Analysis of HIV-1 variants by cloning DNA generated with the ViroSeq™ HIV-1 Genotyping System

BioTechniques

Volumn 35, Issue 3, 2003, Pages 614-622

  Eshleman, Susan H ^a   Jones, Dana ^a   Flys, Tamara ^a   Petrauskene, Olga ^b   Jackson, J Brooks ^a  

^a DEPARTMENT OF PATHOLOGY   (United States)

^b APPLIED BIOSYSTEMS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

VIRUS DNA;

DEVICE; GENE AMPLIFICATION; GENE MUTATION; GENOTYPE; HUMAN IMMUNODEFICIENCY VIRUS 1; MOLECULAR CLONING; NONHUMAN; PLASMID; POLYMERASE CHAIN REACTION; REVIEW; VIRUS EXAMINATION;

DNA VIRUSES; HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 0043192554     PISSN: 07366205     EISSN: None     Source Type: Journal    
DOI: 10.2144/03353dd05     Document Type: Review

References (17)

1. Leitner, T., E. Halapi, G. Scarlatti, P. Rossi, J. Albert, E.M. Fenyo, and M. Uhlen. 1993. Analysis of heterogeneous viral populations by direct DNA sequencing. BioTechniques 15:120-127.
2. Chadwick, R.B., M.P. Conrad, M.D. McGinnis, L. Johnston-Dow, S.L. Spurgeon, and M.N. Kronick. 1996. Heterozygote and mutation detection by direct automated fluorescent DNA sequencing using a mutant Taq DNA polymerase. BioTechniques 20:676-683.
3. Larder, B.A., A. Kohli, S.D. Kemp, M.N. Kronick, and R.D. Henfrey. 1993. Quantitative detection of HIV-1 drug resistance mutations by automated DNA sequencing. Nature 365:671-673.
4. Shafer, R.W., K. Dupnik, M.A. Winters, and S.H. Eshleman. 2001. A guide to HIV-1 reverse transcriptase and protease sequencing for drug resistance studies. In Human Retroviruses and AIDS 2001: A Compilation and Analysis of Nucleic Acid and Amino Acid Sequences. Los Alamos National Laboratory, Los Alamos, NM.
5. Cunningham, S., B. Ank, D. Lewis, L. Wei, J. Dileanis, J.B. Jackson, P. Palumbo, P. Krogstad, and S.H. Eshleman. 2001. Performance of the Applied Biosystems ViroSeq HIV-1 Genotyping System for analysis of HIV-1 in pediatric plasma samples. J. Clin. Microbiol. 39:1254-1257.
6. Mracna, M., G. Becker-Pergola, J. Dileanis, L.A. Guay, S. Cunningham, J.B. Jackson, and S.H. Eshleman. 2001. Performance of the Applied Biosystems ViroSeq HIV-1 Genotyping System for sequence-based analysis of non-subtype B HIV-1 from Uganda. J. Clin. Microbiol. 39:4323-4327.
7. Fontaine, E., C. Riva, M. Peeters, J.C. Schmit, E. Delaporte, K. Van Laethem, K. Van Vaerenbergh, J. Snoeck, et al. 2001. Evaluation of two commercial kits for the detection of genotypic drug resistance on a panel of HIV type 1 subtypes A through J. J. Acquir. Immune Defic. Syndr. 28:254-258.
8. Jagodzinski, L.L., J.D. Cooley, M. Weber and N.L. Michael. 2003. Performance characteristics of human immunodeficiency virus type 1 (HIV-1) genotyping systems in sequence-based analysis of subtypes other than HIV-1 subtype B. J. Clin. Microbiol. 41:998-1003.
9. Longo, M.C., M.S. Berninger and J.L. Hartley. 1990. Use of uracil DNA glycosylase to control carry-over contamination in polymerase chain reactions. Gene 93:125-128.
10. Guay, L.A., P. Musoke, T. Fleming, D. Bagenda, M. Allen, C. Nakabiito, J. Sherman, P. Bakaki, et al. 1999. Intrapartum and neonatal single-dose nevirapine compared with zidovudine for prevention of mother-to-infant transmission of HIV-1 in Kampala, Uganda: HIVNET-012 randomised trial. Lancet 354:795-802.
11. Duncan, B.K. 1985. Isolation of insertion, deletion, and nonsense mutations of the uracil- DNA glycosylase (ung) gene of Escherichia coli K-12. J. Bacteriol. 164:689-695.
12. Seidman, C.E., K. Struhl, and J. Sheen. 1997. Introduction of plasmid DNA into cells: High efficiency transformation by electroporation, p. 1.22-21.23. In F.M. Ausubel, R. Brent, R.E. Kingston, D.D. Moore, J.G. Seidman, J.A. Smith, and K. Struhl (Eds.), Short Protocols in Molecular Biology. John Wiley & Sons, New York.
13. Clark, J.M. 1988. Novel non-templated nucleotide addition reactions catalyzed by procaryotic and eucaryotic DNA polymerases. Nucleic Acids Res. 16:9677-9686.
14. Sambrook, S. and D.W. Russell. 2001. Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
15. Duncan, B.K. and B. Weiss. 1982. Specific mutator effects of ung (uracil-DNA glycosylase) mutations in Escherichia coli. J. Bacteriol. 151:750-755.
16. Kuiken, C.L., B. Foley, B. Hahn, B. Korber, P.A. Marx, F. McCutchan, J.W. Mellors, and S. Wolinksy. 2001. HIV Sequence Compendium. Los Alamos National Laboratory, Los Alamos, NM.
17. Shuman, S. 1994. Novel approach to molecular cloning and polynucleotide synthesis using vaccinia DNA topoisomerase. J. Biol. Chem. 269:32678-32684.