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Genetic diversity and identification of putative recombination events in grapevine rupestris stem pitting-associated virus

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Abstract

The impact of recombination on variant classification and the use of different genomic regions to identify virus variants were investigated using a diversity study performed on grapevine rupestris stem pitting-associated virus (GRSPaV). Three surveys were conducted to investigate the genetic diversity of GRSPaV and to compare the ability of the GRSPaV coat protein and replicase domains to classify virus variants. GRSPaV variants identified in the surveys clustered into five of the six currently recognised lineages, and a seventh, previously unclassified lineage was detected. A correlation was observed between the detection of recombinant GRSPaV sequences and inconsistencies in classification when using different genome regions for analysis.

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Acknowledgements

We would like to thank the owners of the wine estates for permission to sample vineyards and for providing information on sampled vines, Winetech for project funding (GenUS 15/2), and the National Research Foundation (NRF) for personal funding (Miss Ilani Mostert). Opinions expressed and conclusions arrived at are those of the author and are not necessarily to be attributed to the NRF. The authors also thank Dr. Rachelle Bester and Mr. Dirk Aldrich for assisting in sampling, processing and RNA extractions.

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Authors and Affiliations

  1. Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa

    Ilani Mostert, Johan T. Burger & Hans J. Maree

  2. Agricultural Research Council, Infruitec-Nietvoorbij (Institute for Deciduous Fruit, Vines and Wine), Private Bag X5026, Stellenbosch, 7599, South Africa

    Hans J. Maree

Authors
  1. Ilani Mostert
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  2. Johan T. Burger
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  3. Hans J. Maree
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Corresponding author

Correspondence to Hans J. Maree.

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All authors declare that they have no conflict of interest.

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

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Handling Editor: Sead Sabanadzovic.

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Below is the link to the electronic supplementary material.

Fig. S1

Comparison of lineage classification of clones based on the CPreg and pREP regions within each survey. Classification results based on both regions were more or less consistent. Recombinant sequences were not taken into consideration. No group IIc could be discerned within tree topologies based on CPreg sequences (PDF 205 kb)

Table S1

Summary of the primers used in this study. The name, sequence, annealing temperature in °C (TA), extension time (Ext), and expected amplicon size are given (PDF 69 kb)

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Mostert, I., Burger, J.T. & Maree, H.J. Genetic diversity and identification of putative recombination events in grapevine rupestris stem pitting-associated virus. Arch Virol 163, 2491–2496 (2018). https://doi.org/10.1007/s00705-018-3883-x

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  • DOI: https://doi.org/10.1007/s00705-018-3883-x

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