirus-1. In VIRUS GENES. ISSN 0920-8569, 2017, vol. 53, no. 4, pp. 667-671. PASIN, F. - TSENG, X.A. - BEDOYA, L.C. - HEYDARNEJAD, J. - DENG, T.C. - GARCIA, J.A. - CHEN, Y.R. Streamlined generation of plant virus infectious clones using the pLX mini binary vectors. In JOURNAL OF VIROLOGICAL METHODS. ISSN 0166-0934, DEC 2018, vol. 262, p. 48-55. ROBERTS, J.M.K. - IRELAND, K.B. - TAY, W.T. - PAINI, D. Honey bee-assisted surveillance for early plant virus detection. In ANNALS OF APPLIED BIOLOGY. ISSN 0003-4746, NOV 2018, vol. 173, no. 3, p. 285-293. KWON, S.J. - CHOI, G.S. - CHOI, B. - SEO, J.K. Molecular characterization of an unusual new plant RNA virus reveals an evolutionary link between two different virus families. In PLOS ONE. ISSN 1932-6203, OCT 22 2018, vol. 13, no. 10. BARATH, D. - JAKSA-CZOTTER, N. - MOLNAR, J. - VARGA, T. - BALASSY, J. - SZABO, L.K. - KIRILLA, Z. - TUSNADY, G.E. - PREININGER, E. - VARALLYAY, E. Small RNA NGS Revealed the Presence of Cherry Virus A and Little Cherry Virus 1 on Apricots in Hungary. In VIRUSES-BASEL. ISSN 1999-4915, JUN 2018, vol. 10, no. 6. SPANO, R. - BOTTALICO, G. - CORRADO, A. - CAMPANALE, A. - DI FRANCO, A. - MASCIA, T. A Protocol for Producing Virus-Free Artichoke Genetic Resources for Conservation, Breeding, and Production. In AGRICULTURE-BASEL. MAR 2018, vol. 8, no. 3. CZOTTER, N. - MOLNAR, J. - SZABO, E. - DEMIAN, E. - KONTRA, L. - BAKSA, I. - SZITTYA, G. - KOCSIS, L. - DEAK, T. - BISZTRAY, G. - TUSNADY, G.E. - BURGYAN, J. - VARALLYAY, E. NGS of Virus-Derived Small RNAs as a Diagnostic Method Used to Determine Viromes of Hungarian Vineyards. In FRONTIERS IN MICROBIOLOGY. ISSN 1664-302X, FEB 6 2018, vol. 9. CZOTTER, N. - MOLNAR, J. - PESTI, R. - DEMIAN, E. - BARATH, D. - VARGA, T. - VARALLYAY, E. Use of siRNAs for Diagnosis of Viruses Associated to Woody Plants in Nurseries and Stock Collections. In VIRAL METAGENOMICS: METHODS AND PROTOCOLS. ISSN 1064-3745, 2018, vol. 1746, p. 115-130. MCLEISH, M.J. - FRAILE, A. - GARCIA-ARENAL, F. Ecological Complexity in Plant Virus Host Range Evolution. In ENVIRONMENTAL VIROLOGY AND VIRUS ECOLOGY. ISSN 0065-3527, 2018, vol. 101, p. 293-339. PIPER, Alexander M. - BATOVSKA, Jana - COGAN, Noel O. - WEISS, John - CUNNINGHAM, John Paul - RODONI, Brendan C. - BLACKET, Mark J. Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance. In GIGASCIENCE. ISSN 2047-217X, 2019, vol. 8, no. 8, pp. HA, Jungmin - JEON, Ho Hwi - WOO, Dong U. - LEE, Yejin - PARK, Halim - LEE, Joohyeong - KANG, Yang Jae. Soybean-VCF2Genomes: a database to identify the closest accession in soybean germplasm collection. In BMC BIOINFORMATICS. ISSN 1471-2105, 2019, vol. 20, no., pp. PESTI, Reka - KONTRA, Levente - PAUL, Kenny - VASS, Imre - CSORBA, Tibor - HAVELDA, Zoltan - VARALLYAY, Eva. Differential gene expression and physiological changes during acute or persistent plant virus interactions may contribute to viral symptom differences. In PLOS ONE. ISSN 1932-6203, 2019, vol. 14, no. 5, pp. FOX, A. - FOWKES, A. R. - SKELTON, A. - HARJU, V. - BUXTON-KIRK, A. - KELLY, M. - FORDE, S. M. D. - PUFAL, H. - CONYERS, C. - WARD, R. - WEEKES, R. - BOONHAM, N. - ADAMS, I. P. Using high-throughput sequencing in support of a plant health outbreak reveals novel viruses in Ullucus tuberosus (Basellaceae). In PLANT PATHOLOGY. ISSN 0032-0862, 2019, vol. 68, no. 3, pp. 576-587. PASIN, Fabio - MENZEL, Wulf - DAROS, Jose-Antonio. Harnessed viruses in the age of metagenomics and synthetic biology: an update on infectious clone assembly and biotechnologies of plant viruses. In PLANT BIOTECHNOLOGY JOURNAL. ISSN 1467-7644, 2019, vol. 17, no. 6, pp. 1010-1026. ZHAN, Binhui - CAO, Mengji - WANG, Kaina - WANG, Xifeng - ZHOU, Xueping. Detection and Characterization of Cucumis melo Cryptic Virus, Cucumis melo Amalgavirus 1, and Melon Necrotic Spot Virus in Cucumis melo. In VIRUSES-BASEL, 2019, vol. 11, no. 1, pp. SOUIRI, Amal - KHATABY, Khadija - KASMI, Yassine - ZEMZAMI, Mustapha - AMZAZI, Saaid - ENNAJI, Moulay Mustapha. Risk assessment and biosecurity considerations in control of emergent plant viruses. In Emerging and Reemerging Viral Pathogens: Volume 2: Applied Virology Approaches Related to Human, Animal and Environmental Pathogens, 2019-01-01, pp. 287-311. ZHAO, M.M. - GARCIA, B. - GALLO, A. - TZANETAKIS, I.E. - SIMON-MATEO, C. - GARCIA, J.A. - PASIN, F. Home-made enzymatic premix and Illumina sequencing allow for one-step Gibson assembly and verification of virus infectious clones. In PHYTOPATHOLOGY RESEARCH. ISSN 2096-5362, DEC 3 2020, vol. 2, no. 1. HANAFI, M. - TAHZIMA, R. - BEN KAAB, S. - TAMISIER, L. - ROUX, N. - MASSART, S. Identification of Divergent Isolates of Banana Mild Mosaic Virus and Development of a New Diagnostic Primer to Improve Detection. In PATHOGENS. DEC 2020, vol. 9, no. 12. JONES, R.A.C. - BOONHAM, N. - ADAMS, I.P. - FOX, A. Historical virus isolate collections: An invaluable resource connecting plant virology's pre-sequencing and post-sequencing eras. In PLANT PATHOLOGY. ISSN 0032-0862, FEB 2021, vol. 70, no. 2, p. 235-248. HOU, W.Y. - LI, S.F. - MASSART, S. Is There a "Biological Desert" With the Discovery of New Plant Viruses? A Retrospective Analysis for New Fruit Tree Viruses. In FRONTIERS IN MICROBIOLOGY. ISSN 1664-302X, NOV 19 2020, vol. 11. GAAFAR, Y.Z.A. - HERZ, K. - HARTRICK, J. - FLETCHER, J. - BLOUIN, A.G. - MACDIARMID, R. - ZIEBELL, H. Investigating the Pea Virome in Germany-Old Friends and New Players in the Field(s). In FRONTIERS IN MICROBIOLOGY. ISSN 1664-302X, NOV 13 2020, vol. 11. JO, Y. - YOON, Y.N. - JANG, Y.W. - CHOI, H. - LEE, Y.H. - KIM, S.M. - CHOI, S.Y. - LEE, B.C. - CHO, W.K. Soybean Viromes in the Republic of Korea Revealed by RT-PCR and Next-Generation Sequencing. In MICROORGANISMS. NOV 2020, vol. 8, no. 11. IBABA, J.D. - GUBBA, A. High-Throughput Sequencing Application in the Diagnosis and Discovery of Plant-Infecting Viruses in Africa, A Decade Later. In PLANTS-BASEL. OCT 2020, vol. 9, no. 10. BEJERMAN, N. - DEBAT, H. - DIETZGEN, R.G. The Plant Negative-Sense RNA Virosphere: Virus Discovery Through New Eyes. In FRONTIERS IN MICROBIOLOGY. ISSN 1664-302X, SEP 16 2020, vol. 11. GAZEL, M. - ROUMI, V. - ORDEK, K. - MACLOT, F. - MASSART, S. - CAGLAYAN, K. Identification and molecular characterization of a novel foveavirus from Rubus spp. in Turkey. In VIRUS RESEARCH. ISSN 0168-1702, SEP 2020, vol. 286. JO, Y. - CHOI, H. - LIAN, S. - CHO, J.K. - CHU, H. - CHO, W.K. Identification of viruses infecting six plum cultivars in Korea by RNA-sequencing. In PEERJ. ISSN 2167-8359, JUL 29 2020, vol. 8. SINGH, K. - JAROSOVA, J. - FOUSEK, J. - HUAN, C. - KUNDU, J.K. Virome identification in wheat in the Czech Republic using small RNA deep sequencing. In JOURNAL OF INTEGRATIVE AGRICULTURE. ISSN 2095-3119, JUL 2020, vol. 19, no. 7, p. 1825-1833. FOX, A. Reconsidering causal association in plant virology. In PLANT PATHOLOGY. ISSN 0032-0862, AUG 2020, vol. 69, no. 6, p. 956-961. DELLA BARTOLA, M. - BYRNE, S. - MULLINS, E. Characterization of Potato Virus Y Isolates and Assessment of Nanopore Sequencing to Detect and Genotype Potato Viruses. In VIRUSES-BASEL. APR 2020, vol. 12, no. 4. DEMIAN, E. - JAKSA-CZOTTER, N. - MOLNAR, J. - TUSNADY, G.E. - KOCSIS, L. - VARALLYAY, E. Grapevine rootstocks can be a source of infection with non-regulated viruses. In EUROPEAN JOURNAL OF PLANT PATHOLOGY. ISSN 0929-1873, MAR 2020, vol. 156, no. 3, p. 897-912. GARCIA, Y.G. - BAENA, L.M. - FERNANDEZ, L.F.T. - SANCHEZ, P.A.G. - MONTOYA, M.M. Detection of RNA viruses in tomato crops from eastern Antioquia (Colombia) using next-generation sequencing (NGS). In BIOAGRO. ISSN 1316-3361, 2020, vol. 32, no. 3, p. 147-158. SOUIRI, A. - KHATABY, K. - KASMI, Y. - ZEMZAMI, M. - AMZAZI, S. - ENNAJI, M.M. Risk Assessment and Biosecurity Considerations in Control of Emergent Plant Viruses. In EMERGING AND REEMERGING VIRAL PATHOGENS, VOL 2: APPLIED VIROLOGY APPROACHES RELATED TO HUMAN, ANIMAL AND ENVIRONMENTAL PATHOGENS. 2020, p. 287-311. SOMERA, M. - KVARNHEDEN, A. - DESBIEZ, C. - BLYSTAD, D.R. - SOOVALI, P. - KUNDU, J.K. - GANTSOVSKI, M. - NYGREN, J. - LECOQ, H. - VERDIN, E. - SPETZ, C. - TAMISIER, L. - TRUVE, E. - MASSART, S. Sixty Years After the First Description: Genome Sequence and Biological Characterization of European Wheat Striate Mosaic Virus Infecting Cereal Crops. In PHYTOPATHOLOGY. ISSN 0031-949X, JAN 2020, vol. 110, no. 1, p. 68-79. FOWKES, A.R. - MCGREIG, S. - PUFAL, H. - DUFFY, S. - HOWARD, B. - ADAMS, I.P. - MACARTHUR, R. - WEEKES, R. - FOX, A. Integrating High throughput Sequencing into Survey Design Reveals Turnip Yellows Virus and Soybean Dwarf Virus in Pea (Pisum Sativum) in the United Kingdom. In VIRUSES-BASEL. DEC 2021, vol. 13, no. 12. FRANOVA, J. - LENZ, O. - PRIBYLOVA, J. - CMEJLA, R. - VALENTOVA, L. - KOLONIUK, I. High Incidence of Strawberry Polerovirus 1 in the Czech Republic and Its Vectors, Genetic Variability and Recombination. In VIRUSES-BASEL. DEC 2021, vol. 13, no. 12. GASKIN, T.R. - TISCHENDORF, M. - GUNTHER, I. - REHANEK, M. - BUTTNER, C. - VON BARGEN, S. Characterization of a Novel Emaravirus Affecting Ash Species (Fraxinus spp.) in Europe. In FORESTS. NOV 2021, vol. 12, no. 11. SOLTANI, N. - STEVENS, K.A. - KLAASSEN, V. - HWANG, M.S. - GOLINO, D.A. - AL RWAHNIH, M. Quality Assessment and Validation of High-Throughput Sequencing for Grapevine Virus Diagnostics. In VIRUSES-BASEL. JUN 2021, vol. 13, no. 6. MAACHI, A. - TORRE, C. - SEMPERE, R.N. - HERNANDO, Y. - ARANDA, M.A. - DONAIRE, L. Use of High-Throughput Sequencing and Two RNA Input Methods to Identify Viruses Infecting Tomato Crops. In MICROORGANISMS. MAY 2021, vol. 9, no. 5. NABESHIMA, T. - ABE, J. High-Throughput Sequencing Indicates Novel Varicosavirus, Emaravirus, and Deltapartitivirus Infections in Vitis coignetiae. In VIRUSES-BASEL. MAY 2021, vol. 13, no. 5. ORFANIDOU, C.G. - XING, F. - ZHOU, J. - LI, S.F. - KATIS, N.I. - MALIOGKA, V.I. Identification and Sequence Analysis of a Novel Ilarvirus Infecting Sweet Cherry. In PLANTS-BASEL. MAR 2021, vol. 10, no. 3. PASIN, F. Oligonucleotide abundance biases aid design of a type IIS synthetic genomics framework with plant virome capacity. In BIOTECHNOLOGY JOURNAL. ISSN 1860-6768, MAY 2021, vol. 16, no. 5. GUTIERREZ, P. - RIVILLAS, A. - TEJADA, D. - GIRALDO, S. - RESTREPO, A. - OSPINA, M. - CADAVID, S. - GALLO, Y. - MARIN, M. PVDP: A portable open source pipeline for detection of plant viruses in RNAseq data. A case study on potato viruses in Antioquia (Colombia). In PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY. ISSN 0885-5765, JAN 2021, vol. 113. SILVA, G. - TOMLINSON, J. - ONKOKESUNG, N. - SOMMER, S. - MRISHO, L. - LEGG, J. - ADAMS, I.P. - GUTIERREZ-VAZQUEZ, Y. - HOWARD, T.P. - LAVERICK, A. - HOSSAIN, O. - WEI, Q.S. - GOLD, K.M. - BOONHAM, N. Plant pest surveillance: from satellites to molecules. In EMERGING TOPICS IN LIFE SCIENCES. ISSN 2397-8554, 2021, vol. 5, no. 2, p. 275-287. GALLO, Y. - MARIN, M. - GUTIERREZ, P. Detection of RNA viruses in Solanum quitoense by high-throughput sequencing (HTS) using total and double stranded RNA inputs. In PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY. ISSN 0885-5765, JAN 2021, vol. 113. ROY, B.G. - FUCHS, M. Herbaceous plant hosts as supermodels for grapevine viruses: a historical perspective. In JOURNAL OF PLANT PATHOLOGY. ISSN 1125-4653, 2022 DEC 27 2022. Dostupné na: https://doi.org/10.1007/s42161-022-01267-z. PASIN, F. Assembly of plant virus agroinfectious clones using biological material or DNA synthesis. In STAR PROTOCOLS. ISSN 2666-1667, DEC 16 2022, vol. 3, no. 4. Dostupné na: https://doi.org/10.1016/j.xpro.2022.101716. TARQUINI, G. - ERMACORA, P. - MARTINI, M. - FIRRAO, G. The conundrum of the connection of grapevine Pinot gris virus with the grapevine leaf mottling and deformation syndrome. In PLANT PATHOLOGY. ISSN 0032-0862, FEB 2023, vol. 72, no. 2, p. 209-217. Dostupné na: https://doi.org/10.1111/ppa.13667. MCLEISH, M.J. - ZAMFIR, A.D. - BABALOLA, B.M. - PELáEZ, A. - FRAILE, A. - GARCíA-ARENAL, F. Metagenomics show high spatiotemporal virus diversity and ecological compartmentalisation: Virus infections of melon, Cucumis melo, crops, and adjacent wild communities. In VIRUS EVOLUTION. NOV 16 2022, vol. 8, no. 2. Dostupné na: https://doi.org/10.1093/ve/veac095. ROBERTS, J.M.K. - JOOSTE, A.E.C. - PRETORIUS, L.S. - GEERING, A.D.W. Surveillance for Avocado Sunblotch Viroid Utilizing the European Honey Bee (iApis mellifera/i). In PHYTOPATHOLOGY. ISSN 0031-949X, MAR 2023, vol. 113, no. 3, p. 559-566. Dostupné na: https://doi.org/10.1094/PHYTO-08-22-0295-R. VáRALLYAY, E. - PRIBYLOVá, J. - GALBACS, Z.N. - JAHAN, A. - VARGA, T. - SPAK, J. - LENZ, O. - FRáNOVá, J. - SEDLáK, J. - KOLONIUK, I. Detection of Apple Hammerhead Viroid, Apple Luteovirus 1 and Citrus Concave Gum-Associated Virus in Apple Propagation Materials and Orchards in the Czech Republic and Hungary. In VIRUSES-BASEL. NOV 2022, vol. 14, no. 11. Dostupné na: https://doi.org/10.3390/v14112347. ROBSON, M. - CHOOI, K.M. - BLOUIN, A.G. - KNIGHT, S. - MACDIARMID, R.M. A National Catalogue of Viruses Associated with Indigenous Species Reveals High-Throughput Sequencing as a Driver of Indigenous Virus Discovery. In VIRUSES-BASEL. NOV 2022, vol. 14, no. 11. Dostupné na: https://doi.org/10.3390/v14112477. VALENZUELA, S.L. - NORAMBUENA, T. - MORGANTE, V. - GARCíA, F. - JIMéNEZ, J.C. - NúñEZ, C. - FUENTES, I. - POLLAK, B. Viroscope: Plant viral diagnosis from high-throughput sequencing data using biologically-informed genome assembly coverage. In FRONTIERS IN MICROBIOLOGY. OCT 21 2022, vol. 13. Dostupné na: https://doi.org/10.3389/fmicb.2022.967021. 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Category ADMA - Scientific papers in foreign impacted journals registered in Web of Sciences or Scopus Category of document (from 2022) V3 - Vedecký výstup publikačnej činnosti z časopisu Type of document článok Year 2017 Registered in WOS Registered in SCOPUS DOI 10.3389/fmicb.2017.00045 
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rok CC IF IF Q (best) JCR Av Jour IF Perc SJR SJR Q (best) CiteScore N rok vydania rok metriky IF IF Q (best) SJR SJR Q (best) 2017 2016 4.076 Q1 1.759 Q1
Number of the records: 1