HLA-Associated Immune Escape Pathways in HIV-1 Subtype B Gag, Pol and Nef Proteins Zabrina L. Brumme1,2.*, Mina John3., Jonathan M. Carlson4, Chanson J. Brumme1, Dennison Chan5, Mark A. Brockman1,2, Luke C. Swenson5, Iris Tao 5 , Sharon Szeto 5 , Pamela Rosato1, Jennifer Sela1, Carl M. Kadie4, Nicole Frahm1¤, Christian Brander1,6,7, David W. Haas8, Sharon A. Riddler9, Richard Haubrich10, Bruce D. Walker1,11, P. Richard Harrigan5,12 , David Heckerman 4 , Simon Mallal3 1 Ragon Institute of MGH, MIT and Harvard, Charlestown, Massachusetts, United States of America, 2 Simon Fraser University, Burnaby, British Columbia, Canada, 3 Center for Clinical Immunology and Biomedical Statistics, Royal Perth Hospital, Murdoch University, Perth, Australia, 4 Microsoft Research, Redmond, Washington, United States of America, 5 BC Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada, 6 AIDS Research Institute irsiCaixa - HIVACAT, Hospital Germans Trias i Pujol, Badalona, Spain, 7 Institucio´ Catalana de Recerca i Estudis Avanc¸ats (ICREA), Barcelona, Spain, 8 Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America, 9 University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America, 10 University of California San Diego, San Diego, California, United States of America, 11 Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America, 12 University of British Columbia, Vancouver, British Columbia, Canada Abstract Background: Despite the extensive genetic diversity of HIV-1, viral evolution in response to immune selective pressures follows broadly predictable mutational patterns. Sites and pathways of Human Leukocyte-Antigen (HLA)-associated polymorphisms in HIV-1 have been identified through the analysis of population-level data, but the full extent of immune escape pathways remains incompletely characterized. Here, in the largest analysis of HIV-1 subtype B sequences undertaken to date, we identify HLA-associated polymorphisms in the three HIV-1 proteins most commonly considered in cellular-based vaccine strategies. Results are organized into protein-wide escape maps illustrating the sites and pathways of HLA-driven viral evolution. Methodology/Principal Findings: HLA-associated polymorphisms were identified in HIV-1 Gag, Pol and Nef in a multicenter cohort of .1500 chronically subtype-B infected, treatment-na¨ıve individuals from established cohorts in Canada, the USA and Western Australia. At q#0.05, 282 codons commonly mutating under HLA-associated immune pressures were identified in these three proteins. The greatest density of associations was observed in Nef (where close to 40% of codons exhibited a significant HLA association), followed by Gag then Pol (where ,15–20% of codons exhibited HLA associations), confirming the extensive impact of immune selection on HIV evolution and diversity. Analysis of HIV codon covariation patterns identified over 2000 codon-codon interactions at q#0.05, illustrating the dense and complex networks of linked escape and secondary/compensatory mutations. Conclusions/Significance: The immune escape maps and associated data are intended to serve as a user-friendly guide to the locations of common escape mutations and covarying codons in HIV-1 subtype B, and as a resource facilitating the systematic identification and classification of immune escape mutations. These resources should facilitate research in HIV epitope discovery and host-pathogen co-evolution, and are relevant to the continued search for an effective CTL-based AIDS vaccine. Citation: Brumme ZL, John M, Carlson JM, Brumme CJ, Chan D, et al. (2009) HLA-Associated Immune Escape Pathways in HIV-1 Subtype B Gag, Pol and Nef Proteins. PLoS ONE 4(8): e6687. doi:10.1371/journal.pone.0006687 Editor: Douglas F. Nixon, University of California San Francisco, United States of America Received May 15, 2009; Accepted May 27, 2009; Published August 19, 2009 Copyright: 2009 Brumme et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: ZLB was supported by a post-doctoral fellowship and currently a New Investigator award from the Canadian Institutes for Health Research (CIHR). This research was supported in part by funds from the Bill and Melinda Gates Foundation and by Award Number U01AI068636 and AI068634 from the National Institute of Allergy and Infectious Diseases. Funding for R Haubrich and UCSD included K24-AI 064086 (to RH) and AI36214 to the UCSD Center for AIDS Research (CFAR). The content of this manuscript is solely the responsibility of the authors and does not necessarily represent the official views of the National Institute of Allergy and Infectious Diseases or the National Institutes of Health. The ACTG Human DNA Repository is supported by grants AI068636 and RR024975. The following is a list of ACTG sites that participated in both A5142 and A5128 protocols, along with their grant numbers: Northwestern University (Site 2701, 2702, 2705) CTU Grant # AI 069471; University of Minnesota (Site 1501, 1504, 1505) CTU Grant #AI 27661; Vanderbilt University (Site 3652) CTU Grant #AI-069439; Indiana University (Site 2601, 2603) CTU Grant #AI25859, GCRC Grant #MO1RR000750; University of Miami School of Medicine (Site 901) CTU Grant # AI069477; University of Cincinnati (Site 2401) CTU Grant # AI-069513; University of Alabama (Site 5801, 5802) CTU Grant # 1 U01 AI069452-01, GCRC Grant # M01 RR-00032; University of Southern California (Site 1201) CTU Grant # AI27673; Cornell CTU (Site 30329, 7803, 7804) CTU Grant # AI069419-01 CTSC# RR024996; The Ohio State University (Site 2301) CTU Grant # AI069474; University of Rochester (Site 1101, 1102, 1107, 1108) CTU Grant # AI69411, GCRC Grant # 5-MO1 RR00044; UNC-Chapel Hill (Site 3201) CFAR Grant # AI50410, CTU Grant # AI69423-01, GCRC Grant #RR00046; University of Pittsburgh (Site 1001, 1008) CTU Grant #AI69494-01; Duke University Medical Center (Site 1601) CTU Grant # 1U01-AI069484; Harvard/BMC CTU (Sites 103, 104, 107) CTU Grant #AI069472, CFAR Grant # AI060354, and GCRC Grant #RR02635; Durban International CTU (Site 11201) Grant # UOIA138858; Case Western Reserve University (Site 2501, 2503, 2508) CTU Grant #AI 069501; University of Pennsylvania, Philadelphia (Site 6201, 6206) CTU Grant # AI 69467-01, CFAR Grant # 5-P30-AI-045008-07; Colorado ACTU (Site 6101) CTU Grant #AI069450 and GCRC Grant # RR00051;UTMB-Galveston (Site 6301) CTU Grant # AI32782; Johns Hopkins University (Site 201) CTU Grant# AI-69465, GCRC Grant # RR-00052; University of California, Los Angeles (Site 601, 603) CTU Grant #AI069424; University of California, Davis Medical Center (Site 3852) CTU Grant AI38858-09S1; University of Maryland, Inst. of Human Virology (Site 4651) CTU Grant # AI069447-01; Washington University in St. Louis (Site 2101) CTU Grant # AI069495; University of California, San Francisco (Site 801) CTU Grant # AI069502-01; Stanford University (Sites 501, 505, 506) CTU Grant # AI069556; University of California, San Diego (Site 701) Grant # AI069432; Beth Israel Medical Center (Site 2851) CTU Grant #AI46370; New York University/NYC HHC at Bellevue Hospital Center (Site 401) CTU Grant #AI069532, GCRC Grant # M01-RR00096; The Miriam Hospital (Site 2951) CTU Grant # AI69472; UT Southwestern Medical Center at Dallas (Site 3751) CTU Grant #AI046376-05; University of Hawaii at Manoa and Queen’s Medical Center (Site 5201) CTU Grant # AI34853; University of Washington, Seattle (Site 1401) CTU Grant #AI069434. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. PLoS ONE | www.plosone.org 1 August 2009 | Volume 4 | Issue 8 | e6687