Fellay J, Ge D, Shianna KV, Colombo S, Ledergerber B, Cirulli ET, Urban TJ, Zhang K, Gumbs CE, Smith JP, et al. Common genetic variation and the control of HIV-1 in humans. PLoS Genet. 2009;5:e1000791.
International HIVCS, Pereyra F, Jia X, McLaren PJ, Telenti A, de Bakker PI, Walker BD, Ripke S, Brumme CJ, Pulit SL, et al. The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. Science. 2010;330:1551–7.
Altfeld M, Kalife ET, Qi Y, Streeck H, Lichterfeld M, Johnston MN, Burgett N, Swartz ME, Yang A, Alter G, et al. HLA alleles associated with delayed progression to AIDS contribute strongly to the initial CD8(+) T cell response against HIV-1. PLoS Med. 2006;3:e403.
Leslie A, Matthews PC, Listgarten J, Carlson JM, Kadie C, Ndung’u T, Brander C, Coovadia H, Walker BD, Heckerman D, Goulder PJ. Additive contribution of HLA class I alleles in the immune control of HIV-1 infection. J Virol. 2010;84:9879–88.
Borrow P, Lewicki H, Hahn BH, Shaw GM, Oldstone MB. Virus-specific CD8+ cytotoxic T-lymphocyte activity associated with control of viremia in primary human immunodeficiency virus type 1 infection. J Virol. 1994;68:6103–10.
Koup RA, Safrit JT, Cao Y, Andrews CA, McLeod G, Borkowsky W, Farthing C, Ho DD. Temporal association of cellular immune responses with the initial control of viremia in primary human immunodeficiency virus type 1 syndrome. J Virol. 1994;68:4650–5.
Price DA, Goulder PJ, Klenerman P, Sewell AK, Easterbrook PJ, Troop M, Bangham CR, Phillips RE. Positive selection of HIV-1 cytotoxic T lymphocyte escape variants during primary infection. Proc Natl Acad Sci USA. 1997;94:1890–5.
Borrow P, Lewicki H, Wei X, Horwitz MS, Peffer N, Meyers H, Nelson JA, Gairin JE, Hahn BH, Oldstone MB, Shaw GM. Antiviral pressure exerted by HIV-1-specific cytotoxic T lymphocytes (CTLs) during primary infection demonstrated by rapid selection of CTL escape virus. Nat Med. 1997;3:205–11.
Masemola A, Mashishi T, Khoury G, Mohube P, Mokgotho P, Vardas E, Colvin M, Zijenah L, Katzenstein D, Musonda R, et al. Hierarchical targeting of subtype C human immunodeficiency virus type 1 proteins by CD8+ T cells: correlation with viral load. J Virol. 2004;78:3233–43.
Kiepiela P, Ngumbela K, Thobakgale C, Ramduth D, Honeyborne I, Moodley E, Reddy S, de Pierres C, Mncube Z, Mkhwanazi N, et al. CD8 + T-cell responses to different HIV proteins have discordant associations with viral load. Nat Med. 2007;13:46–53.
Adland E, Carlson JM, Paioni P, Kloverpris H, Shapiro R, Ogwu A, Riddell L, Luzzi G, Chen F, Balachandran T, et al. Nef-specific CD8+ T cell responses contribute to HIV-1 immune control. PLoS ONE. 2013;8:e73117.
Mothe B, Llano A, Ibarrondo J, Zamarreno J, Schiaulini M, Miranda C, Ruiz Riol M, Berger CT, Herrero MJ, Palou E, et al. CTL responses of high functional avidity and broad variant cross-reactivity are associated with HIV control. PLoS ONE. 2012;7:e29717.
Mothe B, Llano A, Ibarrondo J, Daniels M, Miranda C, Zamarreno J, Bach V, Zuniga R, Perez-Alvarez S, Berger CT, et al. Definition of the viral targets of protective HIV-1-specific T cell responses. J Transl Med. 2011;9:208.
Mothe B, Hu X, Llano A, Rosati M, Olvera A, Kulkarni V, Valentin A, Alicea C, Pilkington GR, Sardesai NY, et al. A human immune data-informed vaccine concept elicits strong and broad T-cell specificities associated with HIV-1 control in mice and macaques. J Transl Med. 2015;13:60.
Sunshine J, Kim M, Carlson JM, Heckerman D, Czartoski J, Migueles SA, Maenza J, McElrath MJ, Mullins JI, Frahm N. Increased sequence coverage through combined targeting of variant and conserved epitopes correlates with control of HIV replication. J Virol. 2014;88:1354–65.
Pereyra F, Heckerman D, Carlson JM, Kadie C, Soghoian DZ, Karel D, Goldenthal A, Davis OB, DeZiel CE, Lin T, et al. HIV control is mediated in part by CD8+ T-cell targeting of specific epitopes. J Virol. 2014;88:12937–48.
Mudd PA, Martins MA, Ericsen AJ, Tully DC, Power KA, Bean AT, Piaskowski SM, Duan L, Seese A, Gladden AD, et al. Vaccine-induced CD8+ T cells control AIDS virus replication. Nature. 2012;491:129–33.
Hancock G, Yang H, Yorke E, Wainwright E, Bourne V, Frisbee A, Payne TL, Berrong M, Ferrari G, Chopera D, et al. Identification of effective subdominant anti-HIV-1 CD8+ T cells within entire post-infection and post-vaccination immune responses. PLoS Pathog. 2015;11:e1004658.
Hammer SM, Sobieszczyk ME, Janes H, Karuna ST, Mulligan MJ, Grove D, Koblin BA, Buchbinder SP, Keefer MC, Tomaras GD, et al. Efficacy trial of a DNA/rAd5 HIV-1 preventive vaccine. N Engl J Med. 2013;369:2083–92.
Janes H, Friedrich DP, Krambrink A, Smith RJ, Kallas EG, Horton H, Casimiro DR, Carrington M, Geraghty DE, Gilbert PB, et al. Vaccine-induced gag-specific T cells are associated with reduced viremia after HIV-1 infection. J Infect Dis. 2013;208:1231–9.
Rosario M, Bridgeman A, Quakkelaar ED, Quigley MF, Hill BJ, Knudsen ML, Ammendola V, Ljungberg K, Borthwick N, Im EJ, et al. Long peptides induce polyfunctional T cells against conserved regions of HIV-1 with superior breadth to single-gene vaccines in macaques. Eur J Immunol. 2010;40:1973–84.
Kulkarni V, Valentin A, Rosati M, Rolland M, Mullins JI, Pavlakis GN, Felber BK. HIV-1 conserved elements p24CE DNA vaccine induces humoral immune responses with broad epitope recognition in macaques. PLoS ONE. 2014;9:e111085.
Kulkarni V, Valentin A, Rosati M, Alicea C, Singh AK, Jalah R, Broderick KE, Sardesai NY, Le Gall S, Mothe B, et al. Altered response hierarchy and increased T-cell breadth upon HIV-1 conserved element DNA vaccination in macaques. PLoS ONE. 2014;9:e86254.
Haynes BF, Gilbert PB, McElrath MJ, Zolla-Pazner S, Tomaras GD, Alam SM, Evans DT, Montefiori DC, Karnasuta C, Sutthent R, et al. Immune-correlates analysis of an HIV-1 vaccine efficacy trial. N Engl J Med. 2012;366:1275–86.
Schell JB, Bahl K, Folta-Stogniew E, Rose N, Buonocore L, Marx PA, Gambhira R, Rose JK. Antigenic requirement for Gag in a vaccine that protects against high-dose mucosal challenge with simian immunodeficiency virus. Virology. 2015;476:405–12.
Schell JB, Rose NF, Bahl K, Diller K, Buonocore L, Hunter M, Marx PA, Gambhira R, Tang H, Montefiori DC, et al. Significant protection against high-dose simian immunodeficiency virus challenge conferred by a new prime-boost vaccine regimen. J Virol. 2011;85:5764–72.
Nabi G, Genannt Bonsmann MS, Tenbusch M, Gardt O, Barouch DH, Temchura V, Uberla K. GagPol-specific CD4(+) T-cells increase the antibody response to Env by intrastructural help. Retrovirology. 2013;10:117.
Genannt Bonsmann MS, Niezold T, Hannaman D, Uberla K, Tenbusch M. The improved antibody response against HIV-1 after a vaccination based on intrastructural help is complemented by functional CD8(+) T cell responses. Vaccine. 2016;34:1744–51.
Kaufman DR, Li F, Cruz AN, Self SG, Barouch DH. Focus and breadth of cellular immune responses elicited by a heterologous insert prime-boost vaccine regimen in rhesus monkeys. Vaccine. 2012;30:506–9.
Walsh SR, Moodie Z, Fiore-Gartland AJ, Morgan C, Wilck MB, Hammer SM, Buchbinder SP, Kalams SA, Goepfert PA, Mulligan MJ, et al. Vaccination with heterologous HIV-1 envelope sequences and heterologous adenovirus vectors increases T-cell responses to conserved regions: HVTN 083. J Infect Dis. 2016;213:541–50.
Andersson AC, Ragonnaud E, Seaton KE, Sawant S, Folgori A, Colloca S, Labranche C, Montefiori DC, Tomaras GD, Holst PJ. Effect of HIV-1 envelope cytoplasmic tail on adenovirus primed virus encoded virus-like particle immunizations. Vaccine. 2016;34:5344–51.
Van Rompay KK, Greenier JL, Cole KS, Earl P, Moss B, Steckbeck JD, Pahar B, Rourke T, Montelaro RC, Canfield DR, et al. Immunization of newborn rhesus macaques with simian immunodeficiency virus (SIV) vaccines prolongs survival after oral challenge with virulent SIVmac251. J Virol. 2003;77:179–90.
Kremer M, Volz A, Kreijtz JH, Fux R, Lehmann MH, Sutter G. Easy and efficient protocols for working with recombinant vaccinia virus MVA. Methods Mol Biol. 2012;890:59–92.
Kent K, Rud E, Corcoran T, Powell C, Thiriart C, Collignon C, Stott E. Identification of two neutralizing and 8 non-neutralizing epitopes on simian immunodeficiency virus envelope using monoclonal antibodies. AIDS Res Hum Retroviruses. 1992;8:1147–51.
Wehrly K, Chesebro B. p24 antigen capture assay for quantification of human immunodeficiency virus using readily available inexpensive reagents. Methods. 1997;12:288–93.
Hill CM, Deng H, Unutmaz D, Kewalramani VN, Bastiani L, Gorny MK, Zolla-Pazner S, Littman DR. Envelope glycoproteins from human immunodeficiency virus types 1 and 2 and simian immunodeficiency virus can use human CCR5 as a coreceptor for viral entry and make direct CD4-dependent interactions with this chemokine receptor. J Virol. 1997;71:6296–304.
Mason RD, Welles HC, Adams C, Chakrabarti BK, Gorman J, Zhou T, Nguyen R, O’Dell S, Lusvarghi S, Bewley CA, et al. Targeted isolation of antibodies directed against major sites of SIV Env vulnerability. PLoS Pathog. 2016;12:e1005537.
Lai L, Vodros D, Kozlowski PA, Montefiori DC, Wilson RL, Akerstrom VL, Chennareddi L, Yu T, Kannanganat S, Ofielu L, et al. GM-CSF DNA: an adjuvant for higher avidity IgG, rectal IgA, and increased protection against the acute phase of a SHIV-89.6P challenge by a DNA/MVA immunodeficiency virus vaccine. Virology. 2007;369:153–67.
Wei X, Decker JM, Liu H, Zhang Z, Arani RB, Kilby JM, Saag MS, Wu X, Shaw GM, Kappes JC. Emergence of resistant human immunodeficiency virus type 1 in patients receiving fusion inhibitor (T-20) monotherapy. Antimicrob Agents Chemother. 2002;46:1896–905.
Montefiori DC. Measuring HIV neutralization in a luciferase reporter gene assay. Methods Mol Biol. 2009;485:395–405.
Reimann KA, Tenner-Racz K, Racz P, Montefiori DC, Yasutomi Y, Lin W, Ransil BJ, Letvin NL. Immunopathogenic events in acute infection of rhesus monkeys with simian immunodeficiency virus of macaques. J Virol. 1994;68:2362–70.
Ragonnaud E, Andersson AM, Pedersen AE, Laursen H, Holst PJ. An adenoviral cancer vaccine co-encoding a tumor associated antigen together with secreted 4-1BBL leads to delayed tumor progression. Vaccine. 2016;34:2147–56.
Jia B, Serra-Moreno R, Neidermyer W, Rahmberg A, Mackey J, Fofana IB, Johnson WE, Westmoreland S, Evans DT. Species-specific activity of SIV Nef and HIV-1 Vpu in overcoming restriction by tetherin/BST2. PLoS Pathog. 2009;5:e1000429.
Earl PL, Wyatt LS, Montefiori DC, Bilska M, Woodward R, Markham PD, Malley JD, Vogel TU, Allen TM, Watkins DI, et al. Comparison of vaccine strategies using recombinant env-gag-pol MVA with or without an oligomeric Env protein boost in the SHIV rhesus macaque model. Virology. 2002;294:270–81.
Capone S, Naddeo M, D’Alise AM, Abbate A, Grazioli F, Del Gaudio A, Del Sorbo M, Esposito ML, Ammendola V, Perretta G, et al. Fusion of HCV nonstructural antigen to MHC class II-associated invariant chain enhances T-cell responses induced by vectored vaccines in nonhuman primates. Mol Ther. 2014;22:1039–47.
Kwa S, Lai L, Gangadhara S, Siddiqui M, Pillai VB, Labranche C, Yu T, Moss B, Montefiori DC, Robinson HL, et al. CD40L-adjuvanted DNA/modified vaccinia virus Ankara simian immunodeficiency virus SIV239 vaccine enhances SIV-specific humoral and cellular immunity and improves protection against a heterologous SIVE660 mucosal challenge. J Virol. 2014;88:9579–89.
Kilgore KM, Murphy MK, Burton SL, Wetzel KS, Smith SA, Xiao P, Reddy S, Francella N, Sodora DL, Silvestri G, et al. Characterization and implementation of a diverse simian immunodeficiency virus SIVsm envelope panel in the assessment of neutralizing antibody breadth elicited in rhesus macaques by multimodal vaccines expressing the SIVmac239 envelope. J Virol. 2015;89:8130–51.
Kulkarni V, Rosati M, Valentin A, Ganneru B, Singh AK, Yan J, Rolland M, Alicea C, Beach RK, Zhang GM, et al. HIV-1 p24(gag) derived conserved element DNA vaccine increases the breadth of immune response in mice. PLoS ONE. 2013;8:e60245.
Kelly C, Swadling L, Brown A, Capone S, Folgori A, Salio M, Klenerman P, Barnes E. Cross-reactivity of hepatitis C virus specific vaccine-induced T cells at immunodominant epitopes. Eur J Immunol. 2015;45:309–16.
Varela-Rohena A, Molloy PE, Dunn SM, Li Y, Suhoski MM, Carroll RG, Milicic A, Mahon T, Sutton DH, Laugel B, et al. Control of HIV-1 immune escape by CD8 T cells expressing enhanced T-cell receptor. Nat Med. 2008;14:1390–5.
Holst PJ, Jensen BA, Ragonnaud E, Thomsen AR, Christensen JP. Targeting of non-dominant antigens as a vaccine strategy to broaden T-cell responses during chronic viral infection. PLoS ONE. 2015;10:e0117242.
Ishii H, Kawada M, Tsukamoto T, Yamamoto H, Matsuoka S, Shiino T, Takeda A, Inoue M, Iida A, Hara H, et al. Impact of vaccination on cytotoxic T lymphocyte immunodominance and cooperation against simian immunodeficiency virus replication in rhesus macaques. J Virol. 2012;86:738–45.