Rare HIV-1 transmitted/founder lineages identified by deep viral sequencing contribute to rapid shifts in dominant quasispecies during acute and early infection

• Gustavo H. Kijak ,

  Roles Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Software, Validation, Visualization, Writing – original draft

  * E-mail: gustavokijak@gmail.com

  Current address: GSK Vaccines, Rockville, MD, United States of America

  Affiliations U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America, Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America

  http://orcid.org/0000-0002-2746-9533

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• Eric Sanders-Buell,

  Roles Conceptualization, Formal analysis, Investigation, Methodology, Validation, Writing – original draft, Writing – review & editing

  Affiliations U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America, Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America

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• Agnes-Laurence Chenine,

  Roles Conceptualization, Investigation, Methodology, Writing – review & editing

  Affiliations U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America, Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America

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• Michael A. Eller,

  Roles Conceptualization, Formal analysis, Investigation, Methodology, Validation, Visualization, Writing – review & editing

  Affiliations U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America, Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America

  http://orcid.org/0000-0003-3905-4877

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• Nilu Goonetilleke,

  Roles Conceptualization, Investigation, Validation, Writing – review & editing

  Affiliation School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America

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• Rasmi Thomas,

  Roles Investigation, Methodology, Writing – review & editing

  Affiliations U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America, Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America

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• Sivan Leviyang,

  Roles Conceptualization, Formal analysis, Methodology, Software, Visualization, Writing – original draft

  Affiliation Department of Mathematics and Statistics, Georgetown University, Washington, DC, United States of America

  http://orcid.org/0000-0002-8315-3146

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• Elizabeth A. Harbolick,

  Roles Investigation, Methodology

  Affiliations U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America, Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America

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• Meera Bose,

  Roles Data curation, Investigation

  Affiliations U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America, Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America

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• Phuc Pham,

  Roles Formal analysis, Methodology, Software

  Affiliations U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America, Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America

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• Celina Oropeza,

  Roles Investigation

  Affiliations U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America, Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America

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• Kultida Poltavee,

  Roles Investigation

  Affiliations U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America, Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America

  ⨯
• Anne Marie O’Sullivan,

  Roles Data curation, Investigation

  Affiliations U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America, Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America

  ⨯
• Erik Billings,

  Roles Data curation, Writing – review & editing

  Affiliations U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America, Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America

  http://orcid.org/0000-0002-8963-0484

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• Melanie Merbah,

  Roles Investigation, Writing – review & editing

  Affiliations U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America, Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America

  http://orcid.org/0000-0002-5641-8612

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• Margaret C. Costanzo,

  Roles Investigation, Writing – review & editing

  Affiliations U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America, Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America

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• Joanna A. Warren,

  Roles Investigation

  Affiliation School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America

  ⨯
• Bonnie Slike,

  Roles Investigation

  Affiliations U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America, Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America

  ⨯
• Hui Li,

  Roles Investigation

  Affiliation Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America

  ⨯
• Kristina K. Peachman,

  Roles Investigation, Writing – review & editing

  Affiliations U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America, Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America

  ⨯
• Will Fischer,

  Roles Methodology, Software, Writing – review & editing

  Affiliation Theoretical Biology, Los Alamos National Laboratory, Los Alamos, NM, United States of America

  http://orcid.org/0000-0003-4579-4062

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• Feng Gao,

  Roles Conceptualization

  Affiliation Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, United States of America

  ⨯
• Claudia Cicala,

  Roles Conceptualization, Methodology

  Affiliation Laboratory of Immunoregulation National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States of America

  ⨯
• James Arthos,

  Roles Conceptualization, Methodology

  Affiliation Laboratory of Immunoregulation National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States of America

  ⨯
• Leigh A. Eller,

  Roles Data curation, Investigation, Project administration

  Affiliations U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America, Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America

  http://orcid.org/0000-0003-2043-1513

  ⨯
• Robert J. O’Connell,

  Roles Resources, Supervision

  Affiliation Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand

  ⨯
• Samuel Sinei,

  Roles Resources

  Affiliation Walter Reed Project, Kericho, Kenya

  ⨯
• Lucas Maganga,

  Roles Resources

  Affiliation Mbeya Medical Research Programme, Mbeya, Tanzania

  ⨯
• Hannah Kibuuka,

  Roles Resources

  Affiliation Makerere University-Walter Reed Project, Kampala, Uganda

  http://orcid.org/0000-0002-2293-1944

  ⨯
• Sorachai Nitayaphan,

  Roles Resources

  Affiliation Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand

  http://orcid.org/0000-0001-6935-1405

  ⨯
• Mangala Rao,

  Roles Conceptualization

  Affiliation U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America

  ⨯
• Mary A. Marovich,

  Roles Conceptualization

  Affiliation Vaccine Research Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, United States of America

  ⨯
• Shelly J. Krebs,

  Roles Conceptualization, Investigation

  Affiliations U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America, Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America

  ⨯
• Morgane Rolland,

  Roles Conceptualization, Formal analysis, Investigation, Methodology, Writing – review & editing

  Affiliations U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America, Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America

  ⨯
• Bette T. Korber,

  Roles Methodology, Software

  Affiliation Theoretical Biology, Los Alamos National Laboratory, Los Alamos, NM, United States of America

  http://orcid.org/0000-0002-2026-5757

  ⨯
• George M. Shaw,

  Roles Conceptualization, Writing – review & editing

  Affiliation Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America

  ⨯
• Nelson L. Michael,

  Roles Conceptualization, Funding acquisition, Supervision, Writing – review & editing

  Affiliation U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America

  http://orcid.org/0000-0001-5882-5548

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• Merlin L. Robb,

  Roles Conceptualization, Funding acquisition, Project administration, Resources, Writing – original draft

  Affiliations U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America, Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America

  http://orcid.org/0000-0003-3949-9649

  ⨯
• Sodsai Tovanabutra,

  Roles Conceptualization, Formal analysis, Methodology, Supervision, Writing – original draft

  Affiliations U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America, Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America

  http://orcid.org/0000-0002-5946-4227

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•  [ ... ],
• Jerome H. Kim

  Roles Conceptualization, Funding acquisition, Supervision, Writing – original draft

  Current address: International Vaccine Institute, Seoul, South Korea

  Affiliation U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America

  http://orcid.org/0000-0003-0461-6438

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