Sieve analysis of breakthrough HIV-1 sequences in HVTN 505 identifies vaccine pressure targeting the CD4 binding site of Env-gp120

• Allan C. deCamp ,

  Contributed equally to this work with: Allan C. deCamp, Morgane Rolland

  Roles Conceptualization, Formal analysis, Resources, Writing – original draft, Writing – review & editing

  * E-mail: adecamp@scharp.org (ACD); mrolland@hivresearch.org (MR); pgilbert@scharp.org (PBG)

  Affiliation Vaccine and Infectious Disease Division and Statistical Center for HIV/AIDS Research and Prevention, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America

  http://orcid.org/0000-0003-1404-4322

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• Morgane Rolland ,

  Contributed equally to this work with: Allan C. deCamp, Morgane Rolland

  Roles Conceptualization, Formal analysis, Resources, Writing – original draft, Writing – review & editing

  * E-mail: adecamp@scharp.org (ACD); mrolland@hivresearch.org (MR); pgilbert@scharp.org (PBG)

  Affiliations US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America, The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America

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• Paul T. Edlefsen,

  Roles Formal analysis, Resources

  Affiliations Vaccine and Infectious Disease Division and Statistical Center for HIV/AIDS Research and Prevention, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America, Department of Biostatistics, University of Washington, Seattle, Washington, United States of America

  ⨯
• Eric Sanders-Buell,

  Roles Investigation

  Affiliations US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America, The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America

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• Breana Hall,

  Roles Investigation

  Affiliation Department of Microbiology, University of Washington, Seattle, Washington, United States of America

  ⨯
• Craig A. Magaret,

  Roles Formal analysis, Resources

  Affiliation Vaccine and Infectious Disease Division and Statistical Center for HIV/AIDS Research and Prevention, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America

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• Andrew J. Fiore-Gartland,

  Roles Formal analysis, Resources

  Affiliation Vaccine and Infectious Disease Division and Statistical Center for HIV/AIDS Research and Prevention, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America

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• Michal Juraska,

  Roles Formal analysis, Resources

  Affiliation Vaccine and Infectious Disease Division and Statistical Center for HIV/AIDS Research and Prevention, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America

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• Lindsay N. Carpp,

  Roles Conceptualization, Writing – original draft, Writing – review & editing

  Affiliation Vaccine and Infectious Disease Division and Statistical Center for HIV/AIDS Research and Prevention, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America

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• Shelly T. Karuna,

  Roles Investigation

  Affiliation Vaccine and Infectious Disease Division and Statistical Center for HIV/AIDS Research and Prevention, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America

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• Meera Bose,

  Roles Investigation

  Affiliations US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America, The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America

  ⨯
• Steven LePore,

  Roles Investigation

  Affiliations US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America, The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America

  ⨯
• Shana Miller,

  Roles Investigation

  Affiliations US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America, The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America

  ⨯
• Annemarie O'Sullivan,

  Roles Investigation

  Affiliations US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America, The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America

  ⨯
• Kultida Poltavee,

  Roles Investigation

  Affiliations US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America, The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America

  ⨯
• Hongjun Bai,

  Roles Formal analysis

  Affiliations US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America, The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America

  ⨯
• Kalpana Dommaraju,

  Roles Formal analysis

  Affiliations US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America, The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America

  ⨯
• Hong Zhao,

  Roles Investigation

  Affiliation Department of Microbiology, University of Washington, Seattle, Washington, United States of America

  ⨯
• Kim Wong,

  Roles Investigation

  Affiliation Department of Microbiology, University of Washington, Seattle, Washington, United States of America

  ⨯
• Lennie Chen,

  Roles Investigation

  Affiliation Department of Microbiology, University of Washington, Seattle, Washington, United States of America

  ⨯
• Hasan Ahmed,

  Roles Formal analysis, Resources

  Affiliation Department of Biology, Emory University, Atlanta, Georgia, United States of America

  ⨯
• Derrick Goodman,

  Roles Formal analysis

  Affiliation Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America

  ⨯
• Matthew Z. Tay,

  Roles Formal analysis

  Affiliation Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America

  ⨯
• Raphael Gottardo,

  Roles Formal analysis, Resources

  Affiliations Vaccine and Infectious Disease Division and Statistical Center for HIV/AIDS Research and Prevention, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America, Department of Biostatistics, University of Washington, Seattle, Washington, United States of America

  ⨯
• Richard A. Koup,

  Roles Conceptualization

  Affiliation Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America

  ⨯
• Robert Bailer,

  Roles Conceptualization

  Affiliation Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America

  ⨯
• John R. Mascola,

  Roles Conceptualization

  Affiliation Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America

  ⨯
• Barney S. Graham,

  Roles Conceptualization

  Affiliation Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America

  ⨯
• Mario Roederer,

  Roles Investigation

  Affiliation Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America

  ⨯
• Robert J. O’Connell,

  Roles Conceptualization

  Affiliations US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America, The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America

  ⨯
• Nelson L. Michael,

  Roles Conceptualization, Resources

  Affiliations US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America, The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America

  ⨯
• Merlin L. Robb,

  Roles Conceptualization

  Affiliations US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America, The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America

  ⨯
• Elizabeth Adams,

  Roles Investigation

  Affiliations The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America, Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America

  ⨯
• Patricia D’Souza,

  Roles Investigation

  Affiliation Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America

  ⨯
• James Kublin,

  Roles Conceptualization, Investigation

  Affiliation Vaccine and Infectious Disease Division and Statistical Center for HIV/AIDS Research and Prevention, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America

  ⨯
• Lawrence Corey,

  Roles Conceptualization, Investigation

  Affiliation Vaccine and Infectious Disease Division and Statistical Center for HIV/AIDS Research and Prevention, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America

  ⨯
• Daniel E. Geraghty,

  Roles Conceptualization

  Affiliation Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America

  ⨯
• Nicole Frahm,

  Roles Conceptualization

  Affiliations Vaccine and Infectious Disease Division and Statistical Center for HIV/AIDS Research and Prevention, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America, Department of Global Health, University of Washington, Seattle, Washington, United States of America

  ⨯
• Georgia D. Tomaras,

  Roles Conceptualization, Investigation

  Affiliation Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America

  ⨯
• M. Juliana McElrath,

  Roles Conceptualization, Investigation

  Affiliations Vaccine and Infectious Disease Division and Statistical Center for HIV/AIDS Research and Prevention, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America, Department of Medicine, University of Washington, Seattle, Washington, United States of America, Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America

  ⨯
• Lisa Frenkel,

  Roles Investigation

  Affiliations Department of Global Health, University of Washington, Seattle, Washington, United States of America, Department of Medicine, University of Washington, Seattle, Washington, United States of America, Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America, Seattle Children’s Research Institute, Seattle, Washington, United States of America, Department of Pediatrics, University of Washington, Seattle, Washington, United States of America

  ⨯
• Sheila Styrchak,

  Roles Investigation

  Affiliation Seattle Children’s Research Institute, Seattle, Washington, United States of America

  ⨯
• Sodsai Tovanabutra,

  Roles Conceptualization

  Affiliations US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America, The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America

  ⨯
• Magdalena E. Sobieszczyk,

  Roles Conceptualization, Investigation

  Affiliation Department of Medicine, Division of Infectious Diseases, Columbia University Medical Center, New York, New York, United States of America

  ⨯
• Scott M. Hammer,

  Roles Conceptualization, Investigation

  Affiliation Department of Medicine, Division of Infectious Diseases, Columbia University Medical Center, New York, New York, United States of America

  ⨯
• Jerome H. Kim ,

  Roles Conceptualization, Resources

  ¶‡ These authors also contributed equally to this work.

  Affiliation International Vaccine Institute, Seoul, Korea

  ⨯
• James I. Mullins ,

  Roles Conceptualization, Resources, Writing – original draft, Writing – review & editing

  ¶‡ These authors also contributed equally to this work.

  Affiliations Department of Microbiology, University of Washington, Seattle, Washington, United States of America, Department of Global Health, University of Washington, Seattle, Washington, United States of America, Department of Medicine, University of Washington, Seattle, Washington, United States of America, Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America

  ⨯
•  [ ... ],
• Peter B. Gilbert

  Roles Conceptualization, Formal analysis, Resources, Writing – original draft, Writing – review & editing

  * E-mail: adecamp@scharp.org (ACD); mrolland@hivresearch.org (MR); pgilbert@scharp.org (PBG)

  ¶‡ These authors also contributed equally to this work.

  Affiliations Vaccine and Infectious Disease Division and Statistical Center for HIV/AIDS Research and Prevention, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America, Department of Biostatistics, University of Washington, Seattle, Washington, United States of America

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