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Research Article

Progression to AIDS in South Africa Is Associated with both Reverting and Compensatory Viral Mutations

  • Kuan-Hsiang Gary Huang equal contributor,

    equal contributor Contributed equally to this work with: Kuan-Hsiang Gary Huang, Dominique Goedhals

    Affiliations: Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom, The James Martin 21st Century School, Oxford, United Kingdom

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  • Dominique Goedhals equal contributor,

    equal contributor Contributed equally to this work with: Kuan-Hsiang Gary Huang, Dominique Goedhals

    Affiliations: University of Free State, Bloemfontein, South Africa, National Health Laboratory Services (NHLS), Johannesburg, South Africa

    X
  • Jonathan M. Carlson,

    Affiliation: eScience Group, Microsoft Research, Los Angeles, California, United States of America

    X
  • Mark A. Brockman,

    Affiliations: Simon Fraser University, Burnaby, British Columbia, Canada, British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada, Ragon Institute of Massachusetts General Hospital, Harvard University and Massachusetts Institute of Technology (MIT), Boston, Massachusetts, United States of America

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  • Swati Mishra,

    Affiliation: Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom

    X
  • Zabrina L. Brumme,

    Affiliations: Simon Fraser University, Burnaby, British Columbia, Canada, British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada, Ragon Institute of Massachusetts General Hospital, Harvard University and Massachusetts Institute of Technology (MIT), Boston, Massachusetts, United States of America

    X
  • Stephen Hickling,

    Affiliation: Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom

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  • Christopher S. W. Tang,

    Affiliation: Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom

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  • Toshiyuki Miura,

    Affiliations: Ragon Institute of Massachusetts General Hospital, Harvard University and Massachusetts Institute of Technology (MIT), Boston, Massachusetts, United States of America, Institute of Medical Science, University of Tokyo, Tokyo, Japan

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  • Chris Seebregts,

    Affiliation: Biomedical Informatics Research Division, Medical Research Council, Cape Town, South Africa

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  • David Heckerman,

    Affiliation: eScience Group, Microsoft Research, Los Angeles, California, United States of America

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  • Thumbi Ndung'u,

    Affiliation: HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa

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  • Bruce Walker,

    Affiliations: HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa, Infectious Disease, Massachusetts General Hospital, Boston, Massachusetts, United States of America, Division of AIDS, Harvard University, Boston, Massachusetts, United States of America

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  • Paul Klenerman,

    Affiliations: Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom, Oxford NIHR Biomedical Research Centre, Oxford, United Kingdom

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  • Dewald Steyn,

    Affiliation: University of Free State, Bloemfontein, South Africa

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  • Philip Goulder,

    Affiliation: Department of Paediatrics, University of Oxford, Oxford, United Kingdom

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  • Rodney Phillips,

    Affiliations: Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom, The James Martin 21st Century School, Oxford, United Kingdom, Oxford NIHR Biomedical Research Centre, Oxford, United Kingdom

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  • Bloemfontein-Oxford Collaborative Group,
  • Cloete van Vuuren,

    Affiliation: University of Free State, Bloemfontein, South Africa

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  • John Frater mail

    john.frater@ndm.ox.ac.uk

    Affiliations: Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom, Oxford NIHR Biomedical Research Centre, Oxford, United Kingdom

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  • Published: April 22, 2011
  • DOI: 10.1371/journal.pone.0019018

About the Authors

Kuan-Hsiang Gary Huang, Swati Mishra, Stephen Hickling, Christopher S. W. Tang, Paul Klenerman, Rodney Phillips, John Frater
Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
Dominique Goedhals, Dewald Steyn, Cloete van Vuuren
University of Free State, Bloemfontein, South Africa
Dominique Goedhals
National Health Laboratory Services (NHLS), Johannesburg, South Africa
Jonathan M. Carlson, David Heckerman
eScience Group, Microsoft Research, Los Angeles, California, United States of America
Mark A. Brockman, Zabrina L. Brumme
Simon Fraser University, Burnaby, British Columbia, Canada
Mark A. Brockman, Zabrina L. Brumme
British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
Mark A. Brockman, Zabrina L. Brumme, Toshiyuki Miura
Ragon Institute of Massachusetts General Hospital, Harvard University and Massachusetts Institute of Technology (MIT), Boston, Massachusetts, United States of America
Toshiyuki Miura
Institute of Medical Science, University of Tokyo, Tokyo, Japan
Chris Seebregts
Biomedical Informatics Research Division, Medical Research Council, Cape Town, South Africa
Thumbi Ndung'u, Bruce Walker
HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
Bruce Walker
Infectious Disease, Massachusetts General Hospital, Boston, Massachusetts, United States of America
Bruce Walker
Division of AIDS, Harvard University, Boston, Massachusetts, United States of America
Philip Goulder
Department of Paediatrics, University of Oxford, Oxford, United Kingdom
Kuan-Hsiang Gary Huang, Rodney Phillips
The James Martin 21st Century School, Oxford, United Kingdom
Paul Klenerman, Rodney Phillips, John Frater
Oxford NIHR Biomedical Research Centre, Oxford, United Kingdom

Corresponding Author

Email: john.frater@ndm.ox.ac.uk

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

Conceived and designed the experiments: K-HGH DG JC MB SM ZB PK DS PG RP CVV JF CS. Performed the experiments: K-HGH DG SM SH CT. Analyzed the data: JC DH JF K-HGH. Contributed reagents/materials/analysis tools: TM MB TN BW. Wrote the paper: K-HGH JF RP.