Mutation patterns of the reverse transcriptase and protease genes in human immunodeficiency virus type 1-infected patients undergoing combination therapy: Survey of 787 sequences

Journal of Clinical Microbiology

Volumn 37, Issue 12, 1999, Pages 4099-4106

  Yahi, Nouara ^a   Tamalet, Catherine ^a   Tourrès, Christian ^a   Tivoli, Natacha ^a   Ariasi, Franck ^b   Volot, Françoise ^a   Gastaut, Jean Albert ^c   Gallais, Hervé ^c   Moreau, Jacques ^c   Fantini, Jacques ^b  

^a TIMONE HOSPITAL   (France)

^b AIX MARSEILLE UNIVERSITY   (France)

^c CISIH   (France)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEINASE; RNA DIRECTED DNA POLYMERASE;

ARTICLE; CODON; FRANCE; GENE DELETION; GENE INSERTION; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; NONHUMAN; PRIORITY JOURNAL; VIREMIA; VIRUS INFECTIVITY; VIRUS MUTATION; VIRUS RESISTANCE;

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1; RNA VIRUSES;

EID: 0032701542     PISSN: 00951137     EISSN: None     Source Type: Journal    
DOI: 10.1128/jcm.37.12.4099-4106.1999     Document Type: Article

References (30)

1. Beard, W. A., and S. H. Wilson. 19958. Reverse transcriptase, p. 15-36. In J. Karn (ed.), HIV: a practical approach, vol. 2. Biochemistry, molecular biology and drug discovery. IRL Press, Oxford, United Kingdom.
2. Boucher, C. A., E. O'Sullivan, J. W. Mulder, C. Ramautarsing, P. Kellam, G. Darby, J. M. Lange, J. Goudsmit, and B. A. Larder. 1992. Ordered appearance of zidovudine resistance mutations during treatment of 18 human immunodeficiency virus-positive subjects. J. Infect. Dis. 165:105-110.
3. Brown, A. J., B. T. Korber, and J. H. Condra. 1999. Associations between amino acids in the evolution of HIV type 1 protease sequences under indinavir therapy. AIDS Res. Hum. Retroviruses 15:247-253.
4. Cleland, A., H. G. Watson, P. Robertson, C. A. Ludlam, and A. J. Brown. 1996. Evolution of zidovudine resistance-associated genotypes in human immunodeficiency virus type 1-infected patients. J. Acquir. Immune Defic. Syndr. Hum. Retrovirol. 12:6-18.
5. Coffin, J. 1995. HIV population dynamics in vivo: implications for genetic variation, pathogenesis, and therapy. Science 267:483-489.
6. Cornelissen, M., R. van den Burg, F. Zorgdrager, V. Lukashov, and J. Goudsmit. 1997. pol gene diversity of five human immunodeficiency virus type 1 subtypes: evidence for naturally occurring mutations that contribute to drug resistance, limited recombination patterns, and common ancestry for subtypes B and D. J. Virol. 71:6348-6358.
7. Domingo, E. 1997. RNA virus mutations and fitness for survival. Annu. Rev. Microbiol. 51:151-178.
8. Hirsch, M. S., B. Conway, R. T. D'Aquila, V. A. Johnson, F. Brun-Vézinet, B. Clotet, L. M. Demeter, S. M. Hammer, D. M. Jacobsen, D. R. Kuritzkes, C. Loveday, J. W. Mellors, S. Vella, and D. D. Richman. 1998. Antiretroviral drug resistance testing in adults with HIV infection: implications for clinical management. JAMA 279:1984-1991.
9. HIV RT and protease database. [Online.] http://hivdb.stanford.edu/hiv.
10. Hooker, D. J., G. Tachedjian, A. E. Solomon, A. D. Gurusinghe, S. Land, C. Birch, J. L. Anderson, B. M. Roy, E. Arnold, and N. J. Deacon. 1996. An in vivo mutation from leucine to tryptophan at position 210 in human immunodeficiency virus type 1 reverse transcriptase contributes to high-level resistance to 3′-azido-3′-deoxythymidine. J. Virol. 70:8010-8018.
11. Hsu, M., P. Inouye, L. Rezende, N. Richard, Z. Li, V. R. Prasad, and M. A. Wainberg. 1997. Higher fidelity of RNA-dependent DNA mispair extension by M184V drug-resistant than wild-type reverse transcriptase of human immunodeficiency virus type 1. Nucleic Acids Res. 25:4532-4536.
12. Ives, K. J., H. Jacobsen, S. A. Galpin, M. M. Garaev, L. Dorrell, J. Mous, K. Bragman, and J. N. Weber. 1997. Emergence of resistant variants of HIV in vivo during monotherapy with the protease inhibitor saquinavir. J. Antimicrob. Chemother. 39:771-779.
13. Jacobo-Molina, A., J. Ding, R. G. Nanni, A. D. Clark, Jr., X. Lu, C. Tantillo, R. L. Williams, G. Kramer, A. L. Ferris, P. Clark, A. Hizi, S. H. Hugues, and E. Arnold. 1993. Crystal structure of human immunodeficiency virus type 1 reverse transcriptase complexed with double-stranded DNA at 3.0 Å resolution shows bent DNA. Proc. Natl. Acad. Sci. USA 90:6320-6324.
14. Koch, N., N. Yahi, F. Ariasi, J. Fantini, and C. Tamalet. 1999. Comparison of human immunodeficiency virus type 1 (HIV-1) mutations in HIV-1 genomes detected in plasma and in peripheral blood mononuclear cells from patients receiving combination drug therapy. J. Clin. Microbiol. 37:1595-1597
15. Kozal, M. J., N. Shah, N. Shen, R. Yang, R. Facini, T. C. Merrigan, D. D. Richman, D. Morris, E. Hubbell, M. Chee, and T. R. Gingeras. 1996. Extensive polymorphisms observed in HIV-1 clade B protease gene using high-density oligonucleotide arrays. Nat. Med. 2:753-759.
16. Larder, B. A., P. Kellam, and S. Kemp. 1991. Zidovudine resistance predicted by direct detection of mutations in DNA from HIV-infected lymphocytes. AIDS 5:137-144.
17. Learn, G. H., Jr., B. T. Korber, B. Foley, B. H. Hahn, S. M. Wolinsky, and J. I. Mullins. 1996. Maintaining the integrity of human immunodeficiency virus sequence databases. J. Virol. 70:5720-5730.
18. Leitner, T., E. Halapi, G. Scarlatti, P. Rossi, J. Albert, E. M. Fenyö, and M. Uhlen. 1993. Analysis of heterogeneous viral populations by direct DNA sequencing. BioTechniques 15:120-127.
19. Meyerhans, A. E., R. Cheynier, J. Albert, M. Seth, S. Kwok, J. Sninsky, J. Morfeldt-Manson, B. Asjö, and S. Wain-Hobson. 1989. Temporal fluctuations in HIV quasispecies in vivo are not reflected by sequential HIV isolations. Cell 58:901-910.
20. Najera, I., A. Holguin, M. E. Quinones-Mateu, M. A. Munoz-Fernandez, R. Najera, C. Lopez-Galindez, and E. Domingo. 1995. pol gene quasispecies of human immunodeficiency virus: mutations associated with drug resistance in virus from patients undergoing no therapy. J. Virol. 69:25-31.
21. Pandey, V. N., N. Kaushik, N. Rege, S. G. Sarafianos, P. M. Yadav, and M. J. Modak. 1996. Role of methionine 184 of human immunodeficiency virus type-1 reverse transcriptase in the polymerase function and fidelity of DNA synthesis. Biochemistry 35:2168-2179.
22. Pazzani, M. J., D. See, E. Schroeder, and J. Tilles. 1997. Application of an expert system in the management of HIV-infected patients. J. Acquir. Immune Defic. Syndr. Hum. Retrovirol. 15:356-362.
23. Quan, Y., Z. Gu, X. Li, C. Liang, M. A. Parniak, and M. A. Wainberg. 1998. Endogenous reverse transcriptase assays reveal synergy between combinations of the M184V and other drug resistance-conferring mutations in interactions with nucleoside analog triphosphates. J. Mol. Biol. 277:237-247.
24. Rezende, L. F., K. Curr, K. Ueno, H. Mitsuya, and V. R. Prasad. 1998. The impact of multideoxynucleoside resistance-conferring mutations in human immunodeficiency virus type 1 reverse transcriptase on polymerase fidelity and error specificity. J. Virol. 72:2890-2895.
25. Roberts, N. A., J. C. Craig, and J. Sheldon. 1998. Resistance and cross-resistance with saquinavir and other HIV protease inhibitors: theory and practice. AIDS 12:453-460.
26. Shafer, R. W., D. Stevenson, and B. Chan. 1999. Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucleic Acids Res. 27:348-352.
27. Tamalet, C., J. Izopet, N. Koch, J. Fantini, and N. Yahi. 1998. Stable rearrangements of the β3-β4 hairpin loop of HIV-1 reverse transcriptase in plasma viruses from patients receiving combination therapy. AIDS 12:F161-F166.
28. Tantillo, C., J. Ding, A. Jacobo-Molina, R. G. Nanni, P. L. Boyer, S. H. Hugues, R. Pauwels, K. Andries, P. A. Janssen, and E. Arnold. 1994. Locations of anti-AIDS drug binding sites and resistance mutations in the three-dimensional structure of HIV-1 reverse transcriptase. Implications for mechanisms of drug inhibition and resistance. J. Mol. Biol. 243:369-387.
29. Temin, H. 1993. Retrovirus variation and reverse transcription: abnormal strand transfers result in retrovirus genetic variation. Proc. Natl. Acad. Sci. USA 90:6320-6324.
30. Winters, M. A., K. L. Cooley, Y. A. Girard, D. J. Levee, H. Hamdan, R. W. Shafer, D. A. Katzenstein, and T. C. Merrigan. 1998. A 6-basepair insert in the reverse transcriptase gene of human immunodeficiency virus type 1 confers resistance to multiple nucleoside inhibitors. J. Clin. Invest. 102:1769-1775.