Whole Genome Deep Sequencing of HIV-1 Reveals the Impact of Early Minor Variants Upon Immune Recognition During Acute Infection

• Matthew R. Henn,

  Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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• Christian L. Boutwell ,

  Contributed equally to this work with: Christian L. Boutwell, Patrick Charlebois

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

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• Patrick Charlebois ,

  Contributed equally to this work with: Christian L. Boutwell, Patrick Charlebois

  Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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• Niall J. Lennon,

  Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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• Karen A. Power,

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

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• Alexander R. Macalalad,

  Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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• Aaron M. Berlin,

  Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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• Christine M. Malboeuf,

  Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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• Elizabeth M. Ryan,

  Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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• Sante Gnerre,

  Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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• Michael C. Zody,

  Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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• Rachel L. Erlich,

  Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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• Lisa M. Green,

  Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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• Andrew Berical,

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

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• Yaoyu Wang,

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

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• Monica Casali,

  Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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• Hendrik Streeck,

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

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• Allyson K. Bloom,

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

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• Tim Dudek,

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

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• Damien Tully,

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

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• Ruchi Newman,

  Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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• Karen L. Axten,

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

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• Adrianne D. Gladden,

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

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• Laura Battis,

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

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• Michael Kemper,

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

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• Qiandong Zeng,

  Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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• Terrance P. Shea,

  Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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• Sharvari Gujja,

  Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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• Carmen Zedlack,

  Affiliation HIV Clinic Praxis. Jessen, Berlin, Germany

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• Olivier Gasser,

  Affiliation Immunobiology Lab, Department of Biomedicine, University Hospital Basel, Basel, Switzerland

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• Christian Brander,

  Affiliations Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain, Irsicaixa AIDS Research Institute-HIVACAT, Hospital University Germans Trias I Pujol, Badalona, Spain

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• Christoph Hess,

  Affiliation Immunobiology Lab, Department of Biomedicine, University Hospital Basel, Basel, Switzerland

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• Huldrych F. Günthard,

  Affiliation Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland

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• Zabrina L. Brumme,

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

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• Chanson J. Brumme,

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

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• Suzane Bazner,

  Affiliation Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America

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• Jenna Rychert,

  Affiliation Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America

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• Jake P. Tinsley,

  Affiliation The Fenway Institute, Fenway Health, Boston, Massachusetts, United States of America

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• Ken H. Mayer,

  Affiliation The Fenway Institute, Fenway Health, Boston, Massachusetts, United States of America

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• Eric Rosenberg,

  Affiliation Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America

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• Florencia Pereyra,

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

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• Joshua Z. Levin,

  Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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• Sarah K. Young,

  Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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• Heiko Jessen,

  Affiliation HIV Clinic Praxis. Jessen, Berlin, Germany

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• Marcus Altfeld,

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

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• Bruce W. Birren,

  Affiliation Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

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• Bruce D. Walker,

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

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•  [ ... ],
• Todd M. Allen

  * E-mail: tallen2@partners.org

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

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