Mapping sites of positive selection and amino acid diversification in the HIV genome: An alternative approach to vaccine design?

Genetics

Volumn 167, Issue 3, 2004, Pages 1047-1058

  De Oliveira, Tulio ^a   Salemi, Marco ^b   Gordon, Michelle ^a   Vandamme, Anne Mieke ^b   Van Rensburg, Estrelita Janse ^c   Engelbrecht, Susan ^c   Coovadia, Hoosen M ^a   Cassol, Sharon ^a,d  

^a UNIVERSITY OF KWAZULU NATAL   (South Africa)

^b REGA INSTITUTE FOR MEDICAL RESEARCH   (Belgium)

^c STELLENBOSCH UNIVERSITY   (South Africa)

^d UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; CASEIN KINASE II; EPITOPE; HUMAN IMMUNODEFICIENCY VIRUS VACCINE; IMMEDIATE EARLY PROTEIN; PEPTIDE; REV PROTEIN; TRANSACTIVATOR PROTEIN; VIRUS ENVELOPE PROTEIN; VIRUS PROTEIN;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ANTIGENICITY; ARTICLE; CODON; ENZYME PHOSPHORYLATION; GENE MAPPING; HUMAN IMMUNODEFICIENCY VIRUS; MAXIMUM LIKELIHOOD METHOD; MYRISTYLATION; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; VIRUS GENOME;

AMINO ACID SEQUENCE; CHROMOSOME MAPPING; DATABASES, GENETIC; EPITOPES; GENES, REV; GENES, TAT; GENOME, VIRAL; HIV-1; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; SELECTION (GENETICS); SEQUENCE ALIGNMENT; VACCINES; VARIATION (GENETICS);

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1; MACACA; MACACA MULATTA; SIMIAN IMMUNODEFICIENCY VIRUS;

EID: 3843062475     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: 10.1534/genetics.103.018135     Document Type: Article

References (56)

1. ABELE, R., and R. TAMPE, 1999 Function of the transport complex TAP in cellular immune recognition. Biochim. Biophys. Acta 1461: 405-419.
2. ADDO, M., M. ALTFELD, E. S. ROSENBERG, R. L. ELDRIDGE, M. N. PHILIPS et al., 2001 The HIV-1 regulatory proteins Tat and Rev are frequently targeted by cytotoxic T lymphocytes derived from HIV-1-infected individuals. Proc. Natl. Acad. Sci. USA 98: 1783-1796.
3. ALLEN, T. M., D. H. O'CONNOR, P. JING, J. L. DZURIS, B. R. MOTHE et al., 2000 Tat-specific cytotoxic T lymphocytes select for SIV escape variants during resolution of primary viraemia. Nature 407: 386-390.
4. ANISIMOVA, M., J. P. BIELAWSKI and Z. YANG, 2001 Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution. Mol. Biol. Evol. 18: 1585-1592.
5. ANISIMOVA, M., R. NIELSEN and Z. YANG, 2003 Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics 164: 1229-1236.
6. BAROUCH, D. H., J. KUNSTMAN, M. J. KURODA, J. E. SCHMITZ, S. SANTRA et al., 2002 AIDS vaccine failure in a rhesus monkey by viral escape from cytotoxic T lymphocytes. Nature 415: 335-339.
7. BOCHTLER, M., L. DITZEL, M. GROLL, C. HARTMANN and R. HUBER, 1999 The proteasome. Annu. Rev. Biophys. Biomol. Struct. 28: 295-317.
8. BORROW, P., H. LEWICKI, X. WEI, M. S. HORWITZ, N. PEFFER et al., 1997 Antiviral pressure exerted by HIV-1 specific cytotoxic T lymphocytes (CTLs) during primary infection demonstrated by rapid selection of CTL escape virus. Nat. Med. 3: 205-211.
9. BRANDER, C., and P. J. R. GOULDER, 1999 Recent advances in HIV-1 CTL epitope characterization, pp. IV-1-17 in HIV Molecular Immunology Database, edited by T. M. KORBER, C. BRANDER, B. F. HAYNES, R. KOUP, C. KUIKEN et al. Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM.
10. CHECK, E., 2003 AIDS vaccines: back to 'plan A.' Nature 424: 912-914.
11. CHUN, R. F., O. J. SEMMES, C. NEUVEUT and K. T. JEANG, 1998 Modulation of Sp1 phosphorylation by human immunodeficiency virus type 1 Tat. J. Virol. 72: 2615-2629.
12. DANIEL, M. D., F. KIRCHHOFF, S. C. CZAJAK, P. K. SEHGAL and R. C. DESROSIERS, 1992 Protective effects of a live attenuated SIV vaccine with a deletion in the nef gene. Science 258: 1938-1941.
13. DA SILVA, J., and A. L. HUGHES, 1998 Conservation of cytotoxic T lymphocyte (CTL) epitopes as a host strategy to constrain parasite adaptation: evidence from the nef gene of human immunodeficiency virus 1 (HIV-1). Mol. Biol. Evol. 15: 1259-1268.
14. DELWART, E. L., J. I. MULLINS, P. GUPTA, G. H. LEARN and M. HOLODINY, 1998 Human immunodeficiency virus type 1 populations in blood and semen. J. Virol. 72: 617-623.
15. DE OLIVEIRA, T., S. ENGELBRECHT, E. J. VAN RENSBURG, M. GORDON, K. BISHOP et al., 2003a Variability at HIV-1 subtype C protease cleavage sites: An indication of viral fitness? J. Virol. 77: 9422-943.
16. DE OLIVEIRA, T., R. MILLER, M. TARIN and S. CASSOL, 2003b An integrated genetic data environment (GDE)-based LINUX interface for analysis of HIV-1 and other microbial sequences. Bioinformatics 19: 153-154.
17. DUNN, C. S., B. HURTREL, C. BEYER, L. GLOECKLER, T. N. LEDGER et al., 1997 Protection of SIV mac-infected macaque monkeys against superinfection by a simian immunodeficiency virus expressing envelope glycoproteins of HIV type 1. AIDS Res. Hum. Retroviruses 13: 913-922.
18. FOUTS, D. E., H. L. TRUE, K. A. CENGEL and D. CELANDER, 1997 Site-specific phosphorylation of the human immunodeficiency virus type-1 Rev protein accelerates formation of an efficient RNA-binding conformation. Biochemistry 36: 13256-13263.
19. GASCHEN, B., J. TAYLOR, K. YUSIM, B. FOLEY, F. GAO et al., 2002 Diversity considerations in HIV-1 vaccine selection. Science 296: 2354-2360.
20. GOULDER, P. J., R. E. PHILLIPS, R. A. COLBERT, S. MCADAM, G. OGG et al., 1997 Late escape from an immunodominant cytotoxic T-lymphocyte response associated with progression to AIDS. Nat. Med. 3: 212-217.
21. HIRSCH, V. M., S. GOLDSTEIN, N. A. HYNES, W. R. ELKINS, W. T. LONDON et al., 1994 Prolonged clinical latency and survival of macaques given a whole inactivated simian immunodeficiency virus vaccine. J. Infect. Dis. 170: 51-59.
22. HOLMES, A. M., 1996 In vitro phosphorylation of human immunodeficiency virus type 1 Tat protein by protein kinase C: evidence for the phosphorylation of amino acid residue serine-46. Arch. Biochem. Biophys. 335: 8-12.
23. HOOVER, E. A., N. A. PERIGO, S. L. QUACKENBUSH, C. K. MATHIASON-DUBARD, J. M. OVERBAUGH et al., 1991 Protection against feline leukemia virus infection by use of an inactivated virus vaccine. J. Am. Vet. Med. Assoc. 199: 1392-1401.
24. HUELSENBECK, J. P., and F. RONQUIST, 2001 MRBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
25. JEANG, K-T., H. XIAO and E. A. RICH, 1999 Multifaceted activities of the HIV-1 transactivator of transcription, Tat. J. Biol. Chem. 274: 28837-28840.
26. KARLSSON, A. C., S. LINDBACK, H. GAINES and A. SONNERBORG, 1998 Characterization of the viral population during primary HIV-1 infection. AIDS 12: 839-847.
27. KLAUSNER, R. D., A. S. FAUCI, L. COREY, G. J. NABEL, H. GAYLE et al., 2003 The need for a global HIV vaccine enterprise. Science 300 (5628): 2036-2039.
28. KORBER, B., and G. MYERS, 1992 Signature pattern analysis: a method for assessing viral sequence relatedness. AIDS Res. Hum. Retroviruses 8: 1549-1560.
29. MARIN, O., S. SARNO, M. BOSCHETTI, M. A. PAGANO, F. MEGGIO et al., 2000 Unique features of HIV-1 Rev protein phosphorylation by protein kinase CK2. FEBS Lett. 481: 63-67.
30. MCMICHAEL, A. T., 1998 Cell responses and viral escape. Cell 93: 673-676.
31. MCMICHAEL, A. J., and R. E. PHILLIPS, 1997 Escape of human immunodeficiency virus from immune control. Annu. Rev. Immunol. 15: 271-296.
32. MEGGIO, F., D. M. D'AGOSTINO, V. CIMINALE, L. CHIEVO-BIANCHI and L. A. PINNA, 1996 Phosphorylation of HIV-1 Rev protein: implication of protein kinase CK2 and pro-directed kinases. Biochem. Biophys. Res. Commun. 226: 547-554.
33. MELLORS, J. W., C. R. RINALDO, JR., P. GUPTA, R. M. WHITE, J. A. TODD et al., 1996 Prognosis in HIV-1 infection predicted by the quantity of virus in plasma. Science 272: 1167-1170.
34. MELLORS, J. W., A. MUNOZ, J. V. GIORGI, J. B. MARGOLICK, C. J. TASSONI et al., 1997 Plasma viral load and CD4+ lymphocytes as prognostic makers of HIV-1 infection. Ann. Intern. Med. 126: 946-954.
35. NIELSEN, R., and Z. YANG, 1998 Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148: 929-936.
36. NOVITSKY, V., N. RYBAK, M. F. MCLANE, P. GILBERT, P. CHIGWEDERE et al., 2001 Identification of human immunodeficiency virus type I subtype C Gag-, Tat-, Rev-, and Nef-specific Elispot-based cytotoxic T-lymphocyte responses for AIDS vaccine design. J. Virol. 75: 9210-9228.
37. O'CONNOR, D., T. ALLEN and D. I. WATKINS, 2001 Vaccination with CTL epitopes that escape: An alternative approach to HIV vaccine development? Immunol. Lett. 79: 71-84.
38. OVERBAUGH, J., and C. R. M. BANGHAM, 2001 Selection forces and constraints on retroviral sequence variation. Science 292: 1106-1109.
39. PAMER, E., and P. CRESSWELL, 1998 Mechanisms of MHC class I-restricted antigen processing. Annu. Rev. Immunol. 16: 323-358.
40. PARADA, C. A., and R. G. ROEDER, 1996 Enhanced processivity of RNA polymerase II triggered by Tat-induced phosphorylation of its carboxy-terminal domain. Nature 384: 375-378.
41. POLLARD, V. W., and M. H. MALIM, 1998 The HIV-1 Rev protein. Annu. Rev. Microbiol. 52: 491-532.
42. POSADA, D., and K. A. CRANDALL, 1998 MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817-818.
43. PRICE, D. A., P. J. GOULDER, P. KLENERMAN, A. K. SEWELL, P. J. EASTER-BROOK et al., 1997 Positive selection of HIV-1 cytotoxic T lymphocytes escape variants during primary infection. Proc. Natl. Acad. Sci. USA 94: 1890-1895.
44. RAMBAUT, A., D. POSADA, K. A. CRANDALL and E. C. HOLMES, 2004 The causes and consequences of HIV evolution. Nat. Rev. Genet. 5: 52-61.
45. RAMMENSEE, H. G., J. BACHMANN, N. P. EMMERICH, O. A. BACHOR, S. STEVANOVIC et al., 1999 SYFPEITHI: database for MHC ligands and peptide motifs. Immunogenetics 50: 213-219.
46. ROSENBERG, E. S., J. M. BILLINGSLEY, A. M. CALIENDO, S. L. BOSWELL, P. E. SAX et al., 1997 Vigorous HIV-1-specific CD4+ T cell responses associated with control of viremia. Science 278: 1447- 1450.
47. SWOFFORD, D. L., 2002 PAUP* 4.0: Phylogenetic Analysis Using Parsimony (and Other Methods), Version 4.0b2a. Sinauer Associates, Sunderland, MA.
48. WILSON, C., R. C. BROWN, B. T. KORBER, B. M. WILKES, D. J. RUHL et al., 1999 Frequent detection of escape from cytotoxic T-lymphocyte recognition in perinatal human immunodeficiency virus (HIV) type 1 transmission: the Ariel project for the prevention of transmission of HIV from mother to infant. J. Virol. 73: 3975-3985.
49. XIA, X., and Z. XIE, 2001 DAMBE: software package for data analysis in molecular biology and evolution. J. Hered. 92 (4): 371-373.
50. YANG, W., J. P. BIELAWSKI and Z. YANG, 2003 Widespread adaptive evolution in the human immunodeficiency virus type 1 genome. J. Mol. Evol. 57 (2): 212-221.
51. YANG, X., C. H. HERRMAN and A. P. RICE, 1996 The human immunodeficiency virus Tat proteins specifically associated with TAK in vivo and require the carboxyl-terminal domain of RNA polymerase II for function. J. Virol. 70: 4576-4584.
52. YANG, Z. 1997 PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13: 555-556.
53. YANG, Z., 2001 Maximum likelihood analysis of adaptive evolution in HIV-1 gp120 env gene. Pac. Symp. Biocomput. 2001: 226-237.
54. YANG, Z., R. NIELSEN, N. GOLDMAN and A. M. PEDERSEN, 2000 Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155: 431-449.
55. YUSIM, K., C. KESMIR, B. GASCHEN, M. M. ADDO, M. ALTFELD et al., 2002 Clustering patterns of cytotoxic T-lymphocyte epitopes in human immunodeficiency virus type 1 (HIV-1) proteins reveal imprints of immune evasion on HIV-1 global variation. J. Virol. 76: 8757-8768.
56. ZANOTTO, P. M., E. G. KALLAS, R. F. DE SOUZA and E. C. HOLMES, 1999 Genealogical evidence for positive selection in the nef gene of HIV-1. Genetics 153: 1077-1089.