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For: Karlsson AC, Iversen AKN, Chapman JM, de Oliviera T, Spotts G, McMichael AJ, Davenport MP, Hecht FM, Nixon DF. Sequential broadening of CTL responses in early HIV-1 infection is associated with viral escape. PLoS One 2007;2:e225. [PMID: 17311088 PMCID: PMC1790860 DOI: 10.1371/journal.pone.0000225] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2006] [Accepted: 01/10/2007] [Indexed: 01/31/2023]  Open
Number Cited by Other Article(s)
1
Rouzine IM, Rozhnova G. Evolutionary implications of SARS-CoV-2 vaccination for the future design of vaccination strategies. COMMUNICATIONS MEDICINE 2023;3:86. [PMID: 37336956 DOI: 10.1038/s43856-023-00320-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/07/2023] [Indexed: 06/21/2023]  Open
2
Mokaleng B, Choga WT, Bareng OT, Maruapula D, Ditshwanelo D, Kelentse N, Mokgethi P, Moraka NO, Motswaledi MS, Tawe L, Koofhethile CK, Moyo S, Zachariah M, Gaseitsiwe S. No Difference in the Prevalence of HIV-1 gag Cytotoxic T-Lymphocyte-Associated Escape Mutations in Viral Sequences from Early and Late Parts of the HIV-1 Subtype C Pandemic in Botswana. Vaccines (Basel) 2023;11:1000. [PMID: 37243104 PMCID: PMC10221913 DOI: 10.3390/vaccines11051000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023]  Open
3
Alves E, Al-Kaabi M, Keane NM, Leary S, Almeida CAM, Deshpande P, Currenti J, Chopra A, Smith R, Castley A, Mallal S, Kalams SA, Gaudieri S, John M. Adaptation to HLA-associated immune pressure over the course of HIV infection and in circulating HIV-1 strains. PLoS Pathog 2022;18:e1010965. [PMID: 36525463 PMCID: PMC9803285 DOI: 10.1371/journal.ppat.1010965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 12/30/2022] [Accepted: 11/01/2022] [Indexed: 12/23/2022]  Open
4
Sánchez-Martínez A, Acevedo-Sáenz L, Alzate-Ángel JC, Álvarez CM, Guzmán F, Roman T, Urcuqui-Inchima S, Cardona-Maya WD, Velilla PA. Functional Profile of CD8+ T-Cells in Response to HLA-A*02:01-Restricted Mutated Epitopes Derived from the Gag Protein of Circulating HIV-1 Strains from Medellín, Colombia. Front Immunol 2022;13:793982. [PMID: 35392101 PMCID: PMC8980466 DOI: 10.3389/fimmu.2022.793982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 02/28/2022] [Indexed: 11/13/2022]  Open
5
Olusola BA, Olaleye DO, Odaibo GN. Non-synonymous Substitutions in HIV-1 GAG Are Frequent in Epitopes Outside the Functionally Conserved Regions and Associated With Subtype Differences. Front Microbiol 2021;11:615721. [PMID: 33505382 PMCID: PMC7829476 DOI: 10.3389/fmicb.2020.615721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/15/2020] [Indexed: 12/22/2022]  Open
6
Kist NC, Lambert B, Campbell S, Katzourakis A, Lunn D, Lemey P, Iversen AKN. HIV-1 p24Gag adaptation to modern and archaic HLA-allele frequency differences in ethnic groups contributes to viral subtype diversification. Virus Evol 2020;6:veaa085. [PMID: 33343925 PMCID: PMC7733611 DOI: 10.1093/ve/veaa085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]  Open
7
Scharf L, Tauriainen J, Buggert M, Hartogensis W, Nolan DJ, Deeks SG, Salemi M, Hecht FM, Karlsson AC. Delayed Expression of PD-1 and TIGIT on HIV-Specific CD8 T Cells in Untreated HLA-B*57:01 Individuals Followed from Early Infection. J Virol 2020;94:e02128-19. [PMID: 32350076 PMCID: PMC7343205 DOI: 10.1128/jvi.02128-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/16/2020] [Indexed: 12/21/2022]  Open
8
Clinical and evolutionary consequences of HIV adaptation to HLA: implications for vaccine and cure. Curr Opin HIV AIDS 2020;14:194-204. [PMID: 30925534 DOI: 10.1097/coh.0000000000000541] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
9
Impact of Suboptimal APOBEC3G Neutralization on the Emergence of HIV Drug Resistance in Humanized Mice. J Virol 2020;94:JVI.01543-19. [PMID: 31801862 DOI: 10.1128/jvi.01543-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 11/20/2019] [Indexed: 01/05/2023]  Open
10
Boucau J, Le Gall S. Antigen processing and presentation in HIV infection. Mol Immunol 2019;113:67-74. [PMID: 29636181 PMCID: PMC6174111 DOI: 10.1016/j.molimm.2018.03.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 01/09/2018] [Accepted: 03/29/2018] [Indexed: 12/11/2022]
11
John M, Gaudieri S, Mallal S. Immunogenetics and Vaccination. HUMAN VACCINES 2017. [DOI: 10.1016/b978-0-12-802302-0.00005-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
12
Du VY, Bansal A, Carlson J, Salazar-Gonzalez JF, Salazar MG, Ladell K, Gras S, Josephs TM, Heath SL, Price DA, Rossjohn J, Hunter E, Goepfert PA. HIV-1-Specific CD8 T Cells Exhibit Limited Cross-Reactivity during Acute Infection. THE JOURNAL OF IMMUNOLOGY 2016;196:3276-86. [PMID: 26983786 DOI: 10.4049/jimmunol.1502411] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 02/11/2016] [Indexed: 01/03/2023]
13
Impact of APOBEC Mutations on CD8+ T Cell Recognition of HIV Epitopes Varies Depending on the Restricting HLA. J Acquir Immune Defic Syndr 2015;70:172-8. [PMID: 26035050 DOI: 10.1097/qai.0000000000000689] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
14
Newly Exerted T Cell Pressures on Mutated Epitopes following Transmission Help Maintain Consensus HIV-1 Sequences. PLoS One 2015;10:e0120787. [PMID: 25919393 PMCID: PMC4412704 DOI: 10.1371/journal.pone.0120787] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 01/27/2015] [Indexed: 11/19/2022]  Open
15
The route of HIV escape from immune response targeting multiple sites is determined by the cost-benefit tradeoff of escape mutations. PLoS Comput Biol 2014;10:e1003878. [PMID: 25356981 PMCID: PMC4214571 DOI: 10.1371/journal.pcbi.1003878] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Accepted: 08/21/2014] [Indexed: 12/20/2022]  Open
16
Mechanisms of HIV protein degradation into epitopes: implications for vaccine design. Viruses 2014;6:3271-92. [PMID: 25196483 PMCID: PMC4147695 DOI: 10.3390/v6083271] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 08/06/2014] [Accepted: 08/11/2014] [Indexed: 12/02/2022]  Open
17
Buggert M, Norström MM, Salemi M, Hecht FM, Karlsson AC. Functional avidity and IL-2/perforin production is linked to the emergence of mutations within HLA-B*5701-restricted epitopes and HIV-1 disease progression. THE JOURNAL OF IMMUNOLOGY 2014;192:4685-96. [PMID: 24740510 DOI: 10.4049/jimmunol.1302253] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
18
Monajemi M, Woodworth CF, Zipperlen K, Gallant M, Grant MD, Larijani M. Positioning of APOBEC3G/F mutational hotspots in the human immunodeficiency virus genome favors reduced recognition by CD8+ T cells. PLoS One 2014;9:e93428. [PMID: 24722422 PMCID: PMC3982959 DOI: 10.1371/journal.pone.0093428] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 03/05/2014] [Indexed: 11/18/2022]  Open
19
Watanabe K, Murakoshi H, Tamura Y, Koyanagi M, Chikata T, Gatanaga H, Oka S, Takiguchi M. Identification of cross-clade CTL epitopes in HIV-1 clade A/E-infected individuals by using the clade B overlapping peptides. Microbes Infect 2013;15:874-86. [PMID: 23968885 DOI: 10.1016/j.micinf.2013.08.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 08/08/2013] [Accepted: 08/08/2013] [Indexed: 10/26/2022]
20
Perez CL, Milush JM, Buggert M, Eriksson EM, Larsen MV, Liegler T, Hartogensis W, Bacchetti P, Lund O, Hecht FM, Nixon DF, Karlsson AC. Targeting of conserved gag-epitopes in early HIV infection is associated with lower plasma viral load and slower CD4(+) T cell depletion. AIDS Res Hum Retroviruses 2013;29:602-12. [PMID: 23140171 DOI: 10.1089/aid.2012.0171] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
21
Lemey P, Minin VN, Bielejec F, Kosakovsky Pond SL, Suchard MA. A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection. ACTA ACUST UNITED AC 2012;28:3248-56. [PMID: 23064000 DOI: 10.1093/bioinformatics/bts580] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
22
Immunology of infants through adolescents: responses to emulate for HIV vaccines. Curr Opin HIV AIDS 2012;2:391-8. [PMID: 19372917 DOI: 10.1097/coh.0b013e3282e1c633] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
23
Wang W, Qiu C, Qiu C, Wang Y, Zhang X, Xu J. Development of skewed functionality of HIV-1-specific cytotoxic CD8(+) T cells from primary to early chronic phase of HIV infection. PLoS One 2012;7:e44983. [PMID: 23028721 PMCID: PMC3441698 DOI: 10.1371/journal.pone.0044983] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 08/15/2012] [Indexed: 11/18/2022]  Open
24
Combination of immune and viral factors distinguishes low-risk versus high-risk HIV-1 disease progression in HLA-B*5701 subjects. J Virol 2012;86:9802-16. [PMID: 22761389 DOI: 10.1128/jvi.01165-12] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
25
Roy SM, Wodarz D. Infection of HIV-specific CD4 T helper cells and the clonal composition of the response. J Theor Biol 2012;304:143-51. [PMID: 22480435 DOI: 10.1016/j.jtbi.2012.03.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Revised: 03/13/2012] [Accepted: 03/14/2012] [Indexed: 11/24/2022]
26
Keane NM, Roberts SG, Almeida CAM, Krishnan T, Chopra A, Demaine E, Laird R, Tschochner M, Carlson JM, Mallal S, Heckerman D, James I, John M. High-avidity, high-IFNγ-producing CD8 T-cell responses following immune selection during HIV-1 infection. Immunol Cell Biol 2012;90:224-34. [PMID: 21577229 PMCID: PMC3173576 DOI: 10.1038/icb.2011.34] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
27
Skar H, Hedskog C, Albert J. HIV-1 evolution in relation to molecular epidemiology and antiretroviral resistance. Ann N Y Acad Sci 2011;1230:108-18. [PMID: 21824168 DOI: 10.1111/j.1749-6632.2011.06128.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
28
Almeida CAM, Bronke C, Roberts SG, McKinnon E, Keane NM, Chopra A, Kadie C, Carlson J, Haas DW, Riddler SA, Haubrich R, Heckerman D, Mallal S, John M. Translation of HLA-HIV associations to the cellular level: HIV adapts to inflate CD8 T cell responses against Nef and HLA-adapted variant epitopes. THE JOURNAL OF IMMUNOLOGY 2011;187:2502-13. [PMID: 21821798 DOI: 10.4049/jimmunol.1100691] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
29
Wodarz D, Levy DN. Effect of multiple infection of cells on the evolutionary dynamics of HIV in vivo: implications for host adaptation mechanisms. Exp Biol Med (Maywood) 2011;236:926-37. [DOI: 10.1258/ebm.2011.011062] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
30
The immune response to the RT181-189 epitope in HIV-1-infected patients is associated with viral sequence polymorphism flanking the epitope. J Clin Immunol 2011;31:681-9. [PMID: 21491096 DOI: 10.1007/s10875-011-9520-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Accepted: 03/17/2011] [Indexed: 10/18/2022]
31
Hallengärd D, Haller BK, Petersson S, Boberg A, Maltais AK, Isaguliants M, Wahren B, Bråve A. Increased expression and immunogenicity of HIV-1 protease following inactivation of the enzymatic activity. Vaccine 2010;29:839-48. [PMID: 21109032 DOI: 10.1016/j.vaccine.2010.10.083] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Revised: 10/21/2010] [Accepted: 10/25/2010] [Indexed: 10/18/2022]
32
Modelling the evolution and spread of HIV immune escape mutants. PLoS Pathog 2010;6:e1001196. [PMID: 21124991 PMCID: PMC2987822 DOI: 10.1371/journal.ppat.1001196] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Accepted: 10/15/2010] [Indexed: 02/07/2023]  Open
33
Hoof I, Pérez CL, Buggert M, Gustafsson RKL, Nielsen M, Lund O, Karlsson AC. Interdisciplinary Analysis of HIV-Specific CD8+ T Cell Responses against Variant Epitopes Reveals Restricted TCR Promiscuity. THE JOURNAL OF IMMUNOLOGY 2010;184:5383-91. [DOI: 10.4049/jimmunol.0903516] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
34
Tang J, Malhotra R, Song W, Brill I, Hu L, Farmer PK, Mulenga J, Allen S, Hunter E, Kaslow RA. Human leukocyte antigens and HIV type 1 viral load in early and chronic infection: predominance of evolving relationships. PLoS One 2010;5:e9629. [PMID: 20224785 PMCID: PMC2835758 DOI: 10.1371/journal.pone.0009629] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Accepted: 02/18/2010] [Indexed: 11/18/2022]  Open
35
Kopycinski J, Osman M, Griffiths PD, Emery VC. Sequence flexibility of the immunodominant HLA A*0201 restricted ppUL83 CD8 T-cell epitope of human cytomegalovirus. J Med Virol 2010;82:94-103. [DOI: 10.1002/jmv.21668] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
36
Barouch DH, Korber B. HIV-1 vaccine development after STEP. Annu Rev Med 2010;61:153-67. [PMID: 20059334 PMCID: PMC2819364 DOI: 10.1146/annurev.med.042508.093728] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
37
Candidate vaccine sequences to represent intra- and inter-clade HIV-1 variation. PLoS One 2009;4:e7388. [PMID: 19812689 PMCID: PMC2753653 DOI: 10.1371/journal.pone.0007388] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2009] [Accepted: 09/04/2009] [Indexed: 11/24/2022]  Open
38
Bangham CRM. CTL quality and the control of human retroviral infections. Eur J Immunol 2009;39:1700-12. [PMID: 19582737 DOI: 10.1002/eji.200939451] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
39
Dosenovic P, Chakrabarti B, Soldemo M, Douagi I, Forsell MNE, Li Y, Phogat A, Paulie S, Hoxie J, Wyatt RT, Karlsson Hedestam GB. Selective expansion of HIV-1 envelope glycoprotein-specific B cell subsets recognizing distinct structural elements following immunization. THE JOURNAL OF IMMUNOLOGY 2009;183:3373-82. [PMID: 19696434 DOI: 10.4049/jimmunol.0900407] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
40
Brumme ZL, John M, Carlson JM, Brumme CJ, Chan D, Brockman MA, Swenson LC, Tao I, Szeto S, Rosato P, Sela J, Kadie CM, Frahm N, Brander C, Haas DW, Riddler SA, Haubrich R, Walker BD, Harrigan PR, Heckerman D, Mallal S. HLA-associated immune escape pathways in HIV-1 subtype B Gag, Pol and Nef proteins. PLoS One 2009;4:e6687. [PMID: 19690614 PMCID: PMC2723923 DOI: 10.1371/journal.pone.0006687] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2009] [Accepted: 05/27/2009] [Indexed: 02/07/2023]  Open
41
Avila-Rios S, Ormsby CE, Carlson JM, Valenzuela-Ponce H, Blanco-Heredia J, Garrido-Rodriguez D, Garcia-Morales C, Heckerman D, Brumme ZL, Mallal S, John M, Espinosa E, Reyes-Teran G. Unique features of HLA-mediated HIV evolution in a Mexican cohort: a comparative study. Retrovirology 2009;6:72. [PMID: 19664284 PMCID: PMC2734549 DOI: 10.1186/1742-4690-6-72] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2009] [Accepted: 08/10/2009] [Indexed: 11/30/2022]  Open
42
Wodarz D, Levy DN. Multiple HIV-1 infection of cells and the evolutionary dynamics of cytotoxic T lymphocyte escape mutants. Evolution 2009;63:2326-39. [PMID: 19486149 DOI: 10.1111/j.1558-5646.2009.00727.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
43
Ndongala ML, Peretz Y, Boulet S, Doroudchi M, Yassine-Diab B, Boulassel MR, Rouleau D, Tremblay C, LeBlanc R, Routy JP, Sékaly RP, Bernard NF. HIV Gag p24 specific responses secreting IFN-gamma and/or IL-2 in treatment-naïve individuals in acute infection early disease (AIED) are associated with low viral load. Clin Immunol 2009;131:277-87. [PMID: 19135418 DOI: 10.1016/j.clim.2008.11.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2008] [Revised: 11/19/2008] [Accepted: 11/21/2008] [Indexed: 01/29/2023]
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Human immunodeficiency virus type 1 population genetics and adaptation in newly infected individuals. J Virol 2008;83:2715-27. [PMID: 19116249 DOI: 10.1128/jvi.01960-08] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
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Carlson JM, Brumme ZL, Rousseau CM, Brumme CJ, Matthews P, Kadie C, Mullins JI, Walker BD, Harrigan PR, Goulder PJR, Heckerman D. Phylogenetic dependency networks: inferring patterns of CTL escape and codon covariation in HIV-1 Gag. PLoS Comput Biol 2008;4:e1000225. [PMID: 19023406 PMCID: PMC2579584 DOI: 10.1371/journal.pcbi.1000225] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2008] [Accepted: 10/09/2008] [Indexed: 11/18/2022]  Open
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The specificity and polymorphism of the MHC class I prevents the global adaptation of HIV-1 to the monomorphic proteasome and TAP. PLoS One 2008;3:e3525. [PMID: 18949050 PMCID: PMC2569417 DOI: 10.1371/journal.pone.0003525] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2008] [Accepted: 09/29/2008] [Indexed: 11/19/2022]  Open
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Tang J, Shao W, Yoo YJ, Brill I, Mulenga J, Allen S, Hunter E, Kaslow RA. Human leukocyte antigen class I genotypes in relation to heterosexual HIV type 1 transmission within discordant couples. THE JOURNAL OF IMMUNOLOGY 2008;181:2626-35. [PMID: 18684953 DOI: 10.4049/jimmunol.181.4.2626] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Althaus CL, De Boer RJ. Dynamics of immune escape during HIV/SIV infection. PLoS Comput Biol 2008;4:e1000103. [PMID: 18636096 PMCID: PMC2423483 DOI: 10.1371/journal.pcbi.1000103] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2007] [Accepted: 05/28/2008] [Indexed: 01/10/2023]  Open
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Biesinger T, Kimata JT. HIV-1 Transmission, Replication Fitness and Disease Progression. Virology (Auckl) 2008;2008:49-63. [PMID: 20354593 PMCID: PMC2846839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]  Open
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Biesinger T, Kimata JT. HIV-1 Transmission, Replication Fitness and Disease Progression. Virology (Auckl) 2008. [DOI: 10.4137/vrt.s860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]  Open
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