Investigating the specificity of real-time PCR assays using synthetic oligonucleotides

Journal of Virological Methods

Volumn 130, Issue 1-2, 2005, Pages 30-35

  Boonham, N ^a   Fisher, T ^a   Mumford, R A ^a  

^a CENTRAL SCIENCE LABORATORY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE; OLIGONUCLEOTIDE;

ARTICLE; ASSAY; CONTROLLED STUDY; DATA BASE; GENE SEQUENCE; GENETIC VARIABILITY; MEXICAN PAPITA VIROID; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; VIROID; VIRUS DETECTION;

DNA PRIMERS; OLIGONUCLEOTIDES; PLANT DISEASES; POLYMERASE CHAIN REACTION; POLYMORPHISM, GENETIC; SENSITIVITY AND SPECIFICITY; SOLANUM TUBEROSUM; VIROIDS;

MEXICAN PAPITA VIROID; POTATO SPINDLE TUBER VIROID; VIROIDS;

EID: 27744528264     PISSN: 01660934     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jviromet.2005.05.029     Document Type: Article

References (25)

1. N. Boonham, P. Smith, K. Walsh, J. Tame, J. Morris, N. Spence, J. Benison, and I. Barker The detection of tomato spotted wilt virus (TSWV) in individual thrips vectors using real time fluorescent RT-PCR (TaqMan) J. Virol. Meth. 101 2002 37 48
2. N. Boonham, L. González, E. Lilia Peralta, A. Blockley, K. Walsh, I. Barker, and R.A. Mumford Development of a real-time RT-PCR assay for the detection of potato spindle tuber viroid (PSTVd) J. Virol. Meth. 116 2004 139 146
3. F.U. Gast, D. Kempe, R.L. Spieker, and H.L. Sanger Secondary structure probing of potato spindle tuber viroid (PSTVd) and sequence comparison with other small pathogenic RNA replicons provides evidence for central non-canonical base-pairs, large A-rich loops, and a terminal branch J. Mol. Biol. 262 5 1996 652 670
4. M.E. Grasmick, and S.A. Slack Effect of potato spindle tuber viroid on sexual reproduction and viroid transmission in true potato seed Can. J. Bot. 64 1986 336 340
5. Y. Joung, J. Jeon, K. Choi, H. Kim, and H. Joung Detection of potato spindle tuber viroid using RT-PCR technique Kor. J. Plant Pathol. 13 1997 205 209
6. ®) RT-PCR assay J. Virol. Meth. 103 2002 109 120
7. A.E. Mackie, S.J. McKirdy, B. Rodoni, and S. Kumar Potato spindle tuber viroid eradicated in Western Australia Aust. Plant Pathol. 31 3 2002 311 312
8. R.A. Mumford, A. Skelton, E. Metcalfe, K. Walsh, and N. Boonham The reliable detection of barley yellow and mild mosaic viruses using real-time PCR (TaqMan) J. Virol. Meth. 117 2004 153 159
9. R.A. Mumford, K. Walsh, I. Barker, and N. Boonham 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
10. OEPP/EPPO, 2004. Diagnostic protocols for regulated pests: potato spindle tuber pospiviroid. PM 7/33 (1). EPPO Bull. 34, 257-269.
11. M. Ozakman, and N.W. Schaad A real-time BIO-PCR assay for detection of Ralstonia solanacearum race 3, biovar 2, in asymptomatic potato tubers Can. J. Plant Pathol. 25 3 2003 232 239
12. M.A. Pfannenstiel, and S.A. Slack Response of potato cultivars to infection by the potato spindle tuber viroid Phytopathology 70 1980 922 926
13. H. Puchta, T. Herold, K. Verhoven, J.W. Roenhorst, K. Ramm, W. Schmidt-Puchta, and H.L. Sanger A new strain of potato spindle tuber viroid (PSTVd-N) exhibits major sequence differences as compared to all other strains sequenced so far Plant Mol. Biol. 15 3 1990 509 511
14. M. Querci, R.A. Owens, C. Vargas, and L.F. Salazar Detection potato spindle tuber viroid in avocado growing in Peru Plant Dis. 79 2 1995 196 202
15. C. Ratti, G. Budge, L. Ward, G. Clover, C. Rubies-Autonell, and C. Henry Detection and quantitation of soil-borne cereal mosaic virus and Polymyxa graminis in winter wheat using real-time PCR (TaqMan) J. Virol. Meth. 122 2004 95 103
16. L.F. Salazar, M. Querci, I. Bartolini, and V. Lazarte Aphid transmission of potato spindle tuber viroid assisted by potato leafroll virus Fitopathologia 30 1995 56 58
17. N.W. Schaad, R.D. Frederick, J. Shaw, W.L. Schneider, R. Hickson, M.D. Petrillo, and D.G. Luster Advances in molecular-based diagnostics in meeting crop biosecurity and phytosanitary issues Annu. Rev. Phytopathol. 41 2003 305 324
18. N.W. Schaad, and R.D. Frederick Real-time PCR and its application for rapid plant disease diagnostics Can. J. Plant Pathol. 24 3 2002 250 258
19. A.M. Shamloul, F. Faggioli, J.M. Keith, and A. Hadidi A novel multiplex RT-PCR probe capture hybridization (RT-PCR-ELISA) for simultaneous detection of six viroids in four genera: Apscaviroid, Hostuviroid, Pelamoviroid, and Pospiviroid J. Virol. Meth. 105 1 2002 115 121
20. J. Verhoven, and J.W. Roenhorst Virological risks accompanying the increased interest in pepino (Solanum muricatum) Advances in Vegetable Virus Research, Proceedings of the Eighth Conference on Virus Diseases of Vegetables Prague, Czech Republic, 9-15 July 1995 109 112
21. L. Ward, M. Fenn, and C. Henry A rapid method for detection of Polymyxa DNA in soil Plant Pathol. 53 2004 485 490
22. H.L. Weideman, and U. Buchta A simple and rapid method for the detection of potato spindle tuber Potato Res. 41 1998 1 8
23. S.A. Weller, and D.E. Stead Detection of root mat associated Agrobacterium strains from plant material and other sample types by post-enrichment TaqMan PCR J. Appl. Microbiol. 92 1 2002 118 126
24. S.A. Weller, S.A. Simpkins, D.E. Stead, A. Kurdziel, H. Hird, and R.J. Weekes Identification of Agrobacterium spp. present within Brassica napus seed by TaqMan PCR-implications for GM screening procedures Arch. Microbiol. 178 5 2002 338 343
25. S.A. Weller, J.G. Elphinstone, N.C. Smith, N. Boonham, and D.E. Stead Detection of Ralstonia solanacearum strains with a quantitative, multiplex, real-time, fluorogenic PCR (TaqMan) assay Appl. Environ. Microbiol. 66 7 2000 2853 2858