The 2009 H1N1 influenza pandemic showed the speed with which a novel respiratory virus can spread and the ability of a generally mild infection to induce severe morbidity and mortality in a subset of the population. Recent in vitro studies show that the interferon-inducible transmembrane (IFITM) protein family members potently restrict the replication of multiple pathogenic viruses. Both the magnitude and breadth of the IFITM proteins' in vitro effects suggest that they are critical for intrinsic resistance to such viruses, including influenza viruses. Using a knockout mouse model, we now test this hypothesis directly and find that IFITM3 is essential for defending the host against influenza A virus in vivo. Mice lacking Ifitm3 display fulminant viral pneumonia when challenged with a normally low-pathogenicity influenza virus, mirroring the destruction inflicted by the highly pathogenic 1918 'Spanish' influenza. Similar increased viral replication is seen in vitro, with protection rescued by the re-introduction of Ifitm3. To test the role of IFITM3 in human influenza virus infection, we assessed the IFITM3 alleles of individuals hospitalized with seasonal or pandemic influenza H1N1/09 viruses. We find that a statistically significant number of hospitalized subjects show enrichment for a minor IFITM3 allele (SNP rs12252-C) that alters a splice acceptor site, and functional assays show the minor CC genotype IFITM3 has reduced influenza virus restriction in vitro. Together these data reveal that the action of a single intrinsic immune effector, IFITM3, profoundly alters the course of influenza virus infection in mouse and humans.
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Acknowledgements We would like to thank C. Brandt for maintaining mouse colony health and well-being and T. Hussell for provision of A/X-31 virus. We also thank D. Gurdasani and M. Sandhu for statistical analysis of genotype frequencies. We also thank M. Hu and I. Gallego Romero for calculating genome-wide selection statistics. This work was supported by the Wellcome Trust. The MOSAIC work was supported by Imperial’s Comprehensive Biomedical Research Centre (cBRC), the Wellcome Trust (090382/Z/09/Z) and Medical Research Council UK. The GenISIS work was supported by the Chief Scientist Office (Scotland). A.L.B. is the recipient of a Charles H. Hood Foundation Child Health Research Award, and is supported by grants from the Phillip T. and Susan M. Ragon Institute Foundation, the Bill and Melinda Gates Foundation’s Global Health Program and the National Institute of Allergy and Infectious Diseases (R01AI091786). J.K.B. is supported by a Wellcome Trust Clinical Lectureship (090385/Z/09/Z) through the Edinburgh Clinical Academic Track (ECAT). We acknowledge the assistance of K. Alshafi, E. Bailey, A. Bermingham, M. Berry, C. Bloom, E. Brannigan, S. Bremang, J. Clark, M. C. Cox, M. Cross, L. A. Cumming, S. Dyas, J. England-Smith, J. Enstone, D. Ferreira, N. Goddard, A. Godlee, S. Gormley, M. Guiver, M. O. Hassan-Ibrahim, H. Hill, P. Holloway, K. Hoschler, G. Houghton, F. Hughes, R. R. Israel, A. Jepson, K. D. Jones, W. P. Kelleher, M. Kidd, K. Knox, A. Lackenby, G. Lloyd, H. Longworth, M. Minns, S. Mookerjee, S. Mt-Isa, D. Muir, A. Paras, V. Pascual, L. Rae, S. Rodenhurst, F. Rozakeas, E. Scott, E. Sergi, N. Shah, V. Sutton, J. Vernazza, A. W. Walker, C. Wenden, T. Wotherspoon, A. D. Wright, F. Wurie and the clinical and laboratory staff of the Alder Hey Children’s NHS Foundation Trust, Brighton & Sussex University Hospitals NHS Trust, Central Manchester University Hospitals NHS Foundation Trust, Chelsea and Westminster Hospital NHS Foundation Trust, Alder Hey Children’s Hospital and Liverpool School of Tropical Medicine, Health Protection Agency Microbiology Services Colindale, Imperial College Healthcare NHS Trust, Liverpool Women’s NHS Foundation Trust, Royal Liverpool and Broadgreen University Hospitals NHS Trust, Royal Brompton and Harefield NHS Foundation Trust, The Roslin Institute, Edinburgh, University Hospitals Coventry and Warwickshire NHS Trust. The MOSAIC consortium was supported by several Comprehensive Local Research Networks (CLRNs), the National Institute for Health Research (NIHR), UK, and by the Biomedical Research Centre (BRC) and Unit (BRU) funds. Finally, we thank all patients and their relatives for their generous agreement to inclusion in this study.