A rapid agarose-free protocol for preparing human organotypic lung cultures to study respiratory virus infection and evaluate antivirals ex vivo

2026 · doi:10.64898/2026.02.12.705542
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Abstract

Summary We describe a standardized and reproducible procedure to generate human organotypic lung cultures from surgical lung resection for the study of respiratory infections. The protocol details tissue harvesting, biopsy punching, mechanical slicing, culture at the air–liquid interface. This technique enables robust ex vivo infections of human lung tissue with respiratory viruses, including Influenza A and Nipah. The described system can be used to study host-pathogen interactions, analyze innate immune responses, and evaluate antiviral candidates in physiologically relevant human lung tissue. For complete details on the use and execution of this protocol, please refer to Cezard et al 1 .
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New Results A rapid agarose-free protocol for preparing human organotypic lung cultures to study respiratory virus infection and evaluate antivirals ex vivo View ORCID ProfileLola Canus, View ORCID ProfileFlorentine Jacolin, Virginie Vasseur, View ORCID ProfileAdeline Cezard, View ORCID ProfileEva Ogire, View ORCID ProfileAnne Aublin-Gex, Amelie Bourgeais, Camille David, View ORCID ProfileAlexandra Erny, View ORCID ProfileFabienne Archer, Antoine Legras, Damien Sizaret, View ORCID ProfileAntoine Guillon, View ORCID ProfileVincent Lotteau, View ORCID ProfilePierre-Olivier Vidalain, View ORCID ProfileMustapha Si-Tahar, View ORCID ProfileLaure Perrin-Cocon, View ORCID ProfileCyrille Mathieu doi: https://doi.org/10.64898/2026.02.12.705542 Lola Canus 1CIRI, Centre International de Recherche en Infectiologie, Team NeuroInvasion, Tropism and Viral Encephalitis, Univ Lyon, Inserm, U1111, CNRS, UMR5308, Université Lyon 1, Ecole Normale Supérieure de Lyon, 69007, Lyon, France Florentine Jacolin 2CIRI, Centre International de Recherche en Infectiologie, Team Viral Infection, Metabolism and Immunity, Univ Lyon, Inserm, U1111, CNRS, UMR5308, Université Lyon 1, Ecole Normale Supérieure de Lyon, 69007, Lyon, France Virginie Vasseur 3Inserm, U1100, Centre d’Etude des Pathologies Respiratoires (CEPR), University of Tours, 37000 Tours, France Adeline Cezard 3Inserm, U1100, Centre d’Etude des Pathologies Respiratoires (CEPR), University of Tours, 37000 Tours, France Eva Ogire 1CIRI, Centre International de Recherche en Infectiologie, Team NeuroInvasion, Tropism and Viral Encephalitis, Univ Lyon, Inserm, U1111, CNRS, UMR5308, Université Lyon 1, Ecole Normale Supérieure de Lyon, 69007, Lyon, France Anne Aublin-Gex 2CIRI, Centre International de Recherche en Infectiologie, Team Viral Infection, Metabolism and Immunity, Univ Lyon, Inserm, U1111, CNRS, UMR5308, Université Lyon 1, Ecole Normale Supérieure de Lyon, 69007, Lyon, France Amelie Bourgeais 1CIRI, Centre International de Recherche en Infectiologie, Team NeuroInvasion, Tropism and Viral Encephalitis, Univ Lyon, Inserm, U1111, CNRS, UMR5308, Université Lyon 1, Ecole Normale Supérieure de Lyon, 69007, Lyon, France Camille David 3Inserm, U1100, Centre d’Etude des Pathologies Respiratoires (CEPR), University of Tours, 37000 Tours, France Alexandra Erny 4IVPC, Infections Virales et Pathologie Comparée, UMR754, INRAE, Université Lyon 1, EPHE, 69007, Lyon, France Fabienne Archer 4IVPC, Infections Virales et Pathologie Comparée, UMR754, INRAE, Université Lyon 1, EPHE, 69007, Lyon, France Antoine Legras 5Service de Chirurgie Thoracique, CHRU de Tours, Université de Tours, France Damien Sizaret 6Service de Pathologie, CHRU de Tours, France Antoine Guillon 3Inserm, U1100, Centre d’Etude des Pathologies Respiratoires (CEPR), University of Tours, 37000 Tours, France 7Service de Médecine Intensive –Réanimation, CHRU de Tours, France Vincent Lotteau 8Laboratoire P4 INSERM-Jean Mérieux, Lyon, France Pierre-Olivier Vidalain 2CIRI, Centre International de Recherche en Infectiologie, Team Viral Infection, Metabolism and Immunity, Univ Lyon, Inserm, U1111, CNRS, UMR5308, Université Lyon 1, Ecole Normale Supérieure de Lyon, 69007, Lyon, France Mustapha Si-Tahar 3Inserm, U1100, Centre d’Etude des Pathologies Respiratoires (CEPR), University of Tours, 37000 Tours, France Laure Perrin-Cocon 2CIRI, Centre International de Recherche en Infectiologie, Team Viral Infection, Metabolism and Immunity, Univ Lyon, Inserm, U1111, CNRS, UMR5308, Université Lyon 1, Ecole Normale Supérieure de Lyon, 69007, Lyon, France Cyrille Mathieu 1CIRI, Centre International de Recherche en Infectiologie, Team NeuroInvasion, Tropism and Viral Encephalitis, Univ Lyon, Inserm, U1111, CNRS, UMR5308, Université Lyon 1, Ecole Normale Supérieure de Lyon, 69007, Lyon, France Summary We describe a standardized and reproducible procedure to generate human organotypic lung cultures from surgical lung resection for the study of respiratory infections. The protocol details tissue harvesting, biopsy punching, mechanical slicing, culture at the air–liquid interface. This technique enables robust ex vivo infections of human lung tissue with respiratory viruses, including Influenza A and Nipah. The described system can be used to study host-pathogen interactions, analyze innate immune responses, and evaluate antiviral candidates in physiologically relevant human lung tissue. For complete details on the use and execution of this protocol, please refer to Cezard et al1. Competing Interest Statement The authors have declared no competing interest. Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Posted February 13, 2026. A rapid agarose-free protocol for preparing human organotypic lung cultures to study respiratory virus infection and evaluate antivirals ex vivo Lola Canus, Florentine Jacolin, Virginie Vasseur, Adeline Cezard, Eva Ogire, Anne Aublin-Gex, Amelie Bourgeais, Camille David, Alexandra Erny, Fabienne Archer, Antoine Legras, Damien Sizaret, Antoine Guillon, Vincent Lotteau, Pierre-Olivier Vidalain, Mustapha Si-Tahar, Laure Perrin-Cocon, Cyrille Mathieu bioRxiv 2026.02.12.705542; doi: https://doi.org/10.64898/2026.02.12.705542 A rapid agarose-free protocol for preparing human organotypic lung cultures to study respiratory virus infection and evaluate antivirals ex vivo Lola Canus, Florentine Jacolin, Virginie Vasseur, Adeline Cezard, Eva Ogire, Anne Aublin-Gex, Amelie Bourgeais, Camille David, Alexandra Erny, Fabienne Archer, Antoine Legras, Damien Sizaret, Antoine Guillon, Vincent Lotteau, Pierre-Olivier Vidalain, Mustapha Si-Tahar, Laure Perrin-Cocon, Cyrille Mathieu bioRxiv 2026.02.12.705542; doi: https://doi.org/10.64898/2026.02.12.705542 Subject Area Subject Areas - Biochemistry (17690) - Bioengineering (13892) - Bioinformatics (41936) - Biophysics (21451) - Cancer Biology (18588) - Cell Biology (25499) - Clinical Trials (138) - Developmental Biology (13378) - Ecology (19899) - Epidemiology (2067) - Evolutionary Biology (24320) - Genetics (15609) - Genomics (22506) - Immunology (17736) - Microbiology (40394) - Molecular Biology (17181) - Neuroscience (88603) - Paleontology (666) - Pathology (2832) - Pharmacology and Toxicology (4824) - Physiology (7641) - Plant Biology (15152) - Synthetic Biology (4294) - Systems Biology (9825) - Zoology (2271)

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