Comparison of low-density arrays, RT-PCR and real-time TaqMan® RT-PCR in detection of grapevine viruses

Journal of Virological Methods

Volumn 149, Issue 2, 2008, Pages 292-299

  Osman, Fatima ^a   Leutenegger, Christian ^b   Golino, Deborah ^a   Rowhani, Adib ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b IDEXX LABORATORIES   (United States)

Author keywords

Grapevine virus extraction; Grapevine viruses; RNA; Virus detection methods

Indexed keywords

RNA 18S;

ANALYZER; ARTICLE; CONTROLLED STUDY; GEOGRAPHIC DISTRIBUTION; GRAPE; HIGH THROUGHPUT SCREENING; INTERMETHOD COMPARISON; NONHUMAN; PLANT VIRUS; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ANALYSIS; RNA EXTRACTION; VIRUS DETECTION; VITIVIRUS;

AFRICA; ASIA; AUSTRALIA; DNA PRIMERS; EUROPE; LATIN AMERICA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLANT DISEASES; PLANT VIRUSES; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, VIRAL; UNITED STATES; VITIS;

GRAPEVINE FANLEAF VIRUS; GRAPEVINE FLECK VIRUS; GRAPEVINE LEAFROLL-ASSOCIATED VIRUS 2; TOMATO RINGSPOT VIRUS; VITIS; VITIVIRUS;

EID: 41349098104     PISSN: 01660934     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jviromet.2008.01.012     Document Type: Article

References (22)

1. Agindotan B.O., Shiel P.J., and Berger P.H. Simultaneous detection of potato viruses, PLRV, PVA, PVX and PVY from dormant potato tubers by TaqMan real-time RT-PCR. J. Virol. Methods 142 (2007) 1-9
2. Alkowni R., Rowhani A., Daubert S., and Golino D. Partial characterization of a new ampelovirus associated with Grapevine leafroll disease. J. Plant Pathol. 86 (2004) 123-133
3. Balme-Sinibaldi V., Tribodet M., Croizat F., Lefeuvre P., Kerlan C., and Jacquot E. Improvement of Potato virus Y (PVY) detection and quantitation using PVY(N) - and PVY(O)-specific real-time RT-PCR assays. J. Virol. Methods 134 (2006) 261-266
4. Frosline P.L., Hoch J., Limboy W.F., Mc Ferson J.R., Golino D., and Gonsalves D. Comparative effectiveness of symptomatology and ELISA for detecting two isolates of grapevine leafroll in Cabernet Franc. Am. J. Enol. Vitic. 47 (1996) 239-243
5. Harju V.A., Skelton A., Clover G.R., Ratti C., Boonham N., Henry C.M., and Mumford R.A. The use of real-time RT-PCR (TaqMan) and post-ELISA virus release for the detection of Beet necrotic yellow vein virus types containing RNA 5 and its comparison with conventional RT-PCR. J. Virol. Methods 123 (2005) 73-80
6. Holland P.M., Abramson R.D., Watson R., and Ge D.H. Detection of specific polymerase chain reaction product by utilizing the 5′ → 3′ nuclease activity of Thermus aquaticus DNA polymerase. Proc Natl. Acad. Sci. U.S.A. 88 (1991) 7276-7280
7. Lima M.F., Alkowni R., Uyemoto J.K., Golino D., Osman F., and Rowhani A. Molecular analysis of a California strain of Rupestris stem pitting-associated virus isolated from declining Syrah grapevines. Arch. Virol. 151 9 (2006) 1889-1894
8. Lopez R., Asensio C., Cuzman M.M., and Boonham N. Development of real-time and conventional RT-PCR assays for the detection of potato yellow vein virus (PYVV). J. Virol. Methods 136 1/2 (2006) 24-29
9. Lunello P., Mansilla C., Conci V., and Ponz F. Ultra-sensitive detection of two garlic potyviruses using a real-time fluorescent (TaqMan) RT-PCR assay. J. Virol. Methods 118 (2004) 15-21
10. Martelli G.P., Agranovsky A.A., Bar-Joseph M., Boscia D., Candresse T., Coutts R.H., Dolja V.V., Falk B.W., Gonsalves D., Jelkmann W., Karasev A.V., Minafra A., Namba S., Vetten H.J., Wisler G.C., and Yoshikawa N. ICTV Study Group on closteroviruses. The family Closteroviridae revised. Arch. Virol. 147 (2002) 2039-2044
11. Minafra A., Saldarelli P., Grieco F., and Martelli G.P. Nucleotide sequence of the 3′ terminal region of the RNA of two filamentous grapevine viruses. Arch. Virol. 137 (1994) 249-261
12. Mumford R., Mumford K., Walsh I., Barker I., and Boonham N. Detection of potato mop top virus and tobacco rattle virus using a multiplex real-time fluorescent reverse-transcription polymerase chain reaction assay. Phytopathology 90 (2000) 448-453
13. Mumford R., Skelton A., Metcalfe E., Walsh K., and Boonham N. The reliable detection of Barley yellow and mild mosaic viruses using real-time PCR (TaqMan). J. Virol. Methods 117 (2004) 153-159
14. Newbury H.J., and Possingham J.V. Factors affecting the extraction of intact ribonucleic acid from plant tissue containing interfering phenolic compounds. Plant Phys. 60 (1977) 543-547
15. ®) assays for the detection of Grapevine leafroll associated viruses 1-5 and 9. J. Virol. Methods 141 (2007) 22-29
16. Osman F., and Rowhani A. Application of a spotting sample preparation technique for the detection of pathogens in woody plants by RT-PCR and real-time PCR (TaqMan). J. Virol. Methods 133 (2006) 130-136
17. Rezaian M.A., and Krake L.R. Nucleic acid extraction and virus detection in grapevine. J. Virol. Methods 17 (1987) 277-285
18. Rowhani A. Use of (ab′)2 antibody fragment in ELISA for detection of grapevine viruses. Am. J. Enol. Vitic. 43 (1992) 38-40
19. Rowhani A., Biardi L., Johnson R., Saldarelli P., Zhang Y.P., Chin J., and Green M. Simplified sample preparation method and one-tube RT-PCR for grapevine viruses. Proceedings of XIII International Council for the Study of Viruses and Virus-Like Diseases of the Grapevine. Adelaide 2000 (2000) 82
20. Sanchez F., Chay C., Borja M.J., Rowhani A., Romero J., Bruening G., and Ponz F. cDNA sequence of the capsid protein gene and 3 «untranslated region of a fanleaf isolate of Grapevine fanleaf virus. Nucleic Acids Res. 19 (1991) 5440
21. Schaad N.W., and Frederick R.D. Real-time PCR and its application for rapid plant disease diagnostics. Can. J. Plant Pathol. Rev. 24 3 (2002) 250-258
22. Schneider W.L., Sherman D.J., Stone A.L., Damsteegt V.D., and Frederick R.D. Specific detection and quantification of Plum pox virus by real-time fluorescent reverse transcription-PCR. J. Virol. Methods 120 (2004) 97-105