2012-2014

Impact of HLA-driven HIV adaptation on virulence in populations of high HIV seroprevalence. Payne R, Muenchhoff M, Mann J, Roberts HE, Matthews P, Adland E, Hempenstall A, Huang KH, Brockman M, Brumme Z, Sinclair M, Miura T, Frater J, Essex M, Shapiro R, Walker BD, Ndung'u T, McLean AR, Carlson JM, Goulder PJ. Proc Natl Acad Sci U S A. 2014 Dec 16;111(50):E5393-400. doi: 10.1073/pnas.1413339111. Epub 2014 Dec 1.

GWATCH: a web platform for automated gene association discovery analysis. Svitin A, Malov S, Cherkasov N, Geerts P, Rotkevich M, Dobrynin P, Shevchenko A, Guan L, Troyer J, Hendrickson S, Dilks HH, Oleksyk TK, Donfield S, Gomperts E, Jabs DA, Sezgin E, Van Natta M, Harrigan PR, Brumme ZL, O'Brien SJ. Gigascience. 2014 Nov 5;3:18. doi: 10.1186/2047-217X-3-18. eCollection 2014.

Early immune adaptation in HIV-1 revealed by population-level approaches. Martin E, Carlson JM, Le AQ, Chopera DR, McGovern R, Rahman MA, Ng C, Jessen H, Kelleher AD, Markowitz M, Allen TM, Milloy MJ, Carrington M, Wainberg MA, Brumme ZL. Retrovirology. 2014 Aug 29;11:64. doi: 10.1186/s12977-014-0064-1.

Nef-mediated down-regulation of CD4 and HLA class I in HIV-1 subtype C infection: association with disease progression and influence of immune pressure. Mann JK, Chopera D, Omarjee S, Kuang XT, Le AQ, Anmole G, Danroth R, Mwimanzi P, Reddy T, Carlson J, Radebe M, Goulder PJR, Walker BD, Abdool Karim S, Novitsky V, Williamson C, Brockman MA, Brumme ZL, Ndung'u T. Virology. 2014 Nov;468-470:214-225. doi: 10.1016/j.virol.2014.08.009. Epub 2014 Sep 3.

Impaired Nef function is associated with early control of HIV-1 viremia. Kuang XT, Li X, Anmole G, Mwimanzi P, Shahid A, Le AQ, Chong L, Qian H, Miura T, Markle T, Baraki B, Connick E, Daar ES, Jessen H, Kelleher AD, Little S, Markowitz M, Pereyra F, Rosenberg ES, Walker BD, Ueno T, Brumme ZL, Brockman MA. J Virol. 2014 Sep 1;88(17):10200-13. doi: 10.1128/JVI.01334-14. Epub 2014 Jun 25.

Switching and emergence of CTL epitopes in HIV-1 infection. Han C, Kawana-Tachikawa A, Shimizu A, Zhu D, Nakamura H, Adachi E, Kikuchi T, Koga M, Koibuchi T, Gao GF, Sato Y, Yamagata A, Martin E, Fukai S, Brumme ZL, Iwamoto A. Retrovirology. 2014 May 21;11:38. doi: 10.1186/1742-4690-11-38.

HIV-1 Nef and T-cell activation: a history of contradictions. Markle TJ, Philip M, Brockman MA. Future Virol. 2013 Apr 1;8(4):10.2217/fvl.13.20. doi: 10.2217/fvl.13.20.

Genotypic and functional impact of HIV-1 adaptation to its host population during the North American epidemic. Cotton LA, Kuang XT, Le AQ, Carlson JM, Chan B, Chopera DR, Brumme CJ, Markle TJ, Martin E, Shahid A, Anmole G, Mwimanzi P, Nassab P, Penney KA, Rahman MA, Milloy MJ, Schechter MT, Markowitz M, Carrington M, Walker BD, Wagner T, Buchbinder S, Fuchs J, Koblin B, Mayer KH, Harrigan PR, Brockman MA, Poon AF, Brumme ZL. PLoS Genet. 2014 Apr 24;10(4):e1004295. doi: 10.1371/journal.pgen.1004295. eCollection 2014 Apr.

An evaluation of phylogenetic methods for reconstructing transmitted HIV variants using longitudinal clonal HIV sequence data. McCloskey RM, Liang RH, Harrigan PR, Brumme ZL, Poon AF. J Virol. 2014 Jun;88(11):6181-94. doi: 10.1128/JVI.00483-14. Epub 2014 Mar 19.

Host-specific adaptation of HIV-1 subtype B in the Japanese population. Chikata T, Carlson JM, Tamura Y, Borghan MA, Naruto T, Hashimoto M, Murakoshi H, Le AQ, Mallal S, John M, Gatanaga H, Oka S, Brumme ZL, Takiguchi M. J Virol. 2014 May;88(9):4764-75. doi: 10.1128/JVI.00147-14. Epub 2014 Feb 12.

Differential escape patterns within the dominant HLA-B*57:03-restricted HIV Gag epitope reflect distinct clade-specific functional constraints. Payne RP, Branch S, Kløverpris H, Matthews PC, Koofhethile CK, Strong T, Adland E, Leitman E, Frater J, Ndung'u T, Hunter E, Haubrich R, Mothe B, Edwards A, Riddell L, Chen F, Harrigan PR, Brumme ZL, Mallal S, John M, Jooste JP, Shapiro R, Deeks SG, Walker BD, Brander C, Landis C, Carlson JM, Prado JG, Goulder PJ. J Virol. 2014 May;88(9):4668-78. doi: 10.1128/JVI.03303-13. Epub 2014 Feb 5.

Structure of TCR and antigen complexes at an immunodominant CTL epitope in HIV-1 infection. Shimizu A, Kawana-Tachikawa A, Yamagata A, Han C, Zhu D, Sato Y, Nakamura H, Koibuchi T, Carlson J, Martin E, Brumme CJ, Shi Y, Gao GF, Brumme ZL, Fukai S, Iwamoto A. Sci Rep. 2013 Nov 6;3:3097. doi: 10.1038/srep03097.

A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control. Bartha I, Carlson JM, Brumme CJ, McLaren PJ, Brumme ZL, John M, Haas DW, Martinez-Picado J, Dalmau J, López-Galíndez C, Casado C, Rauch A, Günthard HF, Bernasconi E, Vernazza P, Klimkait T, Yerly S, O'Brien SJ, Listgarten J, Pfeifer N, Lippert C, Fusi N, Kutalik Z, Allen TM, Müller V, Harrigan PR, Heckerman D, Telenti A, Fellay J. Elife. 2013 Oct 29;2:e01123. doi: 10.7554/eLife.01123.

Ability of HIV-1 Nef to downregulate CD4 and HLA class I differs among viral subtypes. Mann JK, Byakwaga H, Kuang XT, Le AQ, Brumme CJ, Mwimanzi P, Omarjee S, Martin E, Lee GQ, Baraki B, Danroth R, McCloskey R, Muzoora C, Bangsberg DR, Hunt PW, Goulder PJ, Walker BD, Harrigan PR, Martin JN, Ndung'u T, Brockman MA, Brumme ZL. Retrovirology. 2013 Sep 16;10:100. doi: 10.1186/1742-4690-10-100.

Ability of HIV-1 Nef to downregulate CD4 and HLA class I differs among viral subtypes. Mann JK, Byakwaga H, Kuang XT, Le AQ, Brumme CJ, Mwimanzi P, Omarjee S, Martin E, Lee GQ, Baraki B, Danroth R, McCloskey R, Muzoora C, Bangsberg DR, Hunt PW, Goulder PJ, Walker BD, Harrigan PR, Martin JN, Ndung'u T, Brockman MA, Brumme ZL. Retrovirology. 2013 Sep 16;10:100. doi: 10.1186/1742-4690-10-100.

Influence of HLA-C expression level on HIV control. Apps R, Qi Y, Carlson JM, Chen H, Gao X, Thomas R, Yuki Y, Del Prete GQ, Goulder P, Brumme ZL, Brumme CJ, John M, Mallal S, Nelson G, Bosch R, Heckerman D, Stein JL, Soderberg KA, Moody MA, Denny TN, Zeng X, Fang J, Moffett A, Lifson JD, Goedert JJ, Buchbinder S, Kirk GD, Fellay J, McLaren P, Deeks SG, Pereyra F, Walker B, Michael NL, Weintrob A, Wolinsky S, Liao W, Carrington M. Science. 2013 Apr 5;340(6128):87-91. doi: 10.1126/science.1232685.

A method for killer-cell immunoglobulin-like receptor (KIR) 3DL1/3DS1 genotyping using DNA recovered from frozen plasma. Shahid A, Chopera DR, Martin E, Penney KA, Milloy MJ, Brumme ZL. J Immunol Methods. 2013 May 31;391(1-2):154-62. doi: 10.1016/j.jim.2013.03.005. Epub 2013 Mar 21.

Dynamic range of Nef functions in chronic HIV-1 infection. Mwimanzi P, Markle TJ, Ogata Y, Martin E, Tokunaga M, Mahiti M, Kuang XT, Walker BD, Brockman MA, Brumme ZL, Ueno T. Virology. 2013 May 10;439(2):74-80. doi: 10.1016/j.virol.2013.02.005. Epub 2013 Mar 13.

Frequent and variable cytotoxic-T-lymphocyte escape-associated fitness costs in the human immunodeficiency virus type 1 subtype B Gag proteins. Boutwell CL, Carlson JM, Lin TH, Seese A, Power KA, Peng J, Tang Y, Brumme ZL, Heckerman D, Schneidewind A, Allen TM. J Virol. 2013 Apr;87(7):3952-65. doi: 10.1128/JVI.03233-12. Epub 2013 Jan 30.

Impact of antiretroviral therapy duration and intensification on isolated shedding of HIV-1 RNA in semen. Osborne BJ, Sheth PM, Yi TJ, Kovacs C, Benko E, Porte Cl, Huibner S, Le AQ, Danroth R, Baraki B, Mazzulli T, Brumme ZL, Kaul R. J Infect Dis. 2013 Apr 15;207(8):1226-34. doi: 10.1093/infdis/jit026. Epub 2013 Jan 17.

Attenuation of multiple Nef functions in HIV-1 elite controllers. Mwimanzi P, Markle TJ, Martin E, Ogata Y, Kuang XT, Tokunaga M, Mahiti M, Pereyra F, Miura T, Walker BD, Brumme ZL, Brockman MA, Ueno T. Retrovirology. 2013 Jan 7;10:1. doi: 10.1186/1742-4690-10-1.

Distinct HIV-1 escape patterns selected by cytotoxic T cells with identical epitope specificity. Yagita Y, Kuse N, Kuroki K, Gatanaga H, Carlson JM, Chikata T, Brumme ZL, Murakoshi H, Akahoshi T, Pfeifer N, Mallal S, John M, Ose T, Matsubara H, Kanda R, Fukunaga Y, Honda K, Kawashima Y, Ariumi Y, Oka S, Maenaka K, Takiguchi M. J Virol. 2013 Feb;87(4):2253-63. doi: 10.1128/JVI.02572-12. Epub 2012 Dec 12.

Operationalizing the One Health approach: the global governance challenges. Lee K, Brumme ZL. Health Policy Plan. 2013 Oct;28(7):778-85. doi: 10.1093/heapol/czs127. Epub 2012 Dec 7.

Human leukocyte antigen (HLA) class I down-regulation by human immunodeficiency virus type 1 negative factor (HIV-1 Nef): what might we learn from natural sequence variants? Mwimanzi P, Markle TJ, Ueno T, Brockman MA. Viruses. 2012 Sep;4(9):1711-30. doi: 10.3390/v4091711. Epub 2012 Sep 24.

Significant reductions in Gag-protease-mediated HIV-1 replication capacity during the course of the epidemic in Japan. Nomura S, Hosoya N, Brumme ZL, Brockman MA, Kikuchi T, Koga M, Nakamura H, Koibuchi T, Fujii T, Carlson JM, Heckerman D, Kawana-Tachikawa A, Iwamoto A, Miura T. J Virol. 2013 Feb;87(3):1465-76. doi: 10.1128/JVI.02122-12. Epub 2012 Nov 14.

HERV-K-specific T cells eliminate diverse HIV-1/2 and SIV primary isolates. Jones RB, Garrison KE, Mujib S, Mihajlovic V, Aidarus N, Hunter DV, Martin E, John VM, Zhan W, Faruk NF, Gyenes G, Sheppard NC, Priumboom-Brees IM, Goodwin DA, Chen L, Rieger M, Muscat-King S, Loudon PT, Stanley C, Holditch SJ, Wong JC, Clayton K, Duan E, Song H, Xu Y, SenGupta D, Tandon R, Sacha JB, Brockman MA, Benko E, Kovacs C, Nixon DF, Ostrowski MA. J Clin Invest. 2012 Dec;122(12):4473-89. doi: 10.1172/JCI64560. Epub 2012 Nov 12.

Correlates of protective cellular immunity revealed by analysis of population-level immune escape pathways in HIV-1. Carlson JM, Brumme CJ, Martin E, Listgarten J, Brockman MA, Le AQ, Chui CK, Cotton LA, Knapp DJ, Riddler SA, Haubrich R, Nelson G, Pfeifer N, Deziel CE, Heckerman D, Apps R, Carrington M, Mallal S, Harrigan PR, John M, Brumme ZL; International HIV Adaptation Collaborative. J Virol. 2012 Dec;86(24):13202-16. doi: 10.1128/JVI.01998-12. Epub 2012 Oct 10.

Intersubtype differences in the effect of a rare p24 gag mutation on HIV-1 replicative fitness. Chopera DR, Cotton LA, Zawaira A, Mann JK, Ngandu NK, Ntale R, Carlson JM, Mlisana K, Woodman Z, de Assis Rosa D, Martin E, Miura T, Pereyra F, Walker BD, Gray CM, Martin DP, Ndung'u T, Brockman MA, Karim SA, Brumme ZL, Williamson C; CAPRISA 002 Study Team. J Virol. 2012 Dec;86(24):13423-33. doi: 10.1128/JVI.02171-12. Epub 2012 Sep 26.

Modulation of HIV reservoirs by host HLA: bridging the gap between vaccine and cure. Brumme ZL, Chopera DR, Brockman MA. Curr Opin Virol. 2012 Oct;2(5):599-605. doi: 10.1016/j.coviro.2012.08.003. Epub 2012 Aug 29.

TCR clonotypes modulate the protective effect of HLA class I molecules in HIV-1 infection. Chen H, Ndhlovu ZM, Liu D, Porter LC, Fang JW, Darko S, Brockman MA, Miura T, Brumme ZL, Schneidewind A, Piechocka-Trocha A, Cesa KT, Sela J, Cung TD, Toth I, Pereyra F, Yu XG, Douek DC, Kaufmann DE, Allen TM, Walker BD. Nat Immunol. 2012 Jun 10;13(7):691-700. doi: 10.1038/ni.2342.

Aminopeptidase substrate preference affects HIV epitope presentation and predicts immune escape patterns in HIV-infected individuals. Zhang SC, Martin E, Shimada M, Godfrey SB, Fricke J, Locastro S, Lai NY, Liebesny P, Carlson JM, Brumme CJ, Ogbechie OA, Chen H, Walker BD, Brumme ZL, Kavanagh DG, Le Gall S. J Immunol. 2012 Jun 15;188(12):5924-34. doi: 10.4049/jimmunol.1200219. Epub 2012 May 14.

HLA class I sequence-based typing using DNA recovered from frozen plasma. Cotton LA, Abdur Rahman M, Ng C, Le AQ, Milloy MJ, Mo T, Brumme ZL. J Immunol Methods. 2012 Aug 31;382(1-2):40-7. doi: 10.1016/j.jim.2012.05.003. Epub 2012 May 11.

Minor contribution of HLA class I-associated selective pressure to the variability of HIV-1 accessory protein Vpu. Hasan Z, Carlson JM, Gatanaga H, Le AQ, Brumme CJ, Oka S, Brumme ZL, Ueno T. Biochem Biophys Res Commun. 2012 May 4;421(2):291-5. doi: 10.1016/j.bbrc.2012.04.002. Epub 2012 Apr 7.

Uncommon pathways of immune escape attenuate HIV-1 integrase replication capacity. Brockman MA, Chopera DR, Olvera A, Brumme CJ, Sela J, Markle TJ, Martin E, Carlson JM, Le AQ, McGovern R, Cheung PK, Kelleher AD, Jessen H, Markowitz M, Rosenberg E, Frahm N, Sanchez J, Mallal S, John M, Harrigan PR, Heckerman D, Brander C, Walker BD, Brumme ZL. J Virol. 2012 Jun;86(12):6913-23. doi: 10.1128/JVI.07133-11. Epub 2012 Apr 11.

Characteristics and outcomes of initial virologic suppressors during analytic treatment interruption in a therapeutic HIV-1 gag vaccine trial. Li JZ, Brumme CJ, Lederman MM, Brumme ZL, Wang H, Spritzler J, Carrington M, Medvik K, Walker BD, Schooley RT, Kuritzkes DR; AIDS Clinical Trials Group A5197 Study Team. PLoS One. 2012;7(3):e34134. doi: 10.1371/journal.pone.0034134. Epub 2012 Mar 30.

Increasingly successful highly active antiretroviral therapy delays the emergence of new HLA class I-associated escape mutations in HIV-1. Knapp DJ, Brumme ZL, Huang SY, Wynhoven B, Dong WW, Mo T, Harrigan PR, Brumme CJ. Clin Infect Dis. 2012 Jun;54(11):1652-9. doi: 10.1093/cid/cis253. Epub 2012 Mar 28.

Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection. Henn MR, Boutwell CL, Charlebois P, Lennon NJ, Power KA, Macalalad AR, Berlin AM, Malboeuf CM, Ryan EM, Gnerre S, Zody MC, Erlich RL, Green LM, Berical A, Wang Y, Casali M, Streeck H, Bloom AK, Dudek T, Tully D, Newman R, Axten KL, Gladden AD, Battis L, Kemper M, Zeng Q, Shea TP, Gujja S, Zedlack C, Gasser O, Brander C, Hess C, Günthard HF, Brumme ZL, Brumme CJ, Bazner S, Rychert J, Tinsley JP, Mayer KH, Rosenberg E, Pereyra F, Levin JZ, Young SK, Jessen H, Altfeld M, Birren BW, Walker BD, Allen TM. PLoS Pathog. 2012;8(3):e1002529. doi: 10.1371/journal.ppat.1002529. Epub 2012 Mar 8.

Widespread impact of HLA restriction on immune control and escape pathways of HIV-1. Carlson JM, Listgarten J, Pfeifer N, Tan V, Kadie C, Walker BD, Ndung'u T, Shapiro R, Frater J, Brumme ZL, Goulder PJ, Heckerman D. J Virol. 2012 May;86(9):5230-43. doi: 10.1128/JVI.06728-11. Epub 2012 Feb 29.

Impact of HLA-B*81-associated mutations in HIV-1 Gag on viral replication capacity. Wright JK, Naidoo VL, Brumme ZL, Prince JL, Claiborne DT, Goulder PJ, Brockman MA, Hunter E, Ndung'u T. J Virol. 2012 Mar;86(6):3193-9. doi: 10.1128/JVI.06682-11. Epub 2012 Jan 11.

Lack of association between HLA class II alleles and in vitro replication capacities of recombinant viruses encoding HIV-1 subtype C Gag-protease from chronically infected individuals. Wright JK, Brumme ZL, Julg B, van der Stok M, Mncube Z, Gao X, Carlson JM, Goulder PJ, Walker BD, Brockman MA, Ndung'u T. J Virol. 2012 Jan;86(2):1273-6. doi: 10.1128/JVI.06533-11. Epub 2011 Nov 16.