Advertisement

Virus Genes

pp 1–5 | Cite as

Grapevine virus T is relatively widespread in Slovakia and Czech Republic and genetically diverse

  • Miroslav Glasa
  • Lukáš Predajňa
  • Nina Sihelská
  • Katarína Šoltys
  • Ana Belén Ruiz-García
  • Antonio Olmos
  • Thierry Wetzel
  • Sead Sabanadzovic
Article

Abstract

A recently described putative foveavirus, grapevine virus T (GVT), was detected in a Slovak grapevine accession (SK704) using high-throughput sequencing, prompting further studies. Full-length genome sequence of isolate GVT-SK704 was determined. Analyses revealed 86.1% nucleotide identity with the Italian GVT isolate, currently the only available nearly complete sequence of GVT in GenBank. A virus-specific RT-PCR assay was developed, which enabled a survey of GVT incidence in grapevine samples from Slovakia and Czech Republic. Unexpectedly, GVT was present in ~ 30% of tested samples. Analysis of complete CP gene sequences of 20 Slovak and Czech GVT isolates detected in the survey revealed relatively high intra-species variability (up to 11.2% nucleotide divergence), suggesting multiple introductions from different sources, possibly over an extended period of time.

Keywords

GVT Foveavirus Grapevine High-throughput sequencing Diversity 

Notes

Acknowledgements

We are grateful to Dr. P. Kominek for providing the grapevine samples from the Czech Republic.

Author Contributions

MG, AO and TW conceived the study. MG, LP, NS, ABRG, AO, TW and SS participated in the conduct of the study, HTS assays and screening of the grapevine plants. KŠ performed the deep sequencing assays, KŠ, ABRG, AO, MG and SS analyzed the sequence data. MG and SS drafted and reviewed the manuscript. All authors critically revised and approved the manuscript.

Funding

This work was supported by Grants VEGA 2/0036/16 from the Scientific Grant Agency of the Ministry of Education and Slovak Academy of Sciences and APVV-15-0232 from the Slovak Research and Development Agency. KŠ was supported by the Grant ITMS313021D075 from the Research & Development Operational Program funded by the ERDF. SS acknowledges partial support from Special Research Initiative Grant—Mississippi Agriculture and Forest Experiment Station (MAFES), Mississippi State University. The research was conducted within the framework of COST Action FA1407 (DIVAS) supported by COST (European Cooperation in Science and Technology).

Compliance with ethical standards

Conflict of interest

All authors declare that they have no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

11262_2018_1587_MOESM1_ESM.pptx (2.1 mb)
Supplementary Fig. A. Phylogram depicting the relationships of coat proteins encoded by studied grapevine virus T isolates. The tree was generated with MrBayes [10] using complete amino acid sequences aligned with MUSCLE [22]. Bootstrap support indicated on branching point—Supplementary material 1 (PPTX 2158 KB)
11262_2018_1587_MOESM2_ESM.pptx (1 mb)
Supplementary Fig. B: MUSCLE-generated alignment of amino acid sequences of 22 GVT isolates from Slovakia and Czech Republic and two previously available sequences. Note that dark shaded columns indicate perfect conservation among all isolates for a given amino acid. Light blue and/or white columns represent amino acid positions differing in at least one of studied isolates. Notice clear-cut difference in level of aa conservation between N- and C- termini—Supplementary material 2 (PPTX 1069 KB)

References

  1. 1.
    Saldarelli P, Giampetruzzi A, Maree HJ, Al Rwahnih M (2017) High-throughput sequencing: advantages beyond virus identification. In: Meng B, Martelli G, Golino D, Fuchs M (eds) Grapevine viruses: molecular biology, diagnostics and management. Springer, Cham, pp 625–642.  https://doi.org/10.1007/978-3-319-57706-7_30 CrossRefGoogle Scholar
  2. 2.
    Al Rwahnih M, Daubert S, Golino D, Rowhani A (2009) Deep sequencing analysis of RNAs from a grapevine showing Syrah decline symptoms reveals a multiple virus infection that includes a novel virus. Virology 387:395–401CrossRefPubMedGoogle Scholar
  3. 3.
    Coetzee B, Freeborough MJ, Maree HJ, Celton JM, Rees DJ, Burger JT (2010) Deep sequencing analysis of viruses infecting grapevines: virome of a vineyard. Virology 400:157–163CrossRefPubMedGoogle Scholar
  4. 4.
    Jo Y, Choi H, Cho JK, Yoon JY, Choi SK, Cho WK (2015) In silico approach to reveal viral populations in grapevine cultivar Tannat using transcriptome data. Sci Rep 5:15841.  https://doi.org/10.1038/srep15841 CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Jo Y, Song MK, Choi H, Park JS, Lee JW, Lian S, Lee BC, Cho WK (2017) Genome sequence of Grapevine Virus T, a novel foveavirus infecting grapevine. Genome Announc 5:e00995–e00917.  https://doi.org/10.1128/genomeA.00995-17 PubMedPubMedCentralGoogle Scholar
  6. 6.
    Ruiz-García AB, Okic A, Nourinejhad-Zarghani S, Olmos A, Wetzel T (2018) First report of grapevine virus T in grapevine in Germany. Plant Dis.  https://doi.org/10.1094/PDIS-01-18-0161-PDN Google Scholar
  7. 7.
    Vončina D, Almeida RPP (2018) Screening of some Croatian autochthonous grapevine varieties reveals a multitude of viruses, including novel ones. Arch Virol.  https://doi.org/10.1007/s00705-018-3850-6 PubMedGoogle Scholar
  8. 8.
    Glasa M, Predajňa L, Šoltys K, Sihelská N, Nagyová A, Wetzel T, Sabanadzovic S (2017) 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 33:34–42CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Martelli GP, Jelkmann W (1998) Foveavirus, a new plant virus genus. Arch Virol 142:1245–1249CrossRefGoogle Scholar
  10. 10.
    Huelsenbeck JP, Ronquist F (2001) MRBAYES: bayesian inference of phylogenetic trees. Bioinformatics 17:754–755CrossRefPubMedGoogle Scholar
  11. 11.
    Garcia-Arenal F, Fraile A, Malpica JM (2001) Variability and genetic structure of plant virus populations. Annu Rev Phytopathol 39:157–186CrossRefPubMedGoogle Scholar
  12. 12.
    Glasa M, Predajňa L, Komínek P, Nagyová A, Candresse T, Olmos A (2014) Molecular characterization of divergent grapevine Pinot gris virus isolates and their detection in Slovak and Czech grapevines. Arch Virol 159:2103–2107CrossRefPubMedGoogle Scholar
  13. 13.
    Glasa M, Predajňa L, Šoltys K, Sabanadzovic S, Olmos A (2015) Detection and molecular characterisation of Grapevine Syrah virus-1 isolates from Central Europe. Virus Genes 51:112–121CrossRefPubMedGoogle Scholar
  14. 14.
    Bouyahia H, Boscia D, Savino V, La Notte P, Pirolo C, Castellano MA, Minafra A, Martelli GP (2005) Grapevine rupestris stem pitting-associated virus is linked with grapevine vein necrosis. Vitis 44:133–137Google Scholar
  15. 15.
    Lunden S, Meng B, Avery J, Qiu W (2009) Characterization of a grapevine vein-clearing complex on Chardonnay. Eur J Plant Pathol 126:135–144CrossRefGoogle Scholar
  16. 16.
    Massart S, Candresse T, Gil J, Lacomme C, Predajňa L, Ravnikar M, Reynard JS, Rumbou A, Saldarelli P, Škorić D, Vainio EJ, Valkonen JPT, Vanderschuren H, Varveri C, Wetzel T (2017) A framework for the evaluation of biosecurity, commercial, regulatory, and scientific impacts of plant viruses and viroids identified by NGS technologies. Front Microbiol 8:45.  https://doi.org/10.3389/fmicb.2017.00045 CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Glasa M, Predajňa L, Komínek P (2011) Grapevine fleck virus isolates split into two distinct molecular groups. J Phytopathol 159:805–807CrossRefGoogle Scholar
  18. 18.
    Glasa M, Predajňa L (2012) Partial sequence analysis of a grapevine leafroll-associated virus 3 isolate from Slovakia. J Plant Pathol 94:675–679Google Scholar
  19. 19.
    Predajňa L, Gažiová A, Holovičová E, Glasa M (2013) Analysis of a short genomic region of grapevine leafroll-associated virus 1 (GLRaV-1) reveals the presence of two different molecular groups of isolates in Slovakia. Acta Virol 57:353–356PubMedGoogle Scholar
  20. 20.
    Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452CrossRefPubMedGoogle Scholar
  21. 21.
    Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874CrossRefPubMedGoogle Scholar
  22. 22.
    Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Miroslav Glasa
    • 1
  • Lukáš Predajňa
    • 1
  • Nina Sihelská
    • 1
  • Katarína Šoltys
    • 2
  • Ana Belén Ruiz-García
    • 3
  • Antonio Olmos
    • 3
  • Thierry Wetzel
    • 4
  • Sead Sabanadzovic
    • 5
  1. 1.Institute of Virology, Biomedical Research CentreSlovak Academy of SciencesBratislavaSlovakia
  2. 2.Comenius University Science ParkComenius UniversityBratislavaSlovakia
  3. 3.Department of Plant PathologyInstituto Valenciano de Investigaciones AgrariasValenciaSpain
  4. 4.Institute of Plant ProtectionDLR RheinpfalzNeustadt an der WeinstrasseGermany
  5. 5.Department of Biochemistry, Molecular Biology, Entomology and Plant PathologyMississippi State UniversityMississippi StateUSA

Personalised recommendations