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Research Article

Evidence of Differential HLA Class I-Mediated Viral Evolution in Functional and Accessory/Regulatory Genes of HIV-1

  • Zabrina L Brumme mail,

    To whom correspondence should be addressed. E-mail: zbrumme@partners.org

    Affiliations: Partners AIDS Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America, Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America, British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada

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  • Chanson J Brumme,

    Affiliations: Partners AIDS Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America, British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada

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  • David Heckerman,

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

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  • Bette T Korber,

    Affiliations: Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America, Santa Fe Institute, Santa Fe, New Mexico, United States of America

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  • Marcus Daniels,

    Affiliation: Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America

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  • Jonathan Carlson,

    Affiliations: Microsoft Research, Redmond, Washington, United States of America, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America

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  • Carl Kadie,

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

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  • Tanmoy Bhattacharya,

    Affiliations: Santa Fe Institute, Santa Fe, New Mexico, United States of America, Department of Computer Science and Engineering, University of Washington, Seattle, Washington, United States of America

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  • Celia Chui,

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

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  • James Szinger,

    Affiliation: Santa Fe Institute, Santa Fe, New Mexico, United States of America

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  • Theresa Mo,

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

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  • Robert S Hogg,

    Affiliations: British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada, Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada

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  • Julio S. G Montaner,

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

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  • Nicole Frahm,

    Affiliation: Partners AIDS Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America

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  • Christian Brander,

    Affiliation: Partners AIDS Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America

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  • Bruce D Walker,

    Affiliations: Partners AIDS Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America, Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America

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  • P. Richard Harrigan

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

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  • Published: July 06, 2007
  • DOI: 10.1371/journal.ppat.0030094

About the Authors

Zabrina L Brumme, Chanson J Brumme, Nicole Frahm, Christian Brander, Bruce D Walker
Partners AIDS Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
Zabrina L Brumme, Bruce D Walker
Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
Zabrina L Brumme, Chanson J Brumme, Celia Chui, Theresa Mo, Robert S Hogg, Julio S. G Montaner, P. Richard Harrigan
British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
David Heckerman, Jonathan Carlson, Carl Kadie
Microsoft Research, Redmond, Washington, United States of America
Bette T Korber, Marcus Daniels, Jonathan Carlson
Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
Bette T Korber, Tanmoy Bhattacharya, James Szinger
Santa Fe Institute, Santa Fe, New Mexico, United States of America
Tanmoy Bhattacharya
Department of Computer Science and Engineering, University of Washington, Seattle, Washington, United States of America
Robert S Hogg
Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
Julio S. G Montaner, P. Richard Harrigan
Department of Medicine, 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

ZLB, CJB, DH, RSH, JSGM, NF, CB, BDW, and PRH conceived and designed the experiments. ZLB, CJB, DH, CC, TM, NF, CB, BDW, and PRH performed the experiments. ZLB, CJB, DH, BTK, MD, JC, CK, TB, JS, and PRH analyzed the data. DH, BTK, MD, TB, and RSH contributed reagents/materials/analysis tools. ZLB, CJB, BDW, and PRH wrote the paper. DH, BTK, JC, CC, and NF critically reviewed the manuscript.