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Research Article

HLA-Associated Immune Escape Pathways in HIV-1 Subtype B Gag, Pol and Nef Proteins

  • Zabrina L. Brumme equal contributor mail,

    equal contributor Contributed equally to this work with: Zabrina L. Brumme, Mina John

    zbrumme@partners.org

    Affiliations: Ragon Institute of MGH, MIT and Harvard, Charlestown, Massachusetts, United States of America, Simon Fraser University, Burnaby, British Columbia, Canada

    X
  • Mina John equal contributor,

    equal contributor Contributed equally to this work with: Zabrina L. Brumme, Mina John

    Affiliation: Center for Clinical Immunology and Biomedical Statistics, Royal Perth Hospital, Murdoch University, Perth, Australia

    X
  • Jonathan M. Carlson,

    Affiliation: Microsoft Research, Redmond, Washington, United States of America

    X
  • Chanson J. Brumme,

    Affiliation: Ragon Institute of MGH, MIT and Harvard, Charlestown, Massachusetts, United States of America

    X
  • Dennison Chan,

    Affiliation: BC Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada

    X
  • Mark A. Brockman,

    Affiliations: Ragon Institute of MGH, MIT and Harvard, Charlestown, Massachusetts, United States of America, Simon Fraser University, Burnaby, British Columbia, Canada

    X
  • Luke C. Swenson,

    Affiliation: BC Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada

    X
  • Iris Tao,

    Affiliation: BC Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada

    X
  • Sharon Szeto,

    Affiliation: BC Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada

    X
  • Pamela Rosato,

    Affiliation: Ragon Institute of MGH, MIT and Harvard, Charlestown, Massachusetts, United States of America

    X
  • Jennifer Sela,

    Affiliation: Ragon Institute of MGH, MIT and Harvard, Charlestown, Massachusetts, United States of America

    X
  • Carl M. Kadie,

    Affiliation: Microsoft Research, Redmond, Washington, United States of America

    X
  • Nicole Frahm,

    Affiliation: Ragon Institute of MGH, MIT and Harvard, Charlestown, Massachusetts, United States of America

    Current address: Fred Hutchinson Cancer Research Center and University of Washington, Seattle, Washington, United States of America

    X
  • Christian Brander,

    Affiliations: Ragon Institute of MGH, MIT and Harvard, Charlestown, Massachusetts, United States of America, AIDS Research Institute irsiCaixa - HIVACAT, Hospital Germans Trias i Pujol, Badalona, Spain, Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain

    X
  • David W. Haas,

    Affiliation: Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America

    X
  • Sharon A. Riddler,

    Affiliation: University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America

    X
  • Richard Haubrich,

    Affiliation: University of California San Diego, San Diego, California, United States of America

    X
  • Bruce D. Walker,

    Affiliations: Ragon Institute of MGH, MIT and Harvard, Charlestown, Massachusetts, United States of America, Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America

    X
  • P. Richard Harrigan,

    Affiliations: BC Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada, University of British Columbia, Vancouver, British Columbia, Canada

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  • David Heckerman,

    Affiliation: Microsoft Research, Redmond, Washington, United States of America

    X
  • Simon Mallal

    Affiliation: Center for Clinical Immunology and Biomedical Statistics, Royal Perth Hospital, Murdoch University, Perth, Australia

    X
  • Published: August 19, 2009
  • DOI: 10.1371/journal.pone.0006687

About the Authors

Zabrina L. Brumme, Chanson J. Brumme, Mark A. Brockman, Pamela Rosato, Jennifer Sela, Nicole Frahm, Christian Brander, Bruce D. Walker
Ragon Institute of MGH, MIT and Harvard, Charlestown, Massachusetts, United States of America
Zabrina L. Brumme, Mark A. Brockman
Simon Fraser University, Burnaby, British Columbia, Canada
Mina John, Simon Mallal
Center for Clinical Immunology and Biomedical Statistics, Royal Perth Hospital, Murdoch University, Perth, Australia
Jonathan M. Carlson, Carl M. Kadie, David Heckerman
Microsoft Research, Redmond, Washington, United States of America
Dennison Chan, Luke C. Swenson, Iris Tao, Sharon Szeto, P. Richard Harrigan
BC Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
Christian Brander
AIDS Research Institute irsiCaixa - HIVACAT, Hospital Germans Trias i Pujol, Badalona, Spain
Christian Brander
Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
David W. Haas
Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
Sharon A. Riddler
University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
Richard Haubrich
University of California San Diego, San Diego, California, United States of America
Bruce D. Walker
Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
P. Richard Harrigan
University of British Columbia, Vancouver, British Columbia, Canada

Corresponding Author

Email: zbrumme@partners.org

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

Conceived and designed the experiments: ZLB MJ JMC DH SAM. Performed the experiments: ZLB MJ JMC CJB LS IT SS DH SAM. Analyzed the data: ZLB MJ JMC CJB PR JS CK DH SAM. Contributed reagents/materials/analysis tools: JMC CJB DC MB CK NF CB DWH SR RH BDW PRH DH SAM. Wrote the paper: ZLB. Critical review of manuscript: MJ JMC CJB MB PR JS NF BDW PRH DH SAM.