Real-time RT-PCR high-resolution melting curve analysis and multiplex RT-PCR to detect and differentiate grapevine leafroll-associated associated virus 3 variant groups I, II, III and VI

Virology Journal

Volumn 9, Issue , 2012, Pages

  Bester, Rachelle ^a   Jooste, Anna E C ^b   Maree, Hans J ^a,c   Burger, Johan T ^a  

^a STELLENBOSCH UNIVERSITY   (South Africa)

^b PLANT PROTECTION RESEARCH INSTITUTE   (South Africa)

^c AGRICULTURAL RESEARCH COUNCIL   (South Africa)

Author keywords

GLRaV 3; Grapevine leafroll associated virus 3; High resolution melting curve analysis; Leafroll disease; Molecular variants; Multiplex RT PCR; Real time RT PCR

Indexed keywords

HEAT SHOCK PROTEIN 70;

ARTICLE; CONFIDENCE INTERVAL; CONTROLLED STUDY; GRAPEVINE LEAFROLL ASSOCIATED VIRUS 3; HIGH RESOLUTION MELTING ANALYSIS; MELTING POINT; MULTIPLEX POLYMERASE CHAIN REACTION; MULTIPLEX REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; NONHUMAN; REAL TIME POLYMERASE CHAIN REACTION; REAL TIME REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; VIRUS DETECTION; VIRUS IDENTIFICATION; VITIVIRUS;

AUTOMATION, LABORATORY; CLOSTEROVIRIDAE; DNA PRIMERS; MULTIPLEX POLYMERASE CHAIN REACTION; REAL-TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, VIRAL; SENSITIVITY AND SPECIFICITY; SOUTH AFRICA; TIME FACTORS; TRANSITION TEMPERATURE; VIROLOGY;

GRAPEVINE LEAFROLL-ASSOCIATED VIRUS 3; VITIS;

EID: 84866671353     PISSN: None     EISSN: 1743422X     Source Type: Journal    
DOI: 10.1186/1743-422X-9-219     Document Type: Article

References (32)

1. The family Closteroviridae revised. Martelli GP, Agranovsky AA, Bar-Joseph M, Boscia D, Candresse T, Coutts RHA, Dolja VV, Falk BW, Gonsalves D, Jelkmann W, Karasev AV, Minafra A, Namba S, Vetten HJ, Wisler GC, Yoshikawa N, Arch Virol 2002 147 10 2039 2044 10.1007/s007050200048 12376765
2. Three genetic grapevine leafroll-associated virus 3 variants identified from South African vineyards show high variability in their 5'UTR. Jooste AEC, Maree HJ, Bellstedt DU, Goszczynski DE, Pietersen G, Burger JT, Arch Virol 2010 155 1997 2006 10.1007/s00705-010-0793-y 20830600
3. 3'-coterminal subgenomic RNAs and putative cis-acting elements of Grapevine leafroll-associated virus 3 reveals 'unique' features of gene expression strategy in the genus Ampelovirus. Jarugula S, Gowda S, Dawson WO, Naidu RA, Virol J 2010 7 180 1 14 20044930
4. Complete nucleotide sequence and genome organization of Grapevine leafroll-associated virus 3, type member of the genus Ampelovirus. Ling K-S, Zhu H-Y, Gonsalves D, J Gen Virol 2004 85 2099 2102 10.1099/vir.0.80007-0 15218195
5. Genome analysis and detection of a Chilean isolate of Grapevine leafroll associated virus-3. Engel EA, Girardi C, Escobar PF, Arredondo V, Dominguez C, Perez-Acle T, Valenzuela PD, Virus Genes 2008 37 1 110 118 10.1007/s11262-008- 0241-1 18498048
6. Complete nucleotide sequence of a South African isolate of grapevine leafroll-associated virus 3 reveals a 5'UTR of 737 nucleotides. Maree HJ, Freeborough M-J, Burger JT, Arch Virol 2008 153 755 757 10.1007/s00705-008-0040- y 18274697
7. Complete nucleotide sequence of a new strain of grapevine leafroll-associated virus 3 in South Africa. Bester R, Maree HJ, Burger JT, Arch Virol 2012 157 9 1815 1819 10.1007/s00705-012-1333-8 22614811
8. Five phylogenetic groups identified in the coat protein gene of grapevine leafroll-associated virus 3 obtained from Portuguese grapevine varieties. Gouveia P, Santos MT, Eiras-Dias JE, Nolasco G, Arch Virol 2010 156 3 413 420 21153745
9. Genetic variability and population structure of grapevine leafroll-associated virus 3 isolates. Turturo C, Salderelli P, Yafeng D, Digiaro M, Minafra A, Savino V, Martelli GP, J Gen Virol 2005 86 217 224 10.1099/vir.0.80395-0 15604449
10. Next-generation sequencing and metagenomic analysis: a universal diagnostic tool in plant virology. Adams IP, Glover RH, Monger WA, Mumford R, Jackeviciene E, Navalinskiene M, Samuitiene M, Boonham N, Mol Plant Path 2009 10 4 537 545 10.1111/j.1364-3703.2009.00545.x
11. Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs: A generic method for diagnosis, discovery and sequencing of viruses. Kreuze JF, Perez A, Untiveros M, Quispe D, Fuentes S, Barker I, Simon R, Virology 2009 388 1 1 7 10.1016/j.virol.2009.03.024 19394993
12. Deep sequencing analysis of RNAs from a grapevine showing Syrah decline symptoms reveals a multiple virus infection that includes a novel virus. Al Rwahnih M, Daubert S, Golino D, Rowhani A, Virology 2009 387 2 395 401 10.1016/j.virol.2009.02.028 19304303
13. Deep sequencing analysis of viruses infecting grapevines: virome of a vineyard. Coetzee B, Freeborough M-J, Maree HJ, Celton J, Rees DJG, Burger JT, Virology 2010 400 2 157 163 10.1016/j.virol.2010.01.023 20172578
14. A review of Grapevine Leafroll associated Virus type 3 (GLRaV-3) for the New Zealand wine industry. Report to New Zealand Winegrowers. Charles JG, Cohen D, Walker JTS, Forgie SA, Bell VA, Breen KC, HortResearch client report 2006 18447 1 79
15. Plant pathogen diagnostics: immunological and nucleic acid-based approaches. Ward E, Foster SJ, Fraaije BA, McCartney HA, Ann Appl Biol 2004 145 1 16 10.1111/j.1744-7348.2004.tb00354.x
16. ®) assays for the detection of grapevine leafroll associated viruses 1-5 and 9. Osman F, Leutenegger C, Colino D, Rowhani A, J Virol Methods 2007 141 22 29 10.1016/j.jviromet.2006.11.035 17223203
17. High-resolution melting analysis as a powerful tool to discriminate and genotype pseudomonas savastanoi pathovars and strains. Gori A, Cerboneschi M, Tegli S, PLoS One 2012 7 1 1 13
18. High-resolution DNA melting analysis for simple and efficient molecular diagnostics. Reed GH, Kent JO, Wittwer CT, Pharmacogenomics 2007 8 6 597 608 10.2217/14622416.8.6.597 17559349
19. Differentiation between vaccine and wild-type varicella-zoster virus genotypes by high-resolution melting analysis of single nucleotide polymorphisms. Toi CS, Dwyer DE, J Clin Virol 2008 43 18 24 10.1016/j.jcv.2008. 03.027 18479962
20. Optimization of high-resolution melting analysis simultaneous genotyping of two 11β-hydoxysteroid dehydrogenase type 1 gene polymorphisms. Dujic T, Ostanek B, Marc J, Causevic A, Minar B, Genet Test Mol Bioma 2011 15 1-2 43 49
21. Classification of mycoplasma synoviae strains using single-strand conformation polymorphism and high-resolution melting-curve analysis of the vlhA gene single-copy region. Jeffery N, Gasser RB, Steer PA, Noormohammadi AH, Microbiology 2007 2007 153 2679 2688
22. Rapid evolution of RNA genomes. Holland J, Spindler K, Horodyski F, Grabau E, Nichol S, VandePol S, Science 1982 215 1577 1585 10.1126/science. 7041255 7041255
23. Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population. Vignuzzi M, Stone JK, Arnold JJ, Cameron CE, Andino R, Nature 2006 439 344 348 10.1038/nature04388 16327776
24. Distribution of grapevine leafroll associated virus-3 variants in South African vineyards. Jooste AEC, Pietersen G, Burger JT, Eur J Plant Pathol 2011 131 371 381 10.1007/s10658-011-9814-2
25. Additive effects of bovine serum albumin, dithiothreitol, and glycerol on PCR. Nagai M, Yoshida A, Sato N, Biochem Mol Biol Int 1998 44 1 157 163 9503159
26. Relief of amplification inhibition in PCR with bovine serum albumin or T4 gene 32 protein. Kreader CA, Appl Environ Microbiol 1996 62 3 1102 1106 8975603
27. An efficient and economic enhancer mix for PCR. Ralser M, Querfurth R, Warnatz HJ, Lehrach H, Yaspo ML, Krobitsch S, Biochem Biophys Res Commun 2006 347 747 751 10.1016/j.bbrc.2006.06.151 16842759
28. Mapping of the 5' terminal nucleotides of Grapevine leafroll-associated virus 3 sgRNAs. Maree HJ, Gardner HFJ, Freeborough M-J, Burger JT, Virus Res 2010 151 252 255 10.1016/j.virusres.2010.05.011 20561952
29. Comparative Effectiveness of ELISA and RT-PCR for Detecting Grapevine Leafroll-Associated Closterovirus-3 in Field Samples. Ling KS, Zhu HY, Petrovic N, Gonsalves D, Am J Enol Viticult 2001 52 1 21 27
30. Modified Cetyltrimethylammonium bromide method improves robustness and versatility: the benchmark for plant RNA extraction. White EJ, Venter M, Hiten NF, Burger JT, Biotechnol J 2008 3 11 1424 1428 10.1002/biot.200800207 19016512
31. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Hall TA, Nucleic Acids Symp Ser 1999 41 95 98
32. An optimized grapevine RNA isolation procedure and statistical determination of reference genes for real-time RT-PCR during berry development. Reid KE, Olsson N, Schlosser J, Peng F, Lund ST, BMC Plant Biol 2006 6 27 1 11 16472405