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

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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.

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Acknowledgements

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

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).

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Authors and Affiliations

  1. Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 84505, Bratislava, Slovakia

    Miroslav Glasa, Lukáš Predajňa & Nina Sihelská

  2. Comenius University Science Park, Comenius University, Ilkovičova 8, 841 04, Bratislava, Slovakia

    Katarína Šoltys

  3. Department of Plant Pathology, Instituto Valenciano de Investigaciones Agrarias, Carretera Moncada a Náquera km 4.5, Moncada, 46113, Valencia, Spain

    Ana Belén Ruiz-García & Antonio Olmos

  4. Institute of Plant Protection, DLR Rheinpfalz, Breitenweg 71, 67435, Neustadt an der Weinstrasse, Germany

    Thierry Wetzel

  5. Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, 39762, USA

    Sead Sabanadzovic

Authors
  1. Miroslav Glasa
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  2. Lukáš Predajňa
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  3. Nina Sihelská
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  4. Katarína Šoltys
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  5. Ana Belén Ruiz-García
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  6. Antonio Olmos
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  7. Thierry Wetzel
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  8. Sead Sabanadzovic
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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.

Corresponding author

Correspondence to Miroslav Glasa.

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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.

Additional information

Edited by Karel Petrzik.

Accession numbers: The full-length genome sequence of GVT-SK704 isolate has been deposited in GenBank under accession number MH182704. The Genbank accession numbers for complete capsid protein gene sequences are MH182685–MH182703.

Electronic supplementary material

Below is the link to the electronic supplementary material.

11262_2018_1587_MOESM1_ESM.pptx

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

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)

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Glasa, M., Predajňa, L., Sihelská, N. et al. Grapevine virus T is relatively widespread in Slovakia and Czech Republic and genetically diverse. Virus Genes 54, 737–741 (2018). https://doi.org/10.1007/s11262-018-1587-7

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  • DOI: https://doi.org/10.1007/s11262-018-1587-7

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