A TaqMan PCR assay using degenerate primers for the quantitative detection of woodchuck hepatitis virus DNA of multiple genotypes

Molecular and Cellular Probes

Volumn 19, Issue 4, 2005, Pages 282-289

  Huang, Zhuhui ^a   Buckwold, Victor E ^a  

^a SOUTHERN RESEARCH INSTITUTE   (United States)

Author keywords

Degenerate primers; Real time PCR; TaqMan; Viral detection; Woodchuck hepatitis virus (WHV)

Indexed keywords

ARTICLE; CONTROLLED STUDY; DNA DETERMINATION; GENE AMPLIFICATION; GENE IDENTIFICATION; GENE LOCATION; GENE SEQUENCE; GENOMICS; GENOTYPE; HEPATITIS B VIRUS; HEPATITIS VIRUS; MOLECULAR DYNAMICS; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; VALIDATION PROCESS;

ANIMALS; BASE SEQUENCE; DNA PRIMERS; DNA, VIRAL; GENOME, VIRAL; GENOTYPE; HEPATITIS B VIRUS, WOODCHUCK; MOLECULAR SEQUENCE DATA; PLASMIDS; POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS; RESEARCH DESIGN; SENSITIVITY AND SPECIFICITY; TAQ POLYMERASE;

ANIMALIA; HEPATITIS B VIRUS; MARMOTA MONAX; WOODCHUCK HEPATITIS B VIRUS;

EID: 22144465869     PISSN: 08908508     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mcp.2005.04.004     Document Type: Article

References (23)

1. B.C. Tennant, and J.L. Gerin The woodchuck model of hepatitis B virus infection ILAR J 42 2001 89 102
2. I.M. MacKay, K.E. Arden, and A. Nitsche Real-time PCR in virology Nucl Acids Res 30 2002 1292 1305
3. V.E. Buckwold, R.J.H. Wilson, A. Nalca, B.E. Beer, T.G. Voss, and J. Turpin Antiviral activity of hop constituents against a series of DNA and RNA viruses Antiviral Res 61 2004 57 62
4. J.I. Cohen, R.H. Miller, B. Rosenblum, K. Denniston, J.L. Gerin, and R.H. Purcell Sequence comparison of woodchuck hepatitis virus replicative forms shows conservation of the genome Virology 162 1988 12 20
5. M.C. Kew, T. Chestnut, B.H. Baldwin, W.E. Hornbuckle, B.C. Tennant, and R.H. Purcell Heterogeneity of the woodchuck hepatitis virus genome in a chronically infected woodchuck Virus Res 27 1993 229 237
6. R. García-Navarro, B. Blanco-Urgoiti, P. Berraondo, R. Sánchez de la Rosa, A. Vales, and S. Hervás-Stubbs Protection against woodchuck hepatitis virus (WHV) infection by gene gun coimmunization with WHV core and interleukin-12 J Virol 75 2001 9068 9076
7. C. Argentini, V. La Sora, R. Bruni, E. D'Ugo, R. Giuseppetti, and M. Rapicetta Hepadnavirus evolution and molecular strategy of adaptation in a new host J Gen Virol 80 1999 617 626
8. M. Dandri, M.R. Burda, H. Will, and J. Petersen Increased hepatocyte turnover and inhibition of woodchuck hepatitis B virus replication by adefovir in vitro do not lead to reduction of the closed circular DNA Hepatology 32 2000 139 146
9. K. Kodama, N. Ogasawara, H. Yoshikawa, and S. Murakami Nucleotide sequence of a cloned woodchuck hepatitis virus genome: evolutional relationship between hepadnaviruses J Virol 56 1985 978 986
10. -ΔΔCt method Methods 25 2001 402 408
11. W. Liu, and D.A. Saint A new quantitative method of real time reverse transcription polymerase chain reaction assay based on simulation of polymerase chain reaction kinetics Anal Biochem 302 2002 52 59
12. S. Kwok, D.E. Kellogg, N. McKinney, D. Spasic, L. Goda, and C. Levenson Effects on primer-template mismatches on the polymerase chain reaction: human immunodeficiency virus type 1 model studies Nucl Acids Res 18 1990 999 1005
13. L.V. Mendelman, J. Petruska, and M.F. Goodman Base mispair extension kinetics. Comparison of DNA polymerase alpha and reverse transcriptase J Biol Chem 265 1990 2338 2346
14. S. Creighton, M.M. Huang, H. Cai, N. Arnheim, and M.F. Goodman Base mispair extension kinetics. Binding of avian myeloblastosis reverse transcriptase to matched and mismatched base pair termini J Biol Chem 267 1992 2633 2639
15. M.M. Huang, N. Arnheim, and M.F. Goodman Extension of bases mispairs by Taq DNA polymerase: implications for single nucleotide discrimination in PCR Nucl Acids Res 20 1992 4567 4573
16. S. Ayyadevara, J.J. Thaden, and R.J.S. Reis Discrimination of primer 3′-nucleotide mismatch by Taq DNA polymerase during polymerase chain reaction Anal Biochem 284 2000 11 18
17. D.R. Kilpatrick, B. Nottay, C.F. Yang, S.J. Yang, M.N. Mulders, and B.P. Holloway Group-specific identification of polioviruses by PCR using primers containing mixed-base or deoxyinosine residue at positions of codon degeneracy J Clin Microbiol 34 1996 2990 2996
18. D.R. Kilpatrick, J. Quay, M.A. Pallansch, and M.S. Oberste Type-specific detection of echovirus 30 isolates using degenerate reverse- transcriptase PCR primers J Clin Microbiol 39 2001 1299 1302
19. B.A. Brown, D.R. Kilpatrick, M.S. Oberste, and M.A. Pallansch Serotype-specific identification of enterovirus 71 by PCR J Clin Virol 16 2000 107 112
20. M. Drogemuller, T. Schnieder, and G. von Samson-Himmelstjerna Evidence of p-glycoprotein sequence diversity in cyathostomins J Parasitol 90 2004 998 1003
21. M.M. van Oers, E.A. Herniou, M. Usmany, G.J. Messelink, and J.M. Vlak Identification and characterization of a DNA photolyase-containing baculovirus from Chrysodeixis chalcites Virology 330 2004 460 470
22. J. Jacobsen, M. Lydolph, and L. Lange Culture independent PCR: an alternative enzyme discovery strategy J Microbiol Methods 60 2005 63 71
23. T. Yamamoto, S. Litwin, T. Zhou, Y. Zhu, L. Condreay, and P. Furman Mutations of the woodchuck hepatitis virus polymerase gene that confer resistance to lamivudine and 2′-fluoro-5-methyl-beta-l- arabinofuranosyluracil J Virol 76 2002 1213 1223