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Open Access
Peer-reviewed
Research Article
Rare HIV-1 transmitted/founder lineages identified by deep viral sequencing contribute to rapid shifts in dominant quasispecies during acute and early infection
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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
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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
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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
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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
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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
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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
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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
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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
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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
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Hui Li,
Roles Investigation
Affiliation Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
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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
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Will Fischer,
Roles Methodology, Software, Writing – review & editing
Affiliation Theoretical Biology, Los Alamos National Laboratory, Los Alamos, NM, United States of America
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Feng Gao,
Roles Conceptualization
Affiliation Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, United States of America
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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
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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
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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
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Robert J. O’Connell,
Roles Resources, Supervision
Affiliation Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
⨯ - Samuel Sinei,
- Lucas Maganga,
- Hannah Kibuuka,
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Sorachai Nitayaphan,
Roles Resources
Affiliation Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
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Mangala Rao,
Roles Conceptualization
Affiliation U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
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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
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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
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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
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Bette T. Korber,
Roles Methodology, Software
Affiliation Theoretical Biology, Los Alamos National Laboratory, Los Alamos, NM, United States of America
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George M. Shaw,
Roles Conceptualization, Writing – review & editing
Affiliation Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
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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
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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
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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
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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
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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,
- Eric Sanders-Buell,
- Agnes-Laurence Chenine,
- Michael A. Eller,
- Nilu Goonetilleke,
- Rasmi Thomas,
- Sivan Leviyang,
- Elizabeth A. Harbolick,
- Meera Bose,
- Phuc Pham
![PLOS](/resource/img/logo-plos.png)
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- Published: July 31, 2017
- https://doi.org/10.1371/journal.ppat.1006510