Long-term adaptation following influenza A virus host shifts results in increased within-host viral fitness due to higher replication rates, broader dissemination within the respiratory epithelium and reduced tissue damage

• Julien A. R. Amat,

  Roles Formal analysis, Funding acquisition, Investigation, Visualization, Writing – original draft

  Affiliations MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom, School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom

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• Veronica Patton,

  Roles Investigation, Writing – review & editing

  Affiliation School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom

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• Caroline Chauché,

  Roles Investigation, Writing – review & editing

  Affiliations MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom, Centre for Inflammation Research, University of Edinburgh, The Queen’s Medical Research Institute, Edinburgh, Scotland, United Kingdom

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• Daniel Goldfarb,

  Roles Methodology, Writing – review & editing

  Affiliation MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom

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• Joanna Crispell,

  Roles Investigation, Writing – review & editing

  Affiliation MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom

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• Quan Gu,

  Roles Data curation, Writing – review & editing

  Affiliation MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom

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• Alice M. Coburn,

  Roles Investigation, Writing – review & editing

  Affiliation MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom

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• Gaelle Gonzalez,

  Roles Investigation, Writing – review & editing

  Affiliations MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom, Ecole Nationale Vétérinaire d’Alfort, Université Paris-Est, Maisons-Alfort, France

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• Daniel Mair,

  Roles Investigation, Writing – review & editing

  Affiliation MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom

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• Lily Tong,

  Roles Investigation, Writing – review & editing

  Affiliation MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom

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• Luis Martinez-Sobrido,

  Roles Conceptualization, Writing – review & editing

  Affiliation Texas Biomedical Research Institute, San Antonio, Texas, United States of America

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• John F. Marshall,

  Roles Investigation, Writing – review & editing

  Affiliation School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom

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• Francesco Marchesi,

  Roles Supervision, Writing – review & editing

  Affiliation School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom

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• Pablo R. Murcia

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

  * E-mail: Pablo.Murcia@Glasgow.ac.uk

  Affiliation MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom

  https://orcid.org/0000-0002-4352-394X

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