Evolution of the HIV-1 nef gene in HLA-B*57 Positive Elite Suppressors

Retrovirology

Volumn 7, Issue , 2010, Pages

  Salgado, Maria ^a   Brennan, Timothy P ^a   O'Connell, Karen A ^a   Bailey, Justin R ^a   Ray, Stuart C ^a   Siliciano, Robert F ^a   Blankson, Joel N ^a  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EPITOPE; GAG PROTEIN; HLA B ANTIGEN; NEF PROTEIN; HLA B57 ANTIGEN; HLA-B57;

ARTICLE; CD8+ T LYMPHOCYTE; GENE MUTATION; GENE SEQUENCE; GENETIC CONSERVATION; GROUP SPECIFIC ANTIGEN GENE; HUMAN IMMUNODEFICIENCY VIRUS 1; NEF GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; VIRUS GENE; VIRUS LOAD; VIRUS REPLICATION; AMINO ACID SEQUENCE; CD4+ T LYMPHOCYTE; GENETICS; HOST PATHOGEN INTERACTION; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; IMMUNOLOGY; MOLECULAR EVOLUTION; MOLECULAR GENETICS; SEQUENCE ALIGNMENT; VIROLOGY;

HUMAN IMMUNODEFICIENCY VIRUS 1;

AMINO ACID SEQUENCE; CD4-POSITIVE T-LYMPHOCYTES; EPITOPES; EVOLUTION, MOLECULAR; HIV INFECTIONS; HIV-1; HLA-B ANTIGENS; HOST-PATHOGEN INTERACTIONS; HUMANS; MOLECULAR SEQUENCE DATA; NEF GENE PRODUCTS, HUMAN IMMUNODEFICIENCY VIRUS; SEQUENCE ALIGNMENT; VIRUS REPLICATION;

EID: 78049469041     PISSN: None     EISSN: 17424690     Source Type: Journal    
DOI: 10.1186/1742-4690-7-94     Document Type: Article

References (36)

1. Baker BM, Block BL, Rothchild AC, Walker BD. Elite control of HIV infection: implications for vaccine design. Expert Opin Biol Ther 2009, 9(1):55-69. 10.1517/14712590802571928, 19063693.
2. Blankson JN. Effector mechanisms in HIV-1 infected elite controllers: highly active immune responses?. Antiviral Res 2010, 85(1):295-302. 10.1016/j.antiviral.2009.08.007, 19733595.
3. Migueles SA, Connors M. Long-term nonprogressive disease among untreated HIV-infected individuals: clinical implications of understanding immune control of HIV. JAMA 2010, 304(2):194-201. 10.1001/jama.2010.925, 20628133.
4. Blankson JN, Bailey JR, Thayil S, Yang HC, Lassen K, Lai J, Gandhi SK, Siliciano JD, Williams TM, Siliciano RF. Isolation and characterization of replication-competent human immunodeficiency virus type 1 from a subset of elite suppressors. J Virol 2007, 81(5):2508-2518. 10.1128/JVI.02165-06, 1865922, 17151109.
5. Lamine A, Caumont-Sarcos A, Chaix ML, Saez-Cirion A, Rouzioux C, Delfraissy JF, Pancino G, Lambotte O. Replication-competent HIV strains infect HIV controllers despite undetectable viremia (ANRS EP36 study). AIDS 2007, 21(8):1043-1045. 10.1097/QAD.0b013e3280d5a7ac, 17457100.
6. Julg B, Pereyra F, Buzon MJ, Piechocka-Trocha A, Clark MJ, Baker BM, Lian J, Miura T, Martinez-Picado J, Addo MM, Walker BD. Infrequent recovery of HIV from but robust exogenous infection of activated CD4(+) T cells in HIV elite controllers. Clin Infect Dis 2010, 51(2):233-238. 10.1086/653677, 20550452.
7. Bailey JR, O'Connell K, Yang HC, Han Y, Xu J, Jilek B, Williams TM, Ray SC, Siliciano RF, Blankson JN. Transmission of human immunodeficiency virus type 1 from a patient who developed AIDS to an elite suppressor. J Virol 2008, 82(15):7395-7410. 10.1128/JVI.00800-08, 2493308, 18495769.
8. Migueles SA, Sabbaghian MS, Shupert WL, Bettinotti MP, Marincola FM, Martino L, Hallahan CW, Selig SM, Schwartz D, Sullivan J, Connors M. HLA B*5701 is highly associated with restriction of virus replication in a subgroup of HIV-infected long term nonprogressors. Proc Natl Acad Sci USA 2000, 97(6):2709-2714. 10.1073/pnas.050567397, 15994, 10694578.
9. Lambotte O, Boufassa F, Madec Y, Nguyen A, Goujard C, Meyer L, Rouzioux C, Venet A, Delfraissy JF, . SEROCO-HEMOCO Study Group HIV controllers: a homogeneous group of HIV-1-infected patients with spontaneous control of viral replication. Clin Infect Dis 2005, 41(7):1053-1056. 10.1086/433188, 16142675, SEROCO-HEMOCO Study Group.
10. Han Y, Lai J, Barditch-Crovo P, Gallant JE, Williams TM, Siliciano RF, Blankson JN. The role of protective HCP5 and HLA-C associated polymorphisms in the control of HIV-1 replication in a subset of elite suppressors. AIDS 2008, 22(4):541-544. 10.1097/QAD.0b013e3282f470e4, 18301071.
11. Emu B, Sinclair E, Hatano H, Ferre A, Shacklett B, Martin JN, McCune JM, Deeks SG. HLA Class I-Restricted T Cell Responses May Contribute to the Control of HIV Infection, but Such Responses are Not Always Necessary for Long-term Virus Control. J Virol 2008, 2395228, 18353945.
12. Pereyra F, Addo MM, Kaufmann DE, Liu Y, Miura T, Rathod A, Baker B, Trocha A, Rosenberg R, Mackey E, Ueda P, Lu Z, Cohen D, Wrin T, Petropoulos CJ, Rosenberg ES, Walker BD. Genetic and immunologic heterogeneity among persons who control HIV infection in the absence of therapy. J Infect Dis 2008, 197(4):563-571. 10.1086/526786, 18275276.
13. Migueles SA, Osborne CM, Royce C, Compton AA, Joshi RP, Weeks KA, Rood JE, Berkley AM, Sacha JB, Cogliano-Shutta NA, Lloyd M, Roby G, Kwan R, McLaughlin M, Stallings S, Rehm C, O'Shea MA, Mican J, Packard BZ, Komoriya A, Palmer S, Wiegand AP, Maldarelli F, Coffin JM, Mellors JW, Hallahan CW, Follman DA, Connors M. Lytic granule loading of CD8+ T cells is required for HIV-infected cell elimination associated with immune control. Immunity 2008, 29(6):1009-1021. 10.1016/j.immuni.2008.10.010, 2622434, 19062316.
14. Sajadi MM, Constantine NT, Mann DL, Charurat M, Dadzan E, Kadlecik P, Redfield RR. Epidemiologic characteristics and natural history of HIV-1 natural viral suppressors. J Acquir Immune Defic Syndr 2009, 50(4):403-408. 10.1097/QAI.0b013e3181945f1e, 2697612, 19214118.
15. Migueles SA, Laborico AC, Imamichi H, Shupert WL, Royce C, McLaughlin M, Ehler L, Metcalf J, Liu S, Hallahan CW, Connors M. The differential ability of HLA B*5701+ long-term nonprogressors and progressors to restrict human immunodeficiency virus replication is not caused by loss of recognition of autologous viral gag sequences. J Virol 2003, 77(12):6889-6898. 10.1128/JVI.77.12.6889-6898.2003, 156173, 12768008.
16. Bailey JR, Williams TM, Siliciano RF, Blankson JN. Maintenance of viral suppression in HIV-1-infected HLA-B*57+ elite suppressors despite CTL escape mutations. J Exp Med 2006, 203(5):1357-1369. 10.1084/jem.20052319, 2121215, 16682496.
17. Miura T, Brockman MA, Schneidewind A, Lobritz M, Pereyra F, Rathod A, Block BL, Brumme ZL, Brumme CJ, Baker B, Rothchild AC, Li B, Trocha A, Cutrell E, Frahm N, Brander C, Toth I, Arts EJ, Allen TM, Walker BD. HLA-B57/B*5801 human immunodeficiency virus type 1 elite controllers select for rare gag variants associated with reduced viral replication capacity and strong cytotoxic T-lymphotye recognition. J Virol 2009, 83(6):2743-2755. 10.1128/JVI.02265-08, 2648254, 19116253.
18. Navis M, Schellens I, van Baarle D, Borghans J, van Swieten P, Miedema F, Kootstra N, Schuitemaker H. Viral replication capacity as a correlate of HLA B57/B5801-associated nonprogressive HIV-1 infection. J Immunol 2007, 179(5):3133-3143.
19. O'Connell KA, Brennan TP, Bailey JR, Ray SC, Siliciano RF, Blankson JN. Control of HIV-1 in elite suppressors despite ongoing replication and evolution in plasma virus. J Virol 2010, 84(14):7018-7028. 10.1128/JVI.00548-10, 20444904.
20. Kiepiela P, Ngumbela K, Thobakgale C, Ramduth D, Honeyborne I, Moodley E, Reddy S, de Pierres C, Mncube Z, Mkhwanazi N, Bishop K, van der Stok M, Nair K, Khan N, Crawford H, Payne R, Leslie A, Prado J, Prendergast A, Frater J, McCarthy N, Brander C, Learn GH, Nickle D, Rousseau C, Coovadia H, Mullins JI, Heckerman D, Walker BD, Goulder P. CD8+ T-cell responses to different HIV proteins have discordant associations with viral load. Nat Med 2007, 13(1):46-53. 10.1038/nm1520, 17173051.
21. Bailey JR, Brennan TP, O'Connell KA, Siliciano RF, Blankson JN. Evidence of CD8+ T-cell-mediated selective pressure on human immunodeficiency virus type 1 nef in HLA-B*57+ elite suppressors. J Virol 2009, 83(1):88-97. 10.1128/JVI.01958-08, 2612327, 18945771.
22. Nei M, Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 1986, 3(5):418-426.
23. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 2007, 24(8):1596-1599. 10.1093/molbev/msm092, 17488738.
24. Migueles SA, Laborico AC, Shupert WL, Sabbaghian MS, Rabin R, Hallahan CW, Van Baarle D, Kostense S, Miedema F, McLaughlin M, Ehler L, Metcalf J, Liu S, Connors M. HIV-specific CD8+ T cell proliferation is coupled to perforin expression and is maintained in nonprogressors. Nat Immunol 2002, 3(11):1061-1068. 10.1038/ni845, 12368910.
25. Betts MR, Nason MC, West SM, De Rosa SC, Migueles SA, Abraham J, Lederman MM, Benito JM, Goepfert PA, Connors M, Roederer M, Koup RA. HIV nonprogressors preferentially maintain highly functional HIV-specific CD8+ T cells. Blood 2006, 107(12):4781-4789. 10.1182/blood-2005-12-4818, 1895811, 16467198.
26. Saez-Cirion A, Lacabaratz C, Lambotte O, Versmisse P, Urrutia A, Boufassa F, Barre-Sinoussi F, Delfraissy JF, Sinet M, Pancino G, Venet A, . Agence Nationale de Recherches sur le Sida EP36 HIV Controllers Study Group HIV controllers exhibit potent CD8 T cell capacity to suppress HIV infection ex vivo and peculiar cytotoxic T lymphocyte activation phenotype. Proc Natl Acad Sci USA 2007, 104(16):6776-6781. 10.1073/pnas.0611244104, 1851664, 17428922, Agence Nationale de Recherches sur le Sida EP36 HIV Controllers Study Group.
27. Saez-Cirion A, Sinet M, Shin SY, Urrutia A, Versmisse P, Lacabaratz C, Boufassa F, Avettand-Fenoel V, Rouzioux C, Delfraissy JF, Barre-Sinoussi F, Lambotte O, Venet A, Pancino G, . ANRS EP36 HIV Controllers Study Group Heterogeneity in HIV suppression by CD8 T cells from HIV controllers: association with Gag-specific CD8 T cell responses. J Immunol 2009, 182(12):7828-7837. 10.4049/jimmunol.0803928, 19494307, ANRS EP36 HIV Controllers Study Group.
28. Hersperger AR, Pereyra F, Nason M, Demers K, Sheth P, Shin LY, Kovacs CM, Rodriguez B, Sieg SF, Teixeira-Johnson L, Gudonis D, Goepfert PA, Lederman MM, Frank I, Makedonas G, Kaul R, Walker BD, Betts MR. Perforin expression directly ex vivo by HIV-specific CD8 T-cells is a correlate of HIV elite control. PLoS Pathog 2010, 6(5):e1000917. 10.1371/journal.ppat.1000917, 2877741, 20523897.
29. Martinez-Picado J, Prado JG, Fry EE, Pfafferott K, Leslie A, Chetty S, Thobakgale C, Honeyborne I, Crawford H, Matthews P, Pillay T, Rousseau C, Mullins JI, Brander C, Walker BD, Stuart DI, Kiepiela P, Goulder P. Fitness cost of escape mutations in p24 Gag in association with control of human immunodeficiency virus type 1. J Virol 2006, 80(7):3617-3623. 10.1128/JVI.80.7.3617-3623.2006, 1440414, 16537629.
30. Brockman MA, Schneidewind A, Lahaie M, Schmidt A, Miura T, Desouza I, Ryvkin F, Derdeyn CA, Allen S, Hunter E, Mulenga J, Goepfert PA, Walker BD, Allen TM. Escape and compensation from early HLA-B57-mediated cytotoxic T-lymphocyte pressure on human immunodeficiency virus type 1 Gag alter capsid interactions with cyclophilin A. J Virol 2007, 81(22):12608-12618. 10.1128/JVI.01369-07, 2169025, 17728232.
31. Leslie AJ, Pfafferott KJ, Chetty P, Draenert R, Addo MM, Feeney M, Tang Y, Holmes EC, Allen T, Prado JG, Altfeld M, Brander C, Dixon C, Ramduth D, Jeena P, Thomas SA, St John A, Roach TA, Kupfer B, Luzzi G, Edwards A, Taylor G, Lyall H, Tudor-Williams G, Novelli V, Martinez-Picado J, Kiepiela P, Walker BD, Goulder PJ. HIV evolution: CTL escape mutation and reversion after transmission. Nat Med 2004, 10(3):282-289. 10.1038/nm992, 14770175.
32. Crawford H, Prado JG, Leslie A, Hue S, Honeyborne I, Reddy S, van der Stok M, Mncube Z, Brander C, Rousseau C, Mullins JI, Kaslow R, Goepfert P, Allen S, Hunter E, Mulenga J, Kiepiela P, Walker BD, Goulder PJ. Compensatory mutation partially restores fitness and delays reversion of escape mutation within the immunodominant HLA-B*5703-restricted Gag epitope in chronic human immunodeficiency virus type 1 infection. J Virol 2007, 81(15):8346-8351. 10.1128/JVI.00465-07, 1951305, 17507468.
33. Leslie A, Kavanagh D, Honeyborne I, Pfafferott K, Edwards C, Pillay T, Hilton L, Thobakgale C, Ramduth D, Draenert R, Le Gall S, Luzzi G, Edwards A, Brander C, Sewell AK, Moore S, Mullins J, Moore C, Mallal S, Bhardwaj N, Yusim K, Phillips R, Klenerman P, Korber B, Kiepiela P, Walker B, Goulder P. Transmission and accumulation of CTL escape variants drive negative associations between HIV polymorphisms and HLA. J Exp Med 2005, 201(6):891-902. 10.1084/jem.20041455, 2213090, 15781581.
34. Dinoso JB, Kim SY, Siliciano RF, Blankson JN. A comparison of viral loads between HIV-1-infected elite suppressors and individuals who receive suppressive highly active antiretroviral therapy. Clin Infect Dis 2008, 47(1):102-104. 10.1086/588791, 2564994, 18494606.
35. Hatano H, Delwart EL, Norris PJ, Lee TH, Dunn-Williams J, Hunt PW, Hoh R, Stramer SL, Linnen JM, McCune JM, Martin JN, Busch MP, Deeks SG. Evidence for persistent low-level viremia in individuals who control human immunodeficiency virus in the absence of antiretroviral therapy. J Virol 2009, 83(1):329-335. 10.1128/JVI.01763-08, 2612329, 18945778.
36. Pereyra F, Palmer S, Miura T, Block BL, Wiegand A, Rothchild AC, Baker B, Rosenberg R, Cutrell E, Seaman MS, Coffin JM, Walker BD. Persistent low-level viremia in HIV-1 elite controllers and relationship to immunologic parameters. J Infect Dis 2009, 200(6):984-990. 10.1086/605446, 19656066.