A de novo approach to inferring within-host fitness effects during untreated HIV-1 infection

• Christopher J. R. Illingworth ,

  Roles Conceptualization, Formal analysis, Funding acquisition, Investigation, Methodology, Project administration, Resources, Software, Validation, Visualization, Writing – original draft, Writing – review & editing

  * E-mail: chris.illingworth@gen.cam.ac.uk (CJRI); katrina.lythgoe@bdi.ox.ac.uk (KAL)

  Affiliations Department of Genetics, University of Cambridge, Cambridge, United Kingdom, Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, United Kingdom, School of Chemical and Biological Sciences, Queen Mary University of London, London, United Kingdom

  http://orcid.org/0000-0002-0030-2784

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• Jayna Raghwani,

  Roles Investigation, Methodology, Writing – review & editing

  Affiliations Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom, Department of Zoology, Peter Medawar Building, University of Oxford, Oxford, United Kingdom

  http://orcid.org/0000-0001-8538-4995

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• David Serwadda,

  Roles Funding acquisition, Supervision

  Affiliation Rakai Health Sciences Program, Kalisizo, Uganda, School of Public Health, Makerere University, Kampala, Uganda

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• Nelson K. Sewankambo,

  Roles Funding acquisition, Supervision

  Affiliations Rakai Health Sciences Program, Kalisizo, Uganda, School of Public Health, Makerere University, Kampala, Uganda, School of Medicine, Makerere University, College of Health Sciences, Kampala, Uganda

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• Merlin L. Robb,

  Roles Funding acquisition, Supervision

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

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• Michael A. Eller,

  Roles Project administration

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

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

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• Andrew R. Redd,

  Roles Investigation, Methodology, Writing – review & editing

  Affiliations Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America, Department of Medicine, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America

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• Thomas C. Quinn,

  Roles Funding acquisition, Methodology, Resources, Writing – review & editing

  Affiliations Department of Medicine, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America, Laboratory of Immunoregulation, Division of Intramural Research, NIAID, NIH, Baltimore Maryland, United States of America

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• Katrina A. Lythgoe

  Roles Conceptualization, Formal analysis, Funding acquisition, Investigation, Methodology, Project administration, Supervision, Visualization, Writing – original draft, Writing – review & editing

  * E-mail: chris.illingworth@gen.cam.ac.uk (CJRI); katrina.lythgoe@bdi.ox.ac.uk (KAL)

  Affiliations Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom, Department of Zoology, Peter Medawar Building, University of Oxford, Oxford, United Kingdom

  http://orcid.org/0000-0002-7089-7680

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