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Three genetic grapevine leafroll-associated virus 3 variants identified from South African vineyards show high variability in their 5′UTR

Abstract

Three genetic variants of grapevine leafroll-associated virus 3 (GLRaV-3) were identified in vineyards of the Western Cape, South Africa. The GLRaV-3 variants were identified by single-strand conformation polymorphism (SSCP) profiles generated from a region amplified in ORF5. ORF5 sequence data confirmed the three genetic variant groups, and a specific SSCP profile was assigned to each variant group. The results of SSCP analysis of this region in ORF5 showed that this method gives a fast and reliable indication of the GLRaV-3 variant status of a plant, which in many instances showed mixed infections. The full genome sequence of one representative of each variant group i.e. isolates 621 (group I), 623 (group II) and PL-20 (group III), was determined by sequencing overlapping cloned fragments of these isolates. The sequences of genomic 5′ ends of these isolates were determined by RLM-RACE. Sequence alignment of the 5′UTRs indicated significant sequence and length variation in this region between the three South African variant groups. Alignment of the Hsp70h and CP gene regions of these isolates with those of isolates from elsewhere in the world, followed by phylogenetic analysis, further supported the presence of three variants of GLRaV-3 in South Africa and the presence of two or three additional variant groups elsewhere in the world.

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References

  1. Angelini E, Bertazzon N, Bazzo I, Borgo M (2006) Molecular characterization of a divergent strain of grapevine leafroll-associated virus 3. In: Extended abstracts 15th Meeting of ICVG. Stellenbosch, South Africa, pp 148–150

    Google Scholar 

  2. Boscia D, Greif C, Gugerli P, Martelli GP, Walter B, Gonsalves D (1995) Nomenclature of grapevine leafroll-associated putative closteroviruses. Vitis 34:171–175

    Google Scholar 

  3. Chooi KM, Pearson MN, Cohen D, Pong JCH (2009) Sequence variation in Grapevine leafroll-associated virus 3 (GLRaV-3) New Zealand isolates. In: Extended abstracts of the 16th Meeting of ICVG. Dijon, France, pp 290–291

    Google Scholar 

  4. Engel EA, Girardi C, Escobar PF, Arredondo V, Domininguez C, Perez-Acle T, Valenzuela PDT (2008) Genome analysis and detection of a Chilean isolate of Grapevine leafroll associated virus-3. Virus Genes 37:110–118

    CAS  Article  PubMed  Google Scholar 

  5. Fuchs M, Martinson TE, Loeb GM, Hoch HC (2009) Survey for the three major leafroll disease-associated viruses in Finger Lakes vineyards in New York. Plant Dis 93:395–401

    CAS  Article  Google Scholar 

  6. Giegerich R, Meyer F, Sleiermacher C (1996) GeneFisher—software support for the detection of postulated genes. Proc Int Conf Intell Syst Mol Biol 4:68–77

    CAS  PubMed  Google Scholar 

  7. Goszczynski DE, Jooste AEC (2002) The application of single-strand conformation polymorphism (SSCP) technique for the analysis of molecular heterogeneity of grapevine virus A. Vitis 41:77–82

    CAS  Google Scholar 

  8. Gouveia P, Esteves F, Teixeira Santos M, Fonseca F, Eiras-Dias JE, Nolasco G (2009) Assessment of GLRaV-3 variants occuring in Portuguese grapevine varieties according to the coat protein gene. In: Extended abstracts of the 16th meeting of ICVG. Dijon, France, pp 316–317

    Google Scholar 

  9. Hall TA (1999) BioEdit: a user-friendly biological sequence and genomic alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98

    CAS  Google Scholar 

  10. Jooste AEC, Goszczynski DE (2005) Single-strand conformation polymorphism (SSCP), cloning and sequencing reveal two major groups of divergent molecular variants of grapevine leafroll-associated virus 3 (GLRaV-3). Vitis 44(1):39–43

    CAS  Google Scholar 

  11. Ling KS, Zhu HY, Drong RF, Slightom JL, McFerson JR, Gonsalves D (1998) Nucleotide sequence of the 3′-terminal two-thirds of the grapevine leafroll-associated virus 3 genome reveals a typical monopartite closterovirus. J Gen Virol 79:1299–1307

    CAS  PubMed  Google Scholar 

  12. Ling KS, Zhu HY, Gonsalves D (2004) Complete nucleotide sequence and genome organization of grapevine leafroll-associated virus 3, type member of the genus Ampelovirus. J Gen Virol 85:2099–2102

    CAS  Article  PubMed  Google Scholar 

  13. López C, Ayllón MA, Navas-Castillo J, Guerri J, Moreno P, Flores R (1998) Molecular variability of the 5′- and 3′-terminal regions of Citrus tristeza virus RNA. Phytopathology 88:685–691

    Article  PubMed  Google Scholar 

  14. Marchler-Bauer A (2009) CDD: specific functional annotation with the conserved domain database. Nucleic Acids Res 37:205–210

    Article  Google Scholar 

  15. Marchler-Bauer A, Bryant SH (2004) CD-Search: protein domain annotations on the fly. Nucleic Acids Res 32:327–331

    Article  Google Scholar 

  16. Maree HJ, Freeborough M-J, Burger JT (2008) Complete nucleotide sequence of a South African isolate of grapevine leafroll-associated virus 3 reveals a 5′UTR of 737 nucleotides. Arch Virol 153:755–757

    CAS  Article  PubMed  Google Scholar 

  17. Martelli GP, Agranovsky AA, Bar-Joseph M, Boscia D, Candresse T, Coutts RHA, Dolja VV, Falk BW, Gonsalves D et al (2002) The family Closteroviridae revised. Arch Virol 147(10):2039–2044

    CAS  Article  PubMed  Google Scholar 

  18. Pietersen G (2004) Spread of grapevine leafroll disease in South Africa—a difficult, but not insurmountable problem. Wynboer—a technical guide for wine producers. June 2004. URL: http://www.wynboer.co.za/recentarticles/articles.php3

  19. Prossser SW, Goszczynski DE, Meng B (2007) Molecular analysis of double-stranded RNAs reveals complex infection of grapevines with multiple viruses. Virus Res 124:151–159

    Article  Google Scholar 

  20. Soule MJ, Eastwell KC, Naidu RA (2006) First report of Grapevine leafroll associated virus-3 in American Vitis spp. Grapevines in Washington State. Plant Dis 90:1461

    Article  Google Scholar 

  21. Swofford DL (2003) PAUP*. Phylogenetic analysis using parsimony (* and other methods). Version 4. Sinauer Associates, Sunderland

    Google Scholar 

  22. Turturo C, Salderelli P, Yafeng D, Digiaro M, Minafra A, Savino V, Martelli GP (2005) Genetic variability and population structure of grapevine leafroll-associated virus 3 isolates. J Gen Virol 86:217–224

    CAS  Article  PubMed  Google Scholar 

  23. White EJ, Venter M, Hiten NF, Burger JT (2008) Modified Cetyltrimethylammonium bromide method improves robustness and versatility: the benchmark for plant RNA extraction. Biotechnol J 3:1424–1428

    CAS  Article  PubMed  Google Scholar 

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Acknowledgments

The research in this study was funded by the South African industry partner, Winetech, in collaboration with the National Research Foundation’s THRIP programme and ARC-PPRI. We acknowledge the assistance of staff at the ARC-PPRI and Stellenbosch University who provided technical assistance. A special word of thanks to Elsa van Niekerk, who assisted with the graphics of the paper.

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Correspondence to A. E. C. Jooste.

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The GenBank/EMBL/DDBJ accession numbers of the sequences reported in this paper are GQ352631, GQ352632 and GQ352633.

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Jooste, A.E.C., Maree, H.J., Bellstedt, D.U. et al. Three genetic grapevine leafroll-associated virus 3 variants identified from South African vineyards show high variability in their 5′UTR. Arch Virol 155, 1997–2006 (2010). https://doi.org/10.1007/s00705-010-0793-y

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  • DOI: https://doi.org/10.1007/s00705-010-0793-y

Keywords

  • Coat Protein
  • Variant Group
  • Coat Protein Gene
  • Citrus Tristeza Virus
  • Online Resource Table