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These authors contributed equally: John T. McCrone, Verity Hill, Sumali Bajaj, Rosario Evans PenaThese authors jointly supervised this work: Oliver G. Pybus, Andrew Rambaut, Moritz U.G. KraemerA list of authors and their affiliations appears in the Supplementary InformationInstitute of Evolutionary Biology, University of Edinburgh, Edinburgh, UKJohn T. McCrone, Verity Hill, Ben Jackson, Rachel Colquhoun, Áine O’Toole & Andrew RambautDepartment of Zoology, University of Oxford, Oxford, UKSumali Bajaj, Rosario Evans Pena, Rhys Inward, Alexander E. Zarebski, Jayna Raghwani, Nuno R. Faria, Louis du Plessis, Oliver G. Pybus & Moritz U. G. KraemerDepartment of Computer Science, University of Oxford, Oxford, UKBen C. LambertMRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UKRhys Inward, Samir Bhatt, Erik Volz & Nuno R. FariaSection of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, DenmarkSamir BhattMolecular Immunity Unit, Department of Medicine, Cambridge University, Cambridge, UKChristopher RuisSpatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, BelgiumSimon DellicourDepartment of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, BelgiumSimon Dellicour & Guy BaeleGoogle, Mountain View, CA, USAAdam Sadilek, Neo Wu & Aaron SchneiderDepartment of Mathematics, School of Science & Engineering, Tulane University, New Orleans, LA, USAXiang JiDepartment of Infectious Disease, Imperial College London, London, UKThomas P. Peacock & Wendy S. BarclayUK Health Security Agency, London, UKThomas P. Peacock, Kate Twohig, Simon Thelwall, Gavin Dabrera, Richard Myers & Meera ChandInstituto de Medicina Tropical, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, BrazilNuno R. FariaBlueDot, Toronto, CanadaCarmen Huber & Kamran KhanDivisions of Internal Medicine & Infectious Diseases, Toronto General Hospital, University Health Network, Toronto, CanadaIsaac I. BogochDepartment of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, ON, CanadaIsaac I. Bogoch & Kamran KhanLi Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, ON, CanadaKamran KhanDepartment of Biosystems Science and Engineering, ETH Zurich, Zurich, SwitzerlandLouis du PlessisWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UKJeffrey C. Barrett & David M. AanensenBig Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UKDavid M. AanensenPathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UKThomas ConnorSchool of Biosciences, The Sir Martin Evans Building, Cardiff University, Cardiff, UKThomas ConnorQuadram Institute, Norwich, UKThomas ConnorInstitute of Microbiology and Infection, University of Birmingham, Birmingham, UKNicholas J. LomanDepartments of Biostatistics, Biomathematics and Human Genetics, University of California, Los Angeles, Los Angeles, CA, USAMarc A. SuchardDepartment of Pathobiology and Population Sciences, Royal Veterinary College London, London, UKOliver G. PybusPandemic Sciences Institute, University of Oxford, Oxford, UKOliver G. Pybus & Moritz U. G. Kraemer More