This study focused on the viruses of the Tymoviridae family that infect grapevines in the Czech Republic. Complete sequences of GFkV (grapevine fleck virus) and GRGV (grapevine red globe virus) from the genus Maculavirus and GRVFV (grapevine rupestris vein feathering virus) and GSyV-1 (grapevine Syrah virus 1) from the genus Marafivirus were obtained using high-throughput sequencing of small RNAs and total RNAs. Mixed infections with these viruses were observed, as well as several variants of these viruses in the same plant. Phylogenetic analysis showed the position of the newly obtained virus isolates within the Tymoviridae family. Recombinant analysis provided evidence of single and multiple intraspecific recombinations in GRGV, GSyV-1, and GRVFV. Additionally, GAMaV, a grapevine virus from the genus Marafivirus, was reported for the first time in the Czech Republic.

Crop Research Institute Prague Research Station for Viticulture Karlštejn Karlštejn 98 267 18 Karlštejn Czech Republic

Department of Plant Protection Faculty of Agrobiology Food and Natural Resources Czech University of Life Sciences Prague Kamýcká 129 165 00 Prague Czech Republic

Ecology Diagnostics and Genetic Resources of Agriculturally Important Viruses Fungi and Phytoplasmas Crop Research Institute Drnovská 507 161 06 Prague Czech Republic

Zobrazit více v PubMed

Fuchs M. Grapevine Viruses: A Multitude of Diverse Species with Simple but Overall Poorly Adopted Management Solutions in the Vineyard. J. Plant Pathol. 2020;102:643–653. doi: 10.1007/s42161-020-00579-2. DOI

Miljanić V., Jakše J., Kunej U., Rusjan D., Škvarč A., Štajner N. Virome Status of Preclonal Candidates of Grapevine Varieties (Vitis vinifera L.) from the Slovenian Wine-Growing Region Primorska as Determined by High-Throughput Sequencing. Front. Microbiol. 2022;13:830866. doi: 10.3389/fmicb.2022.830866. PubMed DOI PMC

Shvets D., Porotikova E., Sandomirsky K., Vinogradova S. Virome of Grapevine Germplasm from the Anapa Ampelographic Collection (Russia) Viruses. 2022;14:1314. doi: 10.3390/v14061314. PubMed DOI PMC

Vinogradova S., Porotikova E., Navrotskaya E., Galbacs Z.N., Massart S., Varallyay E. The First Virome of a Russian Vineyard. Plants. 2023;12:3292. doi: 10.3390/plants12183292. PubMed DOI PMC

Czotter N., Molnar J., Szabó E., Demian E., Kontra L., Baksa I., Szittya G., Kocsis L., Deak T., Bisztray G., et al. NGS of Virus-Derived Small RNAs as a Diagnostic Method Used to Determine Viromes of Hungarian Vineyards. Front. Microbiol. 2018;9:122. doi: 10.3389/fmicb.2018.00122. DOI

Fajardo T.V.M., Silva F.N., Eiras M., Nickel O. High-Throughput Sequencing Applied for the Identification of Viruses Infecting Grapevines in Brazil and Genetic Variability Analysis. Trop. Plant Pathol. 2017;42:250–260. doi: 10.1007/s40858-017-0142-8. DOI

Eichmeier A., Komínková M., Komínek P., Baránek M. Comprehensive Virus Detection Using next Generation Sequencing in Grapevine Vascular Tissues of Plants Obtained from the Wine Regions of Bohemia and Moravia (Czech Republic) PLoS ONE. 2016;11:e0167966. doi: 10.1371/journal.pone.0167966. PubMed DOI PMC

Glasa M., Predajňa L., Komínek P., Nagyová A., Candresse T., Olmos A. Molecular Characterization of Divergent Grapevine Pinot Gris Virus Isolates and Their Detection in Slovak and Czech Grapevines. Arch. Virol. 2014;159:2103–2107. doi: 10.1007/s00705-014-2031-5. PubMed DOI

Komínek P. Distribution of Grapevine Viruses in Vineyards of the Czech Republic. J. Plant Pathol. 2008;90:357–358.

Walker P.J., Siddell S.G., Lefkowitz E.J., Mushegian A.R., Adriaenssens E.M., Alfenas-Zerbini P., Davison A.J., Dempsey D.M., Dutilh B.E., García M.L., et al. Changes to Virus Taxonomy and to the International Code of Virus Classification and Nomenclature Ratified by the International Committee on Taxonomy of Viruses (2021) Arch. Virol. 2021;166:2633–2648. doi: 10.1007/s00705-021-05156-1. PubMed DOI

Zerbini F.M., Siddell S.G., Mushegian A.R., Walker P.J., Lefkowitz E.J., Adriaenssens E.M., Alfenas-Zerbini P., Dutilh B.E., García M.L., Junglen S., et al. Differentiating between Viruses and Virus Species by Writing Their Names Correctly. Arch. Virol. 2022;167:1231–1234. doi: 10.1007/s00705-021-05323-4. PubMed DOI PMC

Sabanadzovic S., Abou-ghanem N., Martelli G.P. Grapevine Fleck and Similar Viruses. In: Meng B., Martelli G.P., Fuchs M., Golino D.A., editors. Grapevine Viruses: Molecular Biology, Diagnostics and Management. Springer; Berlin/Heidelberg, Germany: 2017. pp. 167–195.

Jo Y., Song M.K., Choi H., Park J.S., Lee J.W., Cho W.K. First Report of Grapevine Fleck Virus and Grapevine Virus E in Grapevine in Korea. Plant Dis. 2017;101:1069. doi: 10.1094/PDIS-12-16-1760-PDN. DOI

Crnogorac A., Gašpar M., Davino S., Mandić A., Matić S. First Report of Grapevine Fleck Virus in Vineyards of Bosnia and Herzegovina. J. Plant Pathol. 2020;102:1299. doi: 10.1007/s42161-020-00580-9. DOI

Komínek P., Holleinová V. Evaluation of Sanitary Status of Grapevines in the Czech Republic. Plant Soil Environ. 2003;49:63–66. doi: 10.17221/4091-PSE. DOI

Shi B.J., Habili N., Symons R.H. Nucleotide Sequence Variation in a Small Region of the Grapevine Fleck Virus Replicase Provides Evidence for Two Sequence Variants of the Virus. Ann. Appl. Biol. 2003;142:349–355. doi: 10.1111/j.1744-7348.2003.tb00260.x. DOI

Martelli G.P., Sabanadzovic S., Ghanem-Sabanadzovic N.A., Saldarelli P. Maculavirus, a New Genus of Plant Viruses. Arch. Virol. 2002;147:1847–1853. doi: 10.1007/s007050200046. PubMed DOI

Sabanadzovic S., Abou-Ghanem N., Castellano M.A., Digiaro M., Martelli G.P. Grapevine Fleck Virus-like Viruses in Vitis. Arch. Virol. 2000;145:553–565. doi: 10.1007/s007050050046. PubMed DOI

Ghanem-Sabanadzovic N.A., Sabanadzovic S., Martelli G.P. Sequence Analysis of the 3′ End of Three Grapevine Fleck Virus-like Viruses from Grapevine. Virus Genes. 2003;27:11–16. doi: 10.1023/A:1025164200412. PubMed DOI

El Beaino T., Sabanadzovic S., Digiaro M., Abou Ghanem-Sabanadzovic N., Rowhani A., Kyriakopoulou P.E., Martelli G.P. Molecular Detection of Grapevine Fleck Virus-like Viruses. Vitis. 2001;40:65–68.

Beuve M., Candresse T., Tannières M., Lemaire O. First Report of Grapevine Redglobe Virus (GRGV) in Grapevine in France. Plant Dis. 2015;99:422. doi: 10.1094/PDIS-10-14-1009-PDN. PubMed DOI

Cretazzo E., Padilla C.V., Velasco L. First Report of Grapevine Red Globe Virus in Grapevine in Spain. Plant Dis. 2017;101:264–265. doi: 10.1094/PDIS-06-16-0932-PDN. PubMed DOI

Ruiz-García A.B., Zarghani S.N., Okic A., Olmos A., Wetzel T. First Report of Grapevine Red Globe Virus in Grapevine in Germany. Plant Dis. 2018;102:1675. doi: 10.1094/PDIS-01-18-0105-PDN. PubMed DOI

Candresse T., Faure C., Marais A. First Report of Grapevine Red Globe Virus (GRGV) and Grapevine Rupestris Vein Feathering Virus (GRVFV) Infecting Grapevine (Vitis vinifera) in Portugal. Plant Dis. 2022;107:974. doi: 10.1094/PDIS-06-22-1326-PDN. PubMed DOI

Dixon M., Fowkes A., Hogan C., Adams I., McGreig S., Pufal H., Ward R., Harju V., Skelton A., Fox A. First Report of Grapevine Red Globe Virus in Grapevine in the United Kingdom. New Dis. Rep. 2022;46:e12118. doi: 10.1002/ndr2.12118. DOI

Fan X.D., Dong Y.F., Zhang Z.P., Ren F., Hu G.J., Li Z.N., Zhou J. First Report of Grapevine Red Globe Virus (GRGV) in Grapevines in China. Plant Dis. 2016;100:2340. doi: 10.1094/PDIS-05-16-0701-PDN. DOI

Nourinejhad Zarghani S., Khalili M., Dizadji A., Wetzel T. First Report of Grapevine Red Globe Virus in Grapevine in Iran. J. Plant Pathol. 2021;103:661. doi: 10.1007/s42161-021-00749-w. DOI

Yamamoto T., Sato H., Suzuki T., Miyazaki A., Kitazawa Y., Maejima K., Namba S., Yamaji Y. Complete Genome Sequences of Grapevine Red Globe Virus in Japan. Microbiol. Resour. Announc. 2022;11:12–14. doi: 10.1128/mra.00434-22. PubMed DOI PMC

Wu Q., Habili N., Tyerman S.D., Rinaldo A., Little A., Constable F.E. First Detection of Five Previously Unreported Grapevine Viruses in Australia. Australas. Plant Dis. Notes. 2023;18:27. doi: 10.1007/s13314-023-00511-4. DOI

Massart S., Chiumenti M., De Jonghe K., Glover R., Haegeman A., Koloniuk I., Komínek P., Kreuze J., Kutnjak D., Lotos L., et al. Virus Detection by High-Throughput Sequencing of Small RNAs: Large-Scale Performance Testing of Sequence Analysis Strategies. Phytopathology. 2019;109:488–497. doi: 10.1094/PHYTO-02-18-0067-R. PubMed DOI

Wu Q., Kehoe M.A., Kinoti W.M., Wang C.P., Rinaldo A., Tyerman S., Habili N., Constable F.E. First Report of Grapevine Rupestris Vein Feathering Virus in Grapevine in Australia. Plant Dis. 2021;105:515. doi: 10.1094/PDIS-06-20-1240-PDN. PubMed DOI

Al Rwahnih M., Daubert S., Golino D., Rowhani A. Deep Sequencing Analysis of RNAs from a Grapevine Showing Syrah Decline Symptoms Reveals a Multiple Virus Infection That Includes a Novel Virus. Virology. 2009;387:395–401. doi: 10.1016/j.virol.2009.02.028. PubMed DOI

Engel E.A., Rivera P.A., Valenzuela P.D.T. First Report of Grapevine Syrah Virus-1 in Chilean Grapevines. Plant Dis. 2010;94:633. doi: 10.1094/PDIS-94-5-0633A. PubMed DOI

Giampetruzzi A., Roumi V., Roberto R., Malossini U., Yoshikawa N., La Notte P., Terlizzi F., Credi R., Saldarelli P. A New Grapevine Virus Discovered by Deep Sequencing of Virus- and Viroid-Derived Small RNAs in Cv Pinot Gris. Virus Res. 2012;163:262–268. doi: 10.1016/j.virusres.2011.10.010. PubMed DOI

Czotter N., Szabo E., Molnar J., Kocisz L., Deák T., Bisztray G., Tusnády G., Burgyán J., Várallyay É. First Description of Grapevine Syrah Virus-1 from Grapevine in Hungary. J. Plant Pathol. 2015;97:S74. doi: 10.4454/JPP.V97I4SUP.021. DOI

Oosthuizen K., Coetzee B., Maree H.J., Burger J.T. First Report of Grapevine Syrah Virus 1 in South African Grapevines. Plant Dis. 2016;100:1252. doi: 10.1094/PDIS-12-15-1408-PDN. DOI

Ahmed I., Fan X.D., Zhang Z.P., Ren F., Hu G.J., Li Z.N., Khaskheli M.I., Dong Y.F. First Report of Grapevine Syrah Virus-1 in Grapevines in China. Plant Dis. 2018;102:466. doi: 10.1094/PDIS-09-17-1358-PDN. DOI

Vončina D., Al Rwahnih M., Rowhani A., Gouran M., Almeida R.P.P. Viral Diversity in Autochthonous Croatian Grapevine Cultivars. Plant Dis. 2017;101:1230–1235. doi: 10.1094/PDIS-10-16-1543-RE. PubMed DOI

Ruiz-García A.B., Sabaté J., Lloria O., Laviña A., Batlle A., Olmos A. First Report of Grapevine Syrah Virus-1 in Grapevine in Spain. Plant Dis. 2017;101:1830. doi: 10.1094/PDIS-05-17-0700-PDN. DOI

Cho I.S., Yang C.Y., Kwon S.J., Yoon J.Y., Kim D.H., Choi G.S., Hammond J., Moon J.S., Lim H.S. First Report of Grapevine Syrah Virus 1 Infecting Grapevines in Korea. Plant Dis. 2019;103:2970. doi: 10.1094/PDIS-05-19-1037-PDN. DOI

Navrotskaya E., Porotikova E., Yurchenko E., Galbacs Z.N., Varallyay E., Vinogradova S. High-Throughput Sequencing of Small Rnas for Diagnostics of Grapevine Viruses and Viroids in Russia. Viruses. 2021;13:2432. doi: 10.3390/v13122432. PubMed DOI PMC

Glasa M., Predajňa L., Šoltys K., Sabanadzovic S., Olmos A. Detection and Molecular Characterisation of Grapevine Syrah Virus-1 Isolates from Central Europe. Virus Genes. 2015;51:112–121. doi: 10.1007/s11262-015-1201-1. PubMed DOI

Sabanadzovic S., Ghanem-Sabanadzovic N.A., Gorbalenya A.E. Permutation of the Active Site of Putative RNA-Dependent RNA Polymerase in a Newly Identified Species of Plant Alpha-like Virus. Virology. 2009;394:1–7. doi: 10.1016/j.virol.2009.08.006. PubMed DOI

Di Gaspero G., Radovic S., De Luca E., Spadotto A., Magris G., Falginella L., Cattonaro F., Marroni F. Evaluation of Sensitivity and Specificity in RNA-Seq-Based Detection of Grapevine Viral Pathogens. J. Virol. Methods. 2022;300:114383. doi: 10.1016/j.jviromet.2021.114383. PubMed DOI

Jalili V., Afgan E., Gu Q., Clements D., Blankenberg D., Goecks J., Taylor J., Nekrutenko A. The Galaxy Platform for Accessible, Reproducible and Collaborative Biomedical Analyses: 2020 Update. Nucleic Acids Res. 2021;48:W395–W402. doi: 10.1093/nar/gkaa434. PubMed DOI PMC

Katoh K., Rozewicki J., Yamada K.D. MAFFT Online Service: Multiple Sequence Alignment, Interactive Sequence Choice and Visualization. Brief. Bioinform. 2018;20:1160–1166. doi: 10.1093/bib/bbx108. PubMed DOI PMC

Hall T.A. BioEdit: A User-Friendly Biological Sequence Alignment Editor and Analysis Program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 1999;41:95–98.

Martin D.P., Murrell B., Golden M., Khoosal A., Muhire B. RDP4: Detection and Analysis of Recombination Patterns in Virus Genomes. Virus Evol. 2015;1:vev003. doi: 10.1093/ve/vev003. PubMed DOI PMC

Ben Mansour K., Gibbs A.J., Komínková M., Komínek P., Brožová J., Kazda J., Zouhar M., Ryšánek P. Watermelon Mosaic Virus in the Czech Republic, Its Recent and Historical Origins. Plant Pathol. 2023;72:1528–1538. doi: 10.1111/ppa.13766. DOI

Muhire B.M., Varsani A., Martin D.P. SDT: A Virus Classification Tool Based on Pairwise Sequence Alignment and Identity Calculation. PLoS ONE. 2014;9:e108277. doi: 10.1371/journal.pone.0108277. PubMed DOI PMC

Fiore N., Zamorano A., Sánchez-Diana N., González X., Pallás V., Sánchez-Navarro J. First Detection of Grapevine Rupestris Stem Pitting-Associated Virus and Grapevine Rupestris Vein Feathering Virus, and New Phylogenetic Groups for Grapevine Fleck Virus and Hop Stunt Viroid Isolates, Revealed from Grapevine Field Surveys in Spain. Phytopathol. Mediterr. 2016;55:225–238.

Glasa M., Predajňa L., Šoltys K., Sihelská N., Nagyová A., Wetzel T., Sabanadzovic S. Analysis of Grapevine Rupestris Stem Pitting-Associated Virus in Slovakia Reveals Differences in Intra-Host Population Diversity and Naturally Occurring Recombination Events. Plant Pathol. J. 2017;33:34–42. doi: 10.5423/PPJ.OA.07.2016.0158. PubMed DOI PMC

Nakaune R., Inoue K., Nasu H., Kakogawa K., Nitta H., Imada J., Nakano M. Detection of Viruses Associated with Rugose Wood in Japanese Grapevines and Analysis of Genomic Variability of Rupestris Stem Pitting-Associated Virus. J. Gen. Plant Pathol. 2008;74:156–163. doi: 10.1007/s10327-008-0079-3. DOI

Komínek P., Glasa M., Bryxiová M. Analysis of the Molecular Variability of Grapevine Leafroll-Associated Virus 1 Reveals the Presence of Two Distinct Virus Groups and Their Mixed Occurrence. Virus Genes. 2005;31:247–255. doi: 10.1007/s11262-005-3236-1. PubMed DOI

Glasa M., Predajňa L., Komínek P. Grapevine Fleck Virus Isolates Split into Two Distinct Molecular Groups. J. Phytopathol. 2011;159:805–807. doi: 10.1111/j.1439-0434.2011.01845.x. DOI

Sabanadzovic S., Abou Ghanem-Sabanadzovic N., Saldarelli P., Martelli G.P. Complete Nucleotide Sequence and Genome Organization of Grapevine Fleck Virus. J. Gen. Virol. 2011;156:875–879. doi: 10.1099/0022-1317-82-8-2009. PubMed DOI

Xiao H., Meng B. First Report of Grapevine Asteroid Mosaic Associated Virus and Grapevine Rupestris Vein Feathering Virus in Grapevines in Canada. Plant Dis. 2016;100:2175. doi: 10.1094/PDIS-03-16-0413-PDN. DOI

Jo Y., Choi H., Kyong Cho J., Yoon J.Y., Choi S.K., Kyong Cho W. In Silico Approach to Reveal Viral Populations in Grapevine Cultivar Tannat Using Transcriptome Data. Sci. Rep. 2015;5:15841. doi: 10.1038/srep15841. PubMed DOI PMC

Candresse T., Faure C., Theil S., Beuve M., Lemaire O., Spilmont A.S., Marais A. First Report of Grapevine Asteroid Mosaic-Associated Virus Infecting Grapevine (Vitis vinifera) in France. Plant Dis. 2017;101:1061. doi: 10.1094/PDIS-01-17-0012-PDN. DOI

Morán F., Canales C., Olmos A., Ruiz-García A. First Report of Grapevine Asteroid Mosaic Associated Virus in Grapevine in Spain. Plant Dis. 2020;105:517. doi: 10.1094/PDIS-07-20-1566-PDN. PubMed DOI

Porceddu A., Sanna M., Prota V.A., Schianchi N., Mercenaro L., Nieddu G., Camiolo S. First Report of Grapevine Asteroid Mosaic-Associated Virus Infecting Grapevines (Vitis vinifera) in Italy. Plant Dis. 2018;102:2049. doi: 10.1094/PDIS-03-18-0460-PDN. PubMed DOI

Gibbs A.J., Hajizadeh M., Ohshima K., Jones R.A.C. The Potyviruses: An Evolutionary Synthesis Is Emerging. Viruses. 2020;12:132. doi: 10.3390/v12020132. PubMed DOI PMC

Acosta-Leal R., Duffy S., Xiong Z., Hammond R.W., Elena S.F. Advances in Plant Virus Evolution: Translating Evolutionary Insights into Better Disease Management. Phytopathology. 2011;101:1136–1148. doi: 10.1094/PHYTO-01-11-0017. PubMed DOI

Hily J.M., Poulicard N., Candresse T., Vigne E., Beuve M., Renault L., Velt A., Spilmont A.S., Lemaire O. Datamining, Genetic Diversity Analyses, and Phylogeographic Reconstructions Redefine the Worldwide Evolutionary History of Grapevine Pinot Gris Virus and Grapevine Berry Inner Necrosis Virus. Phytobiomes J. 2020;4:165–177. doi: 10.1094/PBIOMES-10-19-0061-R. DOI

Cretazzo E., Velasco L. High-throughput Sequencing Allowed the Completion of the Genome of Grapevine Red Globe. Plant Pathol. 2016;66:1202–1213. doi: 10.1111/ppa.12669. DOI

Zakubanskiy A., Mitrofanova I., Sheveleva A., Chirkov S. Analysis of Canna Yellow Streak Virus Complete Genomes Provides Evidence of Multiple Intraspecies Recombination Events. J. Plant Pathol. 2018;100:575–580. doi: 10.1007/s42161-018-0111-1. DOI

Komínek P., Glasa M., Komínková M. Analysis of Multiple Virus-Infected Grapevine Plant Reveals Persistence but Uneven Virus Distribution. Acta Virol. 2009;53:281–285. doi: 10.4149/av_2009_04_281. PubMed DOI

Wang Y.M., Ostendorf B., Pagay V. Evaluating the Potential of High-Resolution Visible Remote Sensing to Detect Shiraz Disease in Grapevines. Aust. J. Grape Wine Res. 2023;2023:7376153. doi: 10.1155/2023/7376153. DOI

Wu Q., Habili N., Kinoti W.M., Tyerman S.D., Rinaldo A., Zheng L., Constable F.E. A Metagenomic Investigation of the Viruses Associated with Shiraz Disease in Australia. Viruses. 2023;15:774. doi: 10.3390/v15030774. PubMed DOI PMC