Using viral diversity to identify HIV-1 variants under HLA-dependent selection in a systematic viral genome-wide screen

• Nadia Neuner-Jehle ,

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

  * E-mail: nadia.neuner-jehle@bluewin.ch (NNJ), roger.kouyos@uzh.ch (RDK)

  Affiliations Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland, Institute of Medical Virology, University of Zurich, Zurich, Switzerland

  https://orcid.org/0009-0001-6829-6448

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• Marius Zeeb,

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

  Affiliations Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland, Institute of Medical Virology, University of Zurich, Zurich, Switzerland

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• Christian W. Thorball,

  Roles Formal analysis, Resources, Writing – review & editing

  Affiliation Precision Medicine Unit, Biomedical Data Science Center, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland

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• Jacques Fellay,

  Roles Resources, Writing – review & editing

  Affiliations Precision Medicine Unit, Biomedical Data Science Center, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland, Swiss Institute of Bioinformatics, Lausanne, Switzerland

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• Karin J. Metzner,

  Roles Resources, Writing – review & editing

  Affiliations Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland, Institute of Medical Virology, University of Zurich, Zurich, Switzerland

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• Paul Frischknecht,

  Roles Formal analysis, Resources, Writing – review & editing

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

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• Kathrin Neumann,

  Roles Resources, Writing – review & editing

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

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• Christine Leeman,

  Roles Resources, Writing – review & editing

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

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• Andri Rauch,

  Roles Resources, Writing – review & editing

  Affiliation Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland

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• Marcel Stöckle,

  Roles Resources, Writing – review & editing

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

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• Michael Huber,

  Roles Resources, Writing – review & editing

  Affiliation Institute of Medical Virology, University of Zurich, Zurich, Switzerland

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• Matthieu Perreau,

  Roles Resources, Writing – review & editing

  Affiliation Divisions of Immunology and Allergy, Lausanne University Hospital, Lausanne, Switzerland

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• Enos Bernasconi,

  Roles Resources, Writing – review & editing

  Affiliation Division of Infectious Diseases, Ente Ospedaliero Cantonale, Lugano, University of Geneva and University of Southern Switzerland, Lugano, Switzerland

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• Julia Notter,

  Roles Resources, Writing – review & editing

  Affiliation Division of Infectious Diseases, Infection Prevention and Travel Medicine, Cantonal Hospital St. Gallen, St. Gallen, Switzerland

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• Matthias Hoffmann,

  Roles Resources, Writing – review & editing

  Affiliation Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital Olten, Olten, Switzerland

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• Karoline Leuzinger,

  Roles Resources, Writing – review & editing

  Affiliation Clinical Virology, University Hospital Basel, Basel, Switzerland

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• Huldrych F. Günthard,

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

  Affiliations Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland, Institute of Medical Virology, University of Zurich, Zurich, Switzerland

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• Chloé Pasin ,

  Contributed equally to this work with: Chloé Pasin, Roger D. Kouyos

  Roles Conceptualization, Formal analysis, Funding acquisition, Supervision, Writing – original draft, Writing – review & editing

  Affiliations Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland, Institute of Medical Virology, University of Zurich, Zurich, Switzerland, Collegium Helveticum, Zurich, Switzerland

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• Roger D. Kouyos ,

  Contributed equally to this work with: Chloé Pasin, Roger D. Kouyos

  Roles Conceptualization, Formal analysis, Funding acquisition, Supervision, Writing – original draft, Writing – review & editing

  Affiliations Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland, Institute of Medical Virology, University of Zurich, Zurich, Switzerland

  https://orcid.org/0000-0002-9220-8348

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•  [ ... ],
• the Swiss HIV Cohort Study (SHCS)

  ¶Membership of Swiss HIV Cohort Study (SHCS) is provided in Supporting Information file S1 Acknowledgments.

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