Detection and discrimination of members of the family Luteoviridae by real-time PCR and SYBR® GreenER™ melting curve analysis

Journal of Virological Methods

Volumn 171, Issue 1, 2011, Pages 46-52

  Chomič, Anastasija ^a   Winder, Louise ^b   Armstrong, Karen F ^a   Pearson, Michael N ^c   Hampton, John G ^a  

^a LINCOLN UNIVERSITY   (New Zealand)

^b AGRESEARCH LTD   (New Zealand)

^c UNIVERSITY OF AUCKLAND   (New Zealand)

Author keywords

ABI PRISM 7000; Degenerate primers; Luteovirus; Polerovirus; Synthetic positive control

Indexed keywords

COAT PROTEIN; REAGENT;

AMPLICON; ARTICLE; BEAN LEAFROLL VIRUS; BEET CHLOROSIS VIRUS; BEET MILD YELLOWING VIRUS; CEREAL YELLOW DWARF VIRUS; CONTROLLED STUDY; CUCURBIT APHID BORNE YELLOW VIRUS; LUTEOVIRIDAE; MELTING POINT; NONHUMAN; NUCLEOTIDE SEQUENCE; POLEROVIRUS; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; RNA EXTRACTION; SEQUENCE ANALYSIS; SOYBEAN DWARF VIRUS; SPECIES IDENTIFICATION; TURNIP YELLOWS VIRUS; VIRUS DETECTION;

CAPSID PROTEINS; DNA, VIRAL; FLUORESCENT DYES; LUTEOVIRIDAE; PLANT DISEASES; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; STAINING AND LABELING; TRANSITION TEMPERATURE; VIROLOGY;

BEAN LEAFROLL VIRUS; BEET CHLOROSIS VIRUS; BEET MILD YELLOWING VIRUS; BEET WESTERN YELLOWS VIRUS; CEREAL YELLOW DWARF VIRUS - RPV; CUCURBIT APHID-BORNE YELLOWS VIRUS; LUTEOVIRIDAE; LUTEOVIRUS; POLEROVIRUS; POTATO LEAFROLL VIRUS; REINDEER PAPILLOMAVIRUS; SOYBEAN DWARF VIRUS; TURNIP YELLOWS VIRUS;

EID: 78650583090     PISSN: 01660934     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jviromet.2010.09.028     Document Type: Article

References (29)

1. Afonina I., Ankoudinova I., Mills A., Lokhov S., Huynh P., Mahoney W. Primers with 5' flaps improve real-time PCR. BioTechniques 2007, 43:770. 772, 774.
2. Balaji B., Bucholtz D.B., Anderson J.M. Barley yellow dwarf virus and Cereal yellow dwarf virus quantification by real-time polymerase chain reaction in resistant and susceptible plants. Phytopathology 2003, 93:1386-1392.
3. Castro C., Arnold J.J., Cameron C.E. Incorporation fidelity of the viral RNA-dependent RNA polymerase: a kinetic, thermodynamic and structural perspective. Virus Res. 2005, 107:141-149.
4. Célix A., López-Sesé A., Almarza N., Gómez-Guillamón M.L., Rodríguez-Cerezo E. Characterization of Cucurbit yellow stunting disorder virus, a Bemisia tabaci-transmitted closterovirus. Phytopathology 1996, 86:1370-1376.
5. Chomič A., Pearson M.N., Clover G.R.G., Farreyrol K., Saul D., Hampton J.G., Armstrong K.F. A generic RT-PCR assay for the detection of Luteoviridae. Plant Pathol. 2010, 59:429-442.
6. D'Arcy C.J., Domier L.L., Torrance L. Detection and diagnosis of luteoviruses. The Luteoviridae 1999, 147-168. CABI Publishing, Wallingford, UK. H.G. Smith, H. Barker (Eds.).
7. Fauquet C., Mayo M.A., Maniloff J., Desselberger U., Ball L.A. Virus Taxonomy: The eighth report of the International Committee on Taxonomy of Viruses 2005, Elsevier Academic Press, San Diego, CA.
8. Herrmann M.G., Durtschi J.D., Bromley L.K., Wittwer C.T., Voelkerding K.V. Amplicon DNA melting analysis for mutation scanning and genotyping: cross-platform comparison of instruments and dyes. Clin. Chem. 2006, 52:494-503.
9. Holland J., Spindler K., Horodyski F., Grabau E., Nichol S., VandePol S. Rapid evolution of RNA genomes. Science 1982, 215:1577-1585.
10. Jung M., Muche J.M., Lukowsky A., Jung K., Loening S.A. Dimethyl sulfoxide as additive in ready-to-use reaction mixtures for real-time polymerase chain reaction analysis with SYBR Green I dye. Anal. Biochem. 2001, 289:292-295.
11. Lekanne Deprez R.H., Fijnvandraat A.C., Ruijter J.M., Moorman A.F.M. Sensitivity and accuracy of quantitative real-time polymerase chain reaction using SYBR green I depends on cDNA synthesis conditions. Anal. Biochem. 2002, 307:63-69.
12. Mayo M.A., D'Arcy C.J. Family Luteoviridae: a reclassification of luteoviruses. The Luteoviridae 1999, 15-22. CABI Publishing, Wallingford, UK. H.G. Smith, H. Barker (Eds.).
13. Menzel W., Jelkmann W., Maiss E. Detection of four apple viruses by multiplex RT-PCR assays with coamplification of plant mRNA as internal control. J. Virol. Methods 2002, 99:81-92.
14. Monis P.T., Giglio S., Saint C.P. Comparison of SYTO9 and SYBR Green I for real-time polymerase chain reaction and investigation of the effect of dye concentration on amplification and DNA melting curve analysis. Anal. Biochem. 2005, 340:24-34.
15. Mouillesseaux K.P., Klimpel K.R., Dhar A.K. Improvement in the specificity and sensitivity of detection for the Taura syndrome virus and yellow head virus of penaeid shrimp by increasing the amplicon size in SYBR Green real-time RT-PCR. J. Virol. Methods 2003, 111:121-127.
16. Nicolas L., Milon G., Prina E. Rapid differentiation of Old World Leishmania species by LightCycler polymerase chain reaction and melting curve analysis. J. Microbiol. Methods 2002, 51:295-299.
17. Nicolas L., Prina E., Lang T., Milon G. Real-time PCR for detection and quantitation of Leishmania in mouse tissues. J. Clin. Microbiol. 2002, 40:1666-1669.
18. Pangasa A., Jex A.R., Campbell B.E., Bott N.J., Whipp M., Hogg G., Stevens M.A., Gasser R.B. High resolution melting-curve (HRM) analysis for the diagnosis of cryptosporidiosis in humans. Mol. Cell. Probes 2009, 23:10-15.
19. Pearson M.N., Clover G.R.G., Guy P.L., Fletcher J.D., Beever R.E. A review of the plant virus, viroid and mollicute records for New Zealand. Aust. Plant Pathol. 2006, 35:217-252.
20. Reed G.H., Kent J.O., Wittwer C.T. High-resolution DNA melting analysis for simple and efficient molecular diagnostics. Pharmacogenomics 2007, 8:597-608.
21. Ririe K.M., Rasmussen R.P., Wittwer C.T. Product differentiation by analysis of DNA melting curves during the polymerase chain reaction. Anal. Biochem. 1997, 245:154-160.
22. Robert Y., Lemaire O. Epidemiology and control strategies. The Luteoviridae 1999, 211-279. CABI Publishing, Wallingford, UK. H.G. Smith, H. Barker (Eds.).
23. Singh R.P., Kurz J., Boiteau G., Bernard G. Detection of Potato leafroll virus in single aphids by the reverse transcription polymerase chain reaction and its potential epidemiological application. J. Virol. Methods 1995, 55:133-143.
24. Steger G. Thermal denaturation of double-stranded nucleic acids: prediction of temperatures critical for gradient gel electrophoresis and polymerase chain reaction. Nucleic Acids Res. 1994, 22:2760-2768.
25. Varga A., James D. Detection and differentiation of Plum pox virus using real-time multiplex PCR with SYBR Green and melting curve analysis: a rapid method for strain typing. J. Virol. Methods 2005, 123:213-220.
26. Varga A., James D. Real-time RT-PCR and SYBR Green I melting curve analysis for the identification of Plum pox virus strains C, EA, and W: effect of amplicon size, melt rate, and dye translocation. J. Virol. Methods 2006, 132:146-153.
27. Vossen R.H., Aten E., Roos A., den Dunnen J.T. High-resolution melting analysis (HRMA): more than just sequence variant screening. Hum. Mutat. 2009, 30:860-866.
28. Winder L., Phillips C., Richards N., Ochoa-Corona F., Hardwick S., Vink C. Need organisms identified for biosecurity? Try DNA melting analysis. Proceedings of the Global Biosecurity Conference, 28 February-3 March, 2010 2010.
29. Yvon M., Monsion B., Martin J.F., Gutiérrez S., Blanc S. PCR-based amplification and analysis of specific viral sequences from individual plant cells. J. Virol. Methods 2009, 159:303-307.