Consensus-degenerate hybrid oligonucleotide primers (CODEHOPs) for the detection of novel viruses in non-human primates

Methods

Volumn 49, Issue 1, 2009, Pages 32-41

  Staheli, Jeannette P ^a   Ryan, Jonathan T ^a   Bruce, A Gregory ^a   Boyce, Richard ^b   Rose, Timothy M ^a,c  

^a SEATTLE CHILDREN S RESEARCH INSTITUTE   (United States)

^b UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

Author keywords

CODEHOP; Consensus; consensus degenerate hybrid oligonucleotide primer; Degenerate; L1 protein; Macaque; Non human primate; Oligonucleotide; Papillomavirus; Pathogens; Polymerase chain reaction; Primers; Virus

Indexed keywords

NERVE CELL ADHESION MOLECULE L1; OLIGONUCLEOTIDE;

AMINO ACID SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; COMPUTER PROGRAM; CONSENSUS DEGENERATE HYBRID OLIGONUCLEOTIDE PRIMER; DNA TEMPLATE; GENE AMPLIFICATION; GENE IDENTIFICATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PAPILLOMA VIRUS; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; VIRUS DETECTION; WART VIRUS;

ANIMALS; CONSERVED SEQUENCE; DNA PRIMERS; DNA, VIRAL; HUMANS; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIMATE DISEASES; PRIMATES; VIRUS DISEASES; VIRUSES;

MACACA; MAMMALIA; PAPILLOMAVIRIDAE; PRIMATES;

EID: 68949100483     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2009.05.011     Document Type: Article

References (25)

1. Rose T.M., Schultz E.R., Henikoff J.G., Pietrokovski S., McCallum C.M., and Henikoff S. Nucleic Acids Res. 26 (1998) 1628-1635
2. Rose T.M. Virol. J. 2 (2005) 20
3. Rose T.M., Henikoff J.G., and Henikoff S. Nucleic Acids Res. 31 (2003) 3763-3766
4. Henikoff S., Henikoff J.G., and Pietrokovski S. Bioinformatics 15 (1999) 471-479
5. R. Boyce, J. Henikoff, S. Henikoff, T.M. Rose, 2008. Available from: .
6. VanDevanter D.R., Warrener P., Bennett L., Schultz E.R., Coulter S., Garber R.L., and Rose T.M. J. Clin. Microbiol. 34 (1996) 1666-1671
7. Osterhaus A.D., Pedersen N., van Amerongen G., Frankenhuis M.T., Marthas M., Reay E., Rose T.M., Pamungkas J., and Bosch M.L. Virology 260 (1999) 116-124
8. Wilson C.A., Wong S., Muller J., Davidson C.E., Rose T.M., and Burd P. J. Virol. 72 (1998) 3082-3087
9. Rose T.M., Strand K.B., Schultz E.R., Schaefer G., Rankin Jr. G.W., Thouless M.E., Tsai C.C., and Bosch M.L. J. Virol. 71 (1997) 4138-4144
10. Schultz E.R., Rankin Jr. G.W., Blanc M.P., Raden B.W., Tsai C.C., and Rose T.M. J. Virol. 74 (2000) 4919-4928
11. Rose T.M., Ryan J.T., Schultz E.R., Raden B.W., and Tsai C.-C. J. Virol. 77 (2003) 5084-5097
12. Weiss R.A. Nat. Med. 4 (1998) 391-392
13. Chomel B.B., Belotto A., and Meslin F.X. Emerg. Infect. Dis. 13 (2007) 6-11
14. Chan S.Y., Bernard H.U., Ratterree M., Birkebak T.A., Faras A.J., and Ostrow R.S. J. Virol. 71 (1997) 4938-4943
15. de Villiers E.M., Fauquet C., Broker T.R., Bernard H.U., and Zur Hausen H. Virology 324 (2004) 17-27
16. Chan S.Y., Ostrow R.S., Faras A.J., and Bernard H.U. Virology 228 (1997) 213-217
17. Antonsson A., and Hansson B.G. J. Virol. 76 (2002) 12537-12542
18. Wood C.E., Chen Z., Cline J.M., Miller B.E., and Burk R.D. J. Virol. 81 (2007) 6339-6345
19. Patterson M.M., Rogers A.B., Mansfield K.G., and Schrenzel M.D. Comp. Med. 55 (2005) 75-79
20. Kloster B.E., Manias D.A., Ostrow R.S., Shaver M.K., McPherson S.W., Rangen S.R., Uno H., and Faras A.J. Virology 166 (1988) 30-40
21. Baines J.E., McGovern R.M., Persing D., and Gostout B.S. J. Virol. Methods 123 (2005) 81-87
22. Larkin M.A., Blackshields G., Brown N.P., Chenna R., McGettigan P.A., McWilliam H., Valentin F., Wallace I.M., Wilm A., Lopez R., Thompson J.D., Gibson T.J., and Higgins D.G. Bioinformatics 23 (2007) 2947-2948
23. Rose T.M., Schultz E.R., and Todaro G.J. Proc. Natl. Acad. Sci. USA 89 (1992) 11287-11291
24. Page R.D. Comput. Appl. Biosci. 12 (1996) 357-358
25. Schneider T.D., and Stephens R.M. Nucleic Acids Res. 18 (1990) 6097-6100