Human immunodeficiency virus-specific responses in adult Ugandans: Patterns of cross-clade recognition

Journal of Virology

Volumn 79, Issue 7, 2005, Pages 4132-4139

  Barugahare, Banson ^a   Baker, Chris ^b   K'Aluoch, Okumu ^b   Donovan, Richard ^b   Elrefaei, Mohamed ^b   Eggena, Mark ^c   Jones, Norman ^b   Mutalya, Steven ^a   Kityo, Cissy ^a   Mugyenyi, Peter ^a   Cao, Huyen ^b  

^a JOINT CLINICAL RESEARCH CENTRE   (Uganda)

^b CALIFORNIA DEPARTMENT OF PUBLIC HEALTH   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GAG PROTEIN; NEF PROTEIN; VIRUS ENVELOPE PROTEIN;

ACQUIRED IMMUNE DEFICIENCY SYNDROME; ADULT; AMINO ACID SEQUENCE; ARTICLE; CELLULAR IMMUNITY; CLADISTICS; CONTROLLED STUDY; HUMAN; HUMAN CELL; HUMAN IMMUNODEFICIENCY VIRUS; MAJOR CLINICAL STUDY; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; T LYMPHOCYTE; UGANDA;

ADULT; CELL PROLIFERATION; CONSENSUS SEQUENCE; CONSERVED SEQUENCE; CROSS REACTIONS; EPITOPE MAPPING; EPITOPES; FEMALE; GENE PRODUCTS, ENV; GENE PRODUCTS, GAG; GENE PRODUCTS, NEF; HIV ANTIGENS; HIV INFECTIONS; HIV-1; HUMANS; INTERFERON TYPE II; LYMPHOCYTE ACTIVATION; MALE; MOLECULAR SEQUENCE DATA; SEQUENCE ANALYSIS, DNA; T-LYMPHOCYTES; UGANDA;

EID: 20144372216     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/JVI.79.7.4132-4139.2005     Document Type: Article

References (47)

1. Addo, M. M., X. G. Yu, A. Rathod, D. Cohen, R. L. Eldridge, D. Strick, M. N. Johnston, C. Corcoran, A. G. Wurcel, C. A. Fitzpatrick, M. E. Feeney, W. R. Rodriguez, N. Basgoz, R. Draenert, D. R. Stone, C. Brander, P. J. Goulder, E. S. Rosenberg, M. Altfeld, and B. D. Walker. 2003. Comprehensive epitope analysis of human immunodeficiency virus type 1 (HIV-1)-specific T-cell responses directed against the entire expressed HIV-1 genome demonstrate broadly directed responses, but no correlation to viral load. J. Virol. 77:2081-2092.
2. + T-cell responses: relationship to viral load in untreated HIV infection. J. Virol. 75:11983-11991.
3. 2a. Betts, M. R., J. Krowka, C. Santamaria, K. Balsamo, F. Gao, G. Mulundu, C. C. Luo, N. N'Gandu, H. Sheppard, B. Hahn, S. Allen, and J. A. Frelinger. 1997. Cross-clade human immunodeficiency virus (HIV)-specific cytotoxic T-lymphocyte responses in HIV-infected Zambians. J. Virol. 71:8908-8911.
4. Bruce, C., J. C. Clegg, A. Featherstone, J. Smith, B. Biryahawaho, R. G. Downing, and J. Oram. 1994. Presence of multiple genetic subtypes of human immunodeficiency virus type 1 proviruses in Uganda. AIDS Res. Hum. Retrovir. 10:1543-1550.
5. Burrows, S. R., S. L. Silins, D. J. Moss, R. Khanna, I. S. Misko, and V. P. Argaet. 1995. T cell receptor repertoire for a viral epitope in humans is diversified by tolerance to a background major histocompatibility complex antigen. J. Exp. Med. 182:1703-1715.
6. Cao, H., P. Kaleebu, D. Hom, J. Flores, D. Agrawal, N. Jones, J. Serwanga, M. Okello, C. Walker, H. Sheppard, R. El-Habib, M. Klein, E. Mbidde, P. Mugyenyi, B. D. Walker, J. Ellner, R. Mugerwa, and HIV Network for Prevention Trials. 2003. Immunogenicity of a recombinant human immunodeficiency virus (HIV)-canarypox vaccine in HIV-seronegative Ugandan volunteers: results of the HIV Network for Prevention Trials 007 vaccine study. J. Infect. Dis. 187:887-895.
7. Cao, H., I. Mani, R. Vincent, R. Mugerwa, P. Mugyenyi, P. Kanki, J. Ellner, and B. D. Walker. 2000. Cellular immunity to HIV-1 clades: relevance to HIV-1 vaccine trials in Uganda. J. Infect. Dis. 182:1350-1356.
8. 6a. Cao, H., P. Kanki, J.-L. Sankale, A. Dieng-Sarr, G. P. Mazzara, S. A. Kalams, B. Korber, S. MBoup, and B. D. Walker. 1997. Cytotoxic T-lymphocyte cross-reactivity among different human immunodeficiency virus type 1 clades: implications for vaccine development. J. Virol. 71:8615-8623.
9. + T cells in primary HIV-1 infection. J. Virol. 77:6867-6878.
10. Cao, K., J. Hollenbach, X. Shi, W. Shi, M. Chopek, and M. A. Fernandez-Vina. 2001. Analysis of the frequencies of HLA-A, B, and C alleles and haplotypes in the five major ethnic groups of the United States reveals high levels of diversity in these loci and contrasting distribution patterns in these populations. Hum. Immunol. 62:1009-1030.
11. Cao, K., A. M. Moormann, K. E. Lyke, C. Masaberg, O. P. Sumba, O. K. Doumbo, D. Koech, A. Lancaster, M. Nelson, D. Meyer, R. Single, R. J. Hartzman, C. V. Plowe, J. Kazura, D. L. Mann, M. B. Sztein, G. Thomson, and M. A. Fernandez-Vina. 2004. Differentiation between African populations is evidenced by the diversity of alleles and haplotypes of HLA class I loci. Tissue Antigens 63:293-325.
12. Champagne, P., G. S. Ogg, A. S. King, C. Knabenhans, K. Ellefsen, M. Nobile, V. Appay, G. P. Rizzardi, S. Fleury, M. Lipp, R. Forster, S. Rowland-Jones, R. P. Sekaly, A. J. McMichael, and G. Pantaleo. 2001. Skewed maturation of memory HIV-specific CD8 T lymphocytes. Nature 410:106-111.
13. Collins, K. R., M. E. Quinones-Mateu, M. Wu, H. Luzze, J. L. Johnson, C. Hirsch, Z. Toosi, and E. J. Arts. 2002. Human immunodeficiency virus type 1 (HIV-1) quasispecies at the sites of Mycobacterium tuberculosis infection contribute to systemic HIV-1 heterogeneity. J. Virol. 76:1697-1706.
14. Cornelissen, M., G. Kampinga, F. Zorgdrager, J. Goudsmit, and the UN-AIDS Network for HIV Isolation and Characterization. 1996. Human immunodeficiency virus type 1 subtypes defined by env show high frequency of recombinant gag genes. J. Virol. 70:8209-8212.
15. 12a. Durali, D., J. Morvan, F. Letourneru, D. Schmitt, N. Guegan, M. Dalod, S. Saragosti, D. Sicard, J.-P. Levy, and E. Gomard. 1998. Cross-reactions between the cytotoxic T-lymphocyte responses of human immunodeficiency virus-infected African and European patients. J. Virol. 72:3547-3553.
16. Ellenberger, D. L., B. Li, L. D. Lupo, S. M. Owen, J. Nkengasong, M. S. Kadio-Morokro, J. Smith, H. Robinson, M. Ackers, A. Greenberg, T. Folks, and S. Butera. 2002. Generation of a consensus sequence from prevalent and incident HIV-1 infections in West Africa to guide AIDS vaccine development. Virology 302:155-163.
17. Ferrari, G., J. R. Currier, M. E. Harris, S. Finkelstein, A. de Oliveira, D. Barkhan, J. H. Cox, M. Zeira, K. J. Weinhold, N. Reinsmoen, F. McCutchan, D. L. Birx, S. Osmanov, and S. Maayan. 2004. HLA-A and -B allele expression and ability to develop anti-Gag cross-clade responses in subtype C HIV-1-infected Ethiopians. Hum. Immunol. 65:648-659.
18. 14a. Ferrari, G., W. Humphrey, M. J. McElrath, J. Excler, A. Duliege, M. L. Clements, L. C. Corey, D. P. Bolognesi, and K. J. Weinhold. 1997. Clade B-based HIV-1 vaccines elicit cross-clade cytotoxic T lymphocyte reactivities in uninfected volunteers. Proc. Natl. Acad. Sci. USA 94:1396-1401.
19. Frahm, N., B. T. Korber, C. M. Adams, J. J. Szinger, R. Draenert, M. M. Addo, M. E. Feeney, K. Yusim, K. Sango, N. V. Brown, D. SenGupta, A. Piechocka-Trocha, T. Simonis, F. M. Marincola, A. G. Wurcel, D. R. Stone, C. J. Russell, P. Adolf, D. Cohen, T. Roach, A. StJohn, A. Khatri, K. Davis, J. Mullins, P. J. Goulder, B. D. Walker, and C. Brander. 2004. Consistent cytotoxic-T-lymphocyte targeting of immunodominant regions in human immunodeficiency virus across multiple ethnicities. J. Virol. 78:2187-2200.
20. Gao, F., D. L. Robertson, C. D. Carruthers, S. G. Morrison, B. Jian, Y. Chen, F. Barre-Sinoussi, M. Girard, A. Srinivasan, A. G. Abimiku, G. M. Shaw, P. M. Sharp, and B. H. Hahn. 1998. A comprehensive panel of near-full-length clones and reference sequences for non-subtype B isolates of human immunodeficiency virus type 1. J. Virol. 72:5680-5698.
21. Gao, F., L. Yue, D. L. Robertson, S. C. Hill, H. Hui, R. J. Biggar, A. E. Neequaye, T. M. Whelan, D. D. Ho, and G. M. Shaw. 1994. Genetic diversity of human immunodeficiency virus type 2: evidence for distinct sequence subtypes with differences in virus biology. J. Virol. 68:7433-7447.
22. Gavin, M. A., B. Dere, A. G. Grandea III, K. A. Hogquist, and M. J. Sevan. 1994. Major histocompatibility complex class I allele-specific peptide libraries: identification of peptides that mimic an H-Y T cell epitope. Eur. J. Immunol. 24:2124-2133.
23. Goulder, P. J., C. Brander, K. Annamalai, N. Mngqundaniso, U. Govender, Y. Tang, S. He, K. E. Hartman, C. A. O'Callaghan, G. S. Ogg, M. A. Altfeld, E. S. Rosenberg, H. Cao, S. A. Kalams, M. Hammond, M. Bunce, S. I. Pelton, S. A. Burchett, K. McIntosh, H. M. Coovadia, and B. D. Walker. 2000. Differential narrow focusing of immunodominant human immunodeficiency virus Gag-specific cytotoxic T-lymphocyte responses in infected African and Caucasoid adults and children. J. Virol. 74:5679-5690.
24. Harari, A., S. Petitpierre, F. Vallelian, and G. Pantaleo. 2004. Skewed representation of functionally distinct populations of virus-specific CD4 T cells in HIV-1-infected subjects with progressive disease: changes after antiretroviral therapy. Blood 103:966-972.
25. Hemmer, B., M. Jacobsen, and N. Sommer. 2000. Degeneracy in T-cell antigen recognition-implications for the pathogenesis of autoimmune diseases. J. Neuroimmunol. 107:148-153.
26. Hoelscher, M., W. E. Dowling, E. Sanders-Buell, J. K. Carr, M. E. Harris, A. Thomschke, M. L. Robb, D. L. Birx, and F. McCutchan. 2002. Detection of HIV-1 subtypes, recombinants, and dual infections in east Africa by a multiregion hybridization assay. AIDS 16:2055-2064.
27. Hu, D. J., T. J. Dondero, M. A. Rayfield, R. George, G. Schochetman, H. W. Jaffe, C. C. Luo, M. L. Kalish, B. G. Weniger, C. Pau, C. A. Schable, and J. W. Curran. 1996. The emerging genetic diversity of HIV. The importance of global surveillance for diagnostics, research and prevention. JAMA 275: 210-216.
28. Jacobsen, M., S. Cepok, W. H. Oertel, N. Sommer, and B. Hemmer. 2001. New approaches to dissect degeneracy and specificity in T cell antigen recognition. J. Mol. Med. 79:358-367.
29. Jones, N., D. Agrawal, M. Elrefaei, A. Hanson, V. Novitsky, J. T. Wong, and H. Cao. 2003. Evaluation of antigen-specific responses using in vitro enriched T cells. J. Immunol. Methods 274:139-147.
30. Jubier-Maurin, V., S. Saragosti, J. L. Perret, E. Mpoudi, E. Esu-Williams, C. Mulanga, F. Liegeois, M. Ekwalanga, E. Delaporte, and M. Peeters. 1999. Genetic characterization of the nef gene from human immunodeficiency virus type 1 group M strains representing genetic subtypes A, B, C, E, F, G, and H. AIDS Res. Hum. Retrovir. 15:23-32.
31. Kaleebu, P., J. Whitworth, L. Hamilton, A. Rutebemberwa, F. Lyagoba, D. Morgan, M. Duffield, B. Biryahwaho, B. Magambo, and J. Oram. 2000. Molecular epidemiology of HIV type 1 in a rural community in southwest Uganda. AIDS Res. Hum. Retrovir. 16:393-40.
32. Klenerman, P., S. Rowland-Jones, S. McAdam, J. Edwards, S. Daenke, D. Lalloo, B. Koppe, W. Rosenberg, D. Boyd, A. Edwards, et al. 1994. Cytotoxic T-cell activity antagonized by naturally occurring HIV-1 Gag variants. Nature 369:403-407.
33. Korber, B., B. Gaschen, K. Yusim, R. Thakallapally, C. Kesmir, and V. Detours. 2001. Evolutionary and immunological implications of contemporary HIV-1 variation. Br. Med. Bull. 58:19-42.
34. Mason, D. 1998. A very high level of crossreactivity is an essential feature of the T-cell receptor. Immunol. Today 19:395-404.
35. McAdams, S., P. Kaleebu, P. Krausa, P. Goulder, N. French, B. Collin, T. Blanchard, J. Whitworth, A. McMichael, and F. Gotch. 1998. Cross-clade recognition of p55 by cytotoxic T lymphocytes in HIV-1 infection. AIDS 12:571-579.
36. McKinney, D. M., R. Skvoretz, B. D. Livingston, C. C. Wilson, M. Anders, R. W. Chesnut, A. Sette, M. Essex, V. Novitsky, and M. J. Newman. 2004. Recognition of variant HIV-1 epitopes from diverse viral subtypes by vaccine-induced CTL. J. Immunol. 173:1941-1950.
37. Moore, C. B., M. John, I. R. James, F. T. Christiansen, C. S. Witt, and S. A. Mallal. 2002. Evidence of HIV-1 adaptation to HLA-restricted immune responses at a population level. Science 296:1439-1443.
38. Novitsky, V., H. Cao, N. Rybak, P. Gilbert, M. F. McLane, S. Gaolekwe, T. Peter, I. Thior, T. Ndung'u, R. Marlink, T. H. Lee, and M. Essex. 2002. Magnitude and frequency of cytotoxic T-lymphocyte responses: identification of immunodominant regions of human immunodeficiency virus type 1 subtype C. J. Virol. 76:10155-10168.
39. Novitsky, V., P. Gilbert, T. Peter, M. F. McLane, S. Gaolekwe, N. Rybak, I. Thior, T. Ndung'u, R. Marlink, T. H. Lee, and M. Essex. 2003. Association between virus-specific T-cell responses and plasma viral load in human immunodeficiency virus type 1 subtype C infection. J. Virol. 77:882-890.
40. Novitsky, V., U. R. Smith, P. Gilbert, M. F. McLane, P. Chigwedere, C. Williamson, T. Ndung'u, I. Klein, S. Y. Chang, T. Peter, I. Thior, B. T. Foley, S. Gaolekwe, N. Rybak, S. Gaseitsiwe, F. Vannberg, R. Marlink, T. H. Lee, and M. Essex. 2002. Human immunodeficiency virus type 1 subtype C molecular phylogeny: consensus sequence for an AIDS vaccine design? J. Virol. 76:5435-5451.
41. Raghava, G. P. 2001. A graphical web server for the analysis of protein sequences and alignment. Biotech Software Internet Rep. 2:225-228.
42. Reid, S. W., S. McAdam, K. J. Smith, P. Klenerman, C. A. O'Callaghan, K. Harlos, B. K. Jakobsen, A. J. McMichael, J. I. Bell, D. I. Stuart, and E. Y. Jones. 1996. Antagonist HIV-1 Gag peptides induce structural changes in HLA B8. J. Exp. Med. 184:2279-2286.
43. Rentenaar, R. J., L. E. Gamadia, N. van der Hoek, F. N. van Diepen, P. M. Wertheim-van Dillen, J. F. Weel, S. Surachno, R. A. van Lier, and I. J. ten Berge. 2001. CD8(POS) lymphocyte dynamics in primary CMV infection. Transplant. Proc. 33:1867-1869.
44. Russell, N. D., M. G. Hudgens, R. Ha, C. Havenar-Daughton, and M. J. McElrath. 2003. Moving to human immunodeficiency virus type 1 vaccine efficacy trials: defining T cell responses as potential correlates of immunity. J. Infect. Dis. 187:226-242.
45. Spira, S., M. A. Wainberg, H. Loemba, D. Turner, and B. G. Brenner. 2003. Impact of clade diversity on HIV-1 virulence, antiretroviral drug sensitivity and drug resistance. J. Antimicrob. Chemother. 51:229-240.
46. Wilson, C. C., D. McKinney, M. Anders, S. MaWhinney, J. Forster, C. Crimi, S. Southwood, A. Sette, R. Chesnut, M. J. Newman, and B. D. Livingston. 2003. Development of a DNA vaccine designed to induce cytotoxic T lymphocyte responses to multiple conserved epitopes in HIV-1. J. Immunol. 171:5611-5623.
47. Yirrell, D. L., P. Kaleebu, D. Morgan, C. Watera, B. Magambo, F. Lyagoba, and J. Whitworth. 2002. Inter- and intragenic intersubtype HIV-1 recombination in rural and semiurban Uganda. AIDS 16:279-286.