Maintenance of Nef-mediated modulation of major histocompatibility complex class I and CD4 after sexual transmission of human immunodeficiency virus type 1

Journal of Virology

Volumn 81, Issue 9, 2007, Pages 4776-4786

  Noviello, C M ^a,b   Kosakovsky Pond, S L ^c   Lewis, M J ^e   Richman, D D ^a,b,c,d   Pillai, S K ^b   Yang, O O ^e   Little, S J ^b   Smith, D M ^a,b,d   Guatelli, J C ^a,b,d  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d VA SAN DIEGO HEALTHCARE SYSTEM   (United States)

^e UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CD4 ANTIGEN; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 1; NEF PROTEIN;

ARTICLE; CLINICAL ARTICLE; CLONE; CYTOTOXIC T LYMPHOCYTE; DOWN REGULATION; GENE; GENETIC VARIABILITY; HOST RANGE; HUMAN; HUMAN CELL; HUMAN IMMUNODEFICIENCY VIRUS 1; IMMUNE RESPONSE; IMMUNE SYSTEM; NEF GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; RECIPIENT; SEXUAL TRANSMISSION; VIRUS CELL INTERACTION; VIRUS INFECTIVITY; VIRUS REPLICATION;

AMINO ACID SEQUENCE; ANTIGENS, CD4; BASE SEQUENCE; BLOTTING, WESTERN; EVOLUTION, MOLECULAR; FLOW CYTOMETRY; GENE EXPRESSION REGULATION, VIRAL; GENE PRODUCTS, NEF; GENES, MHC CLASS I; HIV INFECTIONS; HIV-1; HUMANS; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; SELECTION (GENETICS); SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; T-LYMPHOCYTES, CYTOTOXIC; VARIATION (GENETICS);

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 34247625458     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/JVI.01793-06     Document Type: Article

References (48)

1. Ali, A., H. L. Ng, M. D. Dagarag, and O. O. Yang. 2005. Evasion of cytotoxic T lymphocytes is a functional constraint maintaining HIV-1 Nef expression. Eur. J. Immunol. 35:3221-3228.
2. Ali, A., S. Pillai, H. Ng, R. Lubong, D. D. Richman, B. D. Jamieson, Y. Ding, M. J. McElrath, J. C. Guatelli, and O. O. Yang. 2003. Broadly increased sensitivity to cytotoxic T lymphocytes resulting from Nef epitope escape mutations. J. Immunol. 171:3999-4005.
3. + T-cell responses represents a major driving force of human immunodeficiency virus type 1 (HIV-1) sequence diversity and reveals constraints on HIV-1 evolution. J. Virol. 79:13239-13249.
4. Benichou, S., M. Bomsel, M. Bodeus, H. Durand, M. Doute, F. Letourneur, J. Camonis, and R. Benarous. 1994. Physical interaction of the HIV-1 Nef protein with β-COP, a component of non-clathrin-coated vesicles essential for membrane traffic. J. Biol. Chem. 269:30073-30076.
5. Carl, S., T. C. Greenough, M. Krumbiegel, M. Greenberg, J. Skowronski, J. L. Sullivan, and F. Kirchhoff. 2001. Modulation of different human immunodeficiency virus type 1 Nef functions during progression to AIDS. J. Virol. 75:3657-3665.
6. Chohan, B., D. Lang, M. Sagar, B. Korber, L. Lavreys, B. Richardson, and J. Overbaugh. 2005. Selection for human immunodeficiency virus type 1 envelope glycosylation variants with shorter V1-V2 loop sequences occurs during transmission of certain genetic subtypes and may impact viral RNA levels. J. Virol. 79:6528-6531.
7. Coleman, S. H., J. R. Day, and J. C. Guatelli. 2001. The HIV-1 Nef protein as a target for antiretroviral therapy. Emerg. Ther. Targets 5:1-22.
8. Collins, K. L., B. K. Chen, S. A. Kalams, B. D. Walker, and D. Baltimore. 1998. HIV-1 Nef protein protects infected primary cells against killing by cytotoxic T lymphocytes. Nature 391:397-401.
9. Darsow, T., C. G. Burd, and S. D. Emr. 1998. Acidic di-leucine motif essential for AP-3-dependent sorting and restriction of the functional specificity of the Vam3p vacuolar t-SNARE. J. Cell Biol. 142:913-922.
10. Deacon, N. J., A. Tsykin, A. Solomon, K. Smith, M. Ludford-Menting, D. J. Hooker, D. A. McPhee, A. L. Greenway, A. Ellett, C. Chatfield, V. A. Lawson, S. Crowe, A. Maerz, S. Sonza, J. Learmont, J. S. Sullivan, A. Cunningham, D. Dwyer, D. Dowton, and J. Mills. 1995. Genomic structure of an attenuated quasi species of HIV-1 from a blood transfusion donor and recipients. Science 270:988-991.
11. Derdeyn, C. A., J. M. Decker, F. Bibollet-Ruche, J. L. Mokili, M. Muldoon, S. A. Denham, M. L. Heil, F. Kasolo, R. Musonda, B. H. Hahn, G. M. Shaw, B. T. Korber, S. Allen, and E. Hunter. 2004. Envelope-constrained neutralization-sensitive HIV-1 after heterosexual transmission. Science 303:2019-2022.
12. Evans, D. T., D. H. O'Connor, P. Jing, J. L. Dzuris, J. Sidney, J. da Silva, T. M. Allen, H. Horton, J. E. Venham, R. A. Rudersdorf, T. Vogel, C. D. Pauza, R. E. Bontrop, R. DeMars, A. Sette, A. L. Hughes, and D. I. Watkins. 1999. Virus-specific cytotoxic T-lymphocyte responses select for amino-acid variation in simian immunodeficiency virus Env and Nef. Nat. Med. 5:1270-1276.
13. Frater, A. J., C. T. Edwards, N. McCarthy, J. Fox, H. Brown, A. Milicic, N. Mackie, T. Pillay, J. W. Drijfhout, S. Dustan, J. R. Clarke, E. C. Holmes, H. T. Zhang, K. Pfafferott, P. J. Goulder, M. O. McClure, J. Weber, R. E. Phillips, and S. Fidler. 2006. Passive sexual transmission of human immunodeficiency virus type 1 variants and adaptation in new hosts. J. Virol. 80:7226-7234.
14. Friedrich, T. C., E. J. Dodds, L. J. Yant, L. Vojnov, R. Rudersdorf, C. Cullen, D. T. Evans, R. C. Desrosiers, B. R. Mothe, J. Sidney, A. Sette, K. Kunstman, S. Wolinsky, M. Piatak, J. Lifson, A. L. Hughes, N. Wilson, D. H. O'Connor, and D. I. Watkins. 2004. Reversion of CTL escape-variant immunodeficiency viruses in vivo. Nat. Med. 10:275-281.
15. Frost, S., T. Wrin, D. Smith, S. Kosakovsky Pond, Y. Liu, E. Paxinos, C. Chappey, J. Galovich, J. Beauchaine, C. Petropoulos, S. Little, and D. Richman. 2005. Neutralizing antibody responses drive the evolution of human immunodeficiency virus type 1 envelope during recent HIV infection. Proc. Natl. Acad. Sci. USA 102:18514-18519.
16. Frost, S. D. W., Y. Liu, S. L. Kosakovsky Pond, C. Chappey, T. Wrin, C. J. Petropoulos, S. J. Little, and D. D. Richman. 2005. Characterization of human immunodeficiency virus type 1 (HIV-1) envelope variation and neutralizing antibody responses during transmission of HIV-1 subtype B. J. Virol. 79:6523-6527.
17. Furutsuki, T., N. Hosoya, A. Kawana-Tachikawa, M. Tomizawa, T. Odawara, M. Goto, Y. Kitamura, T. Nakamura, A. D. Kelleher, D. A. Cooper, and A. Iwamoto. 2004. Frequent transmission of cytotoxic T-lymphocyte escape mutants of human immunodeficiency virus type 1 in the highly HLA-A24-positive Japanese population. J. Virol. 78:8437-8445.
18. Geyer, M., and B. M. Peterlin. 2001. Domain assembly, surface accessibility and sequence conservation in full length HIV-1 Nef. FEBS Lett. 496:91-95.
19. + T-cell depletion in human lymphoid tissue ex vivo. J. Virol. 75:10113-10117.
20. Haas, G., U. Plikat, P. Debre, M. Lucernari, C. Katlaina, Y. Dudoit, O. Bonduelle, M. Bauer, H. G. Ihlenfeldt, G. Jung, B. Maier, A. Meyerhans, and B. Autran. 1996. Dynamics of viral variants in HIV-1 Nef and specific cytotoxic T lymphocytes in vivo. J. Immunol. 157:4212-4221.
21. Jones, D. T., W. R. Taylor, and J. M. Thornton. 1992. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8:275-282.
22. Kirchhoff, F., P. J. Easterbrook, N. Douglas, M. Troop, T. C. Greenough, J. Weber, S. Carl, J. L. Sullivan, and R. S. Daniels. 1999. Sequence variations in human immunodeficiency virus type 1 Nef are associated with different stages of disease. J. Virol. 73:5497-5508.
23. Kosakovsky Pond, S. L., and S. D. Frost. 2005. Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol. Biol. Evol. 22:1208-1222.
24. Kosakovsky Pond, S. L., and S. D. W. Frost. 2005. A genetic algorithm approach to detecting lineage-specific variation in selection pressure. Mol. Biol. Evol. 22:478-485.
25. Kosakovsky Pond, S. L., and S. D. W. Frost. 2005. A simple hierarchical approach to modeling distributions of substitution rates. Mol. Biol Evol. 22:223-234.
26. Kosakovsky Pond, S. L., D. Posada, M. B. Gravenor, C. H. Woelk, and S. D. Frost. 2006. GARD: a genetic algorithm for recombination detection. Bioinformatics 22:3096-3098.
27. Leslie, A. J., K. J. Pfafferott, P. Chetty, R. Draenert, M. M. Addo, M. Feeney, Y. Tang, E. C. Holmes, T. Allen, J. G. Prado, M. Altfeld, C. Brander, C. Dixon, D. Ramduth, P. Jeena, S. A. Thomas, J. A. St, T. A. Roach, B. Kupfer, G. Luzzi, A. Edwards, G. Taylor, H. Lyall, G. Tudor-Williams, V. Novelli, J. Martinez-Picado, P. Kiepiela, B. D. Walker, and P. J. Goulder. 2004. HIV evolution: CTL escape mutation and reversion after transmission. Nat. Med. 10:282-289.
28. Lichterfeld, M., X. G. Yu, D. Cohen, M. M. Addo, J. Malenfant, B. Perkins, E. Pae, M. N. Johnston, D. Strick, T. M. Allen, E. S. Rosenberg, B. Korber, B. D. Walker, and M. Altfeld. 2004. HIV-1 Nef is preferentially recognized by CD8 T cells in primary HIV-1 infection despite a relatively high degree of genetic diversity. AIDS 18:1383-1392.
29. Lundquist, C. A., M. Tobiume, J. Zhou, D. Unutmaz, and C. Aiken. 2002. Nef-mediatcd downrcgulation of CD4 enhances human immunodeficiency virus type 1 replication in primary T lymphocytes. J. Virol. 76:4625-4633.
30. Martin, A. M., D. Nolan, S. Gaudieri, C. A. Almeida, R. Nolan, I. James, F. Carvalho, E. Phillips, F. T. Christiansen, A. W. Purcell, J. McCluskey, and S. Mallal. 2004. Predisposition to abacavir hypersensitivity conferred by HLA-B*5701 and a haplotypic Hsp70-Hom variant. Proc. Natl. Acad. Sci. USA 101:4180-4185.
31. Milicic, A., C. T. Edwards, S. Hue, J. Fox, H. Brown, T. Pillay, J. W. Drijfhout, J. N. Weber, E. C. Holmes, S. J. Fidler, H. T. Zhang, and R. E. Phillips. 2005. Sexual transmission of single human immunodeficiency virus type 1 virions encoding highly polymorphic multisite cytotoxic T-lymphocyte escape variants. J. Virol. 79:13953-13962.
32. O'Neill, E., L. S. Kuo, J. F. Krisko, D. R. Tomchick, J. V. Garcia, and J. L. Foster. 2006. Dynamic evolution of the human immunodeficiency virus type 1 pathogenic factor, Nef. J. Virol. 80:1311-1320.
33. Piguet, V., F. Gu, M. Foti, N. Demaurex, J. Gruenberg, J.-L. Carpentier, and D. Trono. 1999. Nef-induced CD4 degradation: a diacidic-based motif in nef functions as a lysosomal targeting signal through the binding of β-COP in endosomes. Cell 97:63-73.
34. Pillai, S. K., B. Good, S. K. Pond, J. K. Wong, M. C. Strain, D. D. Richman, and D. M. Smith. 2005. Semen-specific genetic characteristics of human immunodeficiency virus type 1 env. J. Virol. 79:1734-1742.
35. Pond, S. K., and S. V. Muse. 2005. Site-to-site variation of synonymous substitution rates. Mol. Biol. Evol. 22:2375-2385.
36. Pond, S. L., and S. D. Frost. 2005. Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics 21:2531-2533.
37. Pond, S. L., S. D. Frost, Z. Grossman, M. B. Gravenor, U. D. Richman, and A. J. Brown. 2006. Adaptation to different human populations by HIV-1 revealed by codon-based analyses. PLoS Comput. Biol. 2:c62.
38. Pond, S. L., S. D. Frost, and S. V. Muse. 2005. HyPhy: hypothesis testing using phylogenies. Bioinformatics 21:676-679.
39. Richman, D. D., R. J. Whitley, and F. G. Hayden (ed.). 2002. Clinical virology, 2nd ed. ASM Press, Washington, DC.
40. Salvi, R., A. R. Garbuglia, C. A. Di, S. Pulciani, F. Montella, and A. Benedetto. 1998. Grossly defective nef gene sequences in a human immunodeficiency virus type 1-seropositive long-term nonprogressor. J. Virol. 72:3646-3657.
41. + T cell responses and viral evolution in women and infants. J. Immunol. 175: 6976-6986.
42. Schwartz, O., V. Marechal, S. Le Gall, F. Lemonnier, and J. M. Heard. 1996. Endocytosis of major histocompatibility complex class I molecules is induced by the HIV-1 Nef protein. Nat. Med. 2:338-342.
43. Shriner, D., D. C. Nickle, M. A. Jensen, and J. I. Mullins. 2003. Potential impact of recombination on sitewise approaches for detecting positive natural selection. Genet. Res. 81:115-121.
44. Shugars, D. C., M. S. Smith, D. H. Glueck, P. V. Nantermet, F. Seillier-Moiseiwitsch, and R. Swanstrom. 1993. Analysis of human immunodeficiency virus type 1 nef gene sequences present in vivo. J. Virol. 67:4639-4650.
45. Smith, D. M., M. C. Strain, S. D. W. Frost, S. K. Pillai, J. K. Wong, T. Wrin, Y. Liu, C. Petropoulos, E. Daar, S. J. Little, and D. D. Richman. 2006. Lack of neutralizing antibody response to HIV-1 predisposes to superinfection. Virology 355:1-5.
46. Tavare, S. 2006. Some probabilistic and statistical problems in the analysis of DNA sequences. Lect. Math. Life Sci. 17:57-86.
47. Wolfs, T. F. W., G. Zwart, M. Bakker, and J. Goudsmit. 1992. HIV-1 genomic RNA diversification following sexual and parenteral virus transmission. Virology 189:103-110.
48. Zhu, T., H. Mo, N. Wang, D. S. Nam, Y. Cao, R. A. Koup, and D. D. Ho. 1993. Genotypic and phenotypic characterization of HIV-1 in patients with primary infection. Science 261:1179-1184.