Stochastic processes strongly influence HIV-1 evolution during suboptimal protease-inhibitor therapy

Proceedings of the National Academy of Sciences of the United States of America

Volumn 95, Issue 24, 1998, Pages 14441-14446

  Nijhuis, Monique ^a   Boucher, Charles A B ^a   Schipper, Pauline ^a   Leitner, Thomas ^b,c   Schuurman, Rob ^a   Albert, Jan ^b  

^a UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

^b SWEDISH INSTITUTE FOR INFECTIOUS DISEASE CONTROL   (Sweden)

^c LOS ALAMOS NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN INHIBITOR; RITONAVIR;

ARTICLE; ENZYME INHIBITION; EVOLUTION; GENE SEQUENCE; GENETIC ANALYSIS; HUMAN; HUMAN CELL; HUMAN IMMUNODEFICIENCY VIRUS 1; MOLECULAR CLONING; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; PROTEINASE INHIBITION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; STOCHASTIC MODEL;

ACQUIRED IMMUNODEFICIENCY SYNDROME; AMINO ACID SEQUENCE; BASE SEQUENCE; DNA PRIMERS; DRUG RESISTANCE, MICROBIAL; EVOLUTION, MOLECULAR; GENE PRODUCTS, ENV; GENES, ENV; GENOTYPE; HIV PROTEASE INHIBITORS; HIV-1; HUMANS; MOLECULAR SEQUENCE DATA; PHYLOGENY; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RITONAVIR; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; STOCHASTIC PROCESSES; VARIATION (GENETICS);

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

EID: 0032564366     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.95.24.14441     Document Type: Article

References (49)

1. Domingo, E., Escarmis, C., Sevilla, N., Moya, A., Elena, S. F., Quer, J., Novella, I. S. & Holland, J. J. (1996) FASEB J. 10, 859-864.
2. Coffin, J. M. (1992) Curr. Top. Microbiol. Immunol. 176, 143-164.
3. Domingo, E. & Holland, J. J. (1997) Annu. Rev. Microbiol. 51, 151-178.
4. Eigen, M. (1992) Steps Toward Life (Oxford Univ. Press, Oxford).
5. Eigen, M. (1993) Gene 135, 37-47.
6. Piatak, M., Jr., Saag, M. S., Yang, L. C., Clark, S. J., Kappes, J. C., Luk, K. C, Hahn, B. H., Shaw, G. M. & Lifson, J. D. (1993) Science 259, 1749-1754.
7. Wei, X., Ghosh, S. K., Taylor, M. E., Johnson, V. A., Emini, E. A., Deutsch, P., Lifson, J. D., Bonhoeffer, S., Nowak, M. A., Hahn, B. H., et al. (1995) Nature (London) 373, 117-122.
8. Ho, D. D., Neumann, A. U., Perelson, A. S., Chen, W., Leonard, J. M. & Markowitz, M. (1995) Nature (London) 373, 123-126.
9. Perelson, A. S., Neumann, A. U., Markowitz, M., Leonard, J. M. & Ho, D. D. (1996) Science 271, 1582-1586.
10. Coffin, J. M. (1995) Science 267, 483-489.
11. Leigh Brown, A. J. & Richman, D. D. (1997) Nat. Med. 3, 268-271.
12. Leigh Brown, A. J. (1997) Proc. Natl. Acad. Sci. USA 94, 1862-1865.
13. Danner, S. A., Carr, A., Leonard, J. M., Lehman, L., Gudiol, F., Gonzales, J., Raventos, A., Rubio, R., Bouza, E., Pintado, V., et al. (1995) New Engl. J. Med. 333, 1528-1533.
14. Roos, M. T., Miedema, F., Eeftinck Schattenkerk, J. K., de Wolf, F., Goudsmit, J., Lange, J. M., Danner, S. A., Out, T. A. & Schellekens, P. T. (1989) Neth. J. Med. 34, 132-141.
15. Boom, R., Sol, C. J., Salimans, M. M., Jansen, C. L., Wertheimvan Dillen. P. M. & van der Noordaa, J. (1990) J. Clin. Microbiol. 28, 495-503.
16. Mulder, J., McKinney, N., Christopherson, C., Sninsky, J., Greenfield, L. & Kwok. S. (1994) J. Clin. Microbiol. 32, 292-300.
17. Nijhuis, M., Boucher, C. A. B. & Schuurman, R. (1995) Bio-Techniques 19, 178-180.
18. Smith, S. (1992) GDE, Genetic Data Environment (Millipore Imaging Systems. Ann Harbor, MI), Version 2.2.
19. Kumar, S., Tamura, K. & Nei, M. (1993) MEGA, Molecular Evolutionary Genetic Analysis (Institute of Molecular Evolutionary Genetics, Pennsylvania State Univ., University Park, PA), Version 1.01.
20. Leitner, T., Kumar, S. & Albert, J. (1997) J. Virol. 71, 4761-4770.
21. Felsenstein, J. (1991) PHYLIP, Phylogenetic Inference Package (Univ. of Washington, Seattle), Version 3.4.
22. Kuhner, M. K., Yamato, J. & Felsenstein, J. (1997) FLUCTUATE, Metropolis-Hastings Markov Chain Monte Carlo Genealogy Sampler (Univ. of Washington, Seattle), Version 1.1 (beta).
23. Mansky, L. M. & Temin, H. M. (1995) J. Virol. 69, 5087-5094.
24. Ruiz, L, Nijhuis, M., Boucher, C., Puig, T., Bonjoch, A., Martinez-Picado, J., Marfil, S., de Jong, D., Burger, D., Arno, A., et al. (1998) J. Acquired Immune Defic. Syndr. Hum. Retrovirol. 19, 19-28.
25. Molla, A., Korneyeva, M., Gao, Q., Vasavanonda, S., Schipper, P. J., Mo, H. M., Markowitz, M., Chernyavskiy, T., Niu, P., Lyons N., et al. (1996) Nat. Med. 2, 760-766.
26. Markowitz, M., Mo, H., Kempf, D. J., Norbeck, D. W., Bhat, T. N., Erickson, J. W. & Ho, D. D. (1995) J. Virol. 69, 701-706.
27. de Jong, J. J., Goudsmit, J., Keulen, W., Klaver, B., Krone, W. J., Tersmette, M. & de Ronde, A. (1992) J. Virol. 66, 757-765.
28. Fouchier, R. A. M., Groenink, M., Kootstra, N. A., Tersmette, M., Huisman, H. G., Miedema, F. & Schuitemaker, H. (1992) J. Virol. 66, 3183-3187.
29. Zhang, Y. M., Dawson, S. C., Landsman, D., Lane, H. C. & Salzman, N. P. (1994) J. Virol. 68, 425-432.
30. Leigh Brown, A. J. & Cleland, A. (1996) AIDS 10, 1067-1073.
31. Cleland, A., Watson, H. G., Robertson, P., Ludlam, C. A. & Leigh Brown, A. J. (1996) J. Acquired Immune Defic. Syndr. Hum. Retrovirol. 12, 6-18.
32. Kozal, M. J., Shafer, R. W., Winters, M. A., Katzenstein, D. A. & Merigan, T. C. (1993) J. Infect. Dis. 167, 526-532.
33. Kroodsma, K. L., Kozal, M. J., Hamed, K. A., Winters, M. A. & Merigan, T. C. (1994) J. Infect. Dis. 170, 1292-1295.
34. Layne, S. P., Merges, M. J., Dembo, M., Spouge, J. L., Conley, S. R., Moore, J. P., Raina, J. L., Renz, H., Gelderblom, H. R. & Nara, P. L. (1992) Virology 189, 695-714.
35. de Jong, M. D., Veenstra, J., Stilianakis, N. I., Schuurman, R., Lange, J. M. A., de Boer, R. J. & Boucher, C. A. B. (1996) Proc. Natl. Acad. Sci. USA 93, 5501-5506.
36. de Boer, R. J. & Boucher, C. A. B. (1996) Proc. R. Soc. London Ser. B 263, 899-905.
37. de Jong, M. D., de Boer, R. J., de Wolf, F., Foudraine, N., Boucher, C. A. B., Goudsmit, J. & Lange, J. M. A. (1997) AIDS 11, F79-F84.
38. Wong, J. K., Hezareh, M., Günthard, H. F., Havlir, D. V., Ignacio, C. C., Spina, C. A. & Richman, D. D. (1997) Science 278, 1291-1295.
39. Finzi, D., Hermankova, M., Pierson, T., Carruth, L. M., Buck. C., Chaisson, R. E., Quinn, T. C., Chadwick, K., Margolick, J., Brookmeyer, R., et al. (1997) Science 278, 1295-1300.
40. Condra, J. H., Holder, D. J., Schleif, W. A., Blahy, O. M., Danovich, R. M., Gabryelski, L. J., Graham, D. J., Laird, D., Quintero, J. C., Rhodes, A., et al. (1996) J. Virol. 70, 8270-8276.
41. Boucher, C. A., O'Sullivan, E., Mulder, J. W., Ramautarsing, C., Kellam, P., Darby, G., Lange, J. M., Goudsmit, J. & Larder, B. A. (1992) J. Infect. Dis. 165, 105-110.
42. Duarte, E., Clarke, D., Moya, A., Domingo, E. & Holland, J. (1992) Proc. Natl. Acad. Sci. USA 89, 6015-6019.
43. Novella, I. S., Elena, S. F., Moya, A., Domingo, E. & Holland, J. J. (1995) J. Virol. 69, 2869-2872.
44. Clarke, D. K., Duarte, E. A., Moya, A., Elena, S. F., Domingo, E. & Holland, J. (1993) J. Virol. 67, 222-228.
45. Chao, L. (1990) Nature (London) 348, 454-455.
46. Zennou, V., Mammano, F., Paulos, S., Mathez, D. & Clavel, F. (1998) J. Virol. 72, 3300-3306.
47. Croteau, G., Doyon, L., Thibeault, D., McKerchcr, G., Pilote, L. & Lamarre, D. (1997) J. Virol. 71, 1089-1096.
48. Nijhuis, M., Schuurman. R., de Jong, D., Schipper, P. & Boucher, C. (1997) Antiviral Ther. 92, 61-62 (abstr.).
49. Delwart, E. L., Pan, H., Neumann, A. & Markowitz, M. (1998) J. Virol. 72, 2416-2421.