School of Biomedical Engineering and Imaging Sciences, King’s College London, London, UK
Kerstin Kläser, Erika Molteni, Mark Graham, Liane S. Canas, Michela Antonelli, Liyuan Chen, Jie Deng, Benjamin Murray, Eric Kerfoot, Marc Modat, Alexander Hammers, Carole H. Sudre & Sebastien Ourselin
Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, Faculty of Life Sciences and Medicine, King’s College London, St Thomas’ Hospital Campus, 3rd Floor South Wing Block D, Westminster Bridge Road, London, SE1 7EH, UK
Marc F. Österdahl, Tim D. Spector, Claire J. Steves & Emma L. Duncan
Department of Aging and Health, Guy’s and St Thomas’ NHS Foundation Trust, London, UK
Marc F. Österdahl & Claire J. Steves
ZOE Limited, London, UK
Jonathan Wolf, Anna May, Ben Fox & Joan Capdevila
King’s College London & Guy’s and St Thomas’ PET Centre, London, UK
Alexander Hammers
MRC Unit for Lifelong Health and Ageing, Department of Population Health Sciences, University College London, London, UK
Carole H. Sudre
Centre for Medical Image Computing, Department of Computer Science, University College London, London, UK
Carole H. Sudre
Department of Endocrinology, Guy’s and St Thomas’ NHS Foundation Trust, London, UK
Emma L. Duncan
Centre for Genomic Pathogen Surveillance, University of Oxford, Oxford, UK
David M. Aanensen, Khalil Abudahab, Mirko Menegazzo, Ben E. W. Taylor, Anthony P. Underwood & Corin A. Yeats
Betsi Cadwaladr University Health Board, Bangor, UK
Helen Adams
Public Health Wales, Cardiff, UK
Alexander Adams, Tara Annett, Hibo Asad, Alec Birchley, Matthew Bull, Jason Coombes, Sally Corden, Simon Cottrell, Noel Craine, Alisha Davies, Elen De Lacy, Fatima Downing, Sue Edwards, Johnathan M. Evans, Laia Fina, Amy Gaskin, Bree Gatica-Wilcox, Laura Gifford, Lauren Gilbert, Lee Graham, Jessica Hey, David Heyburn, Ember Hilvers, Sophie Jones, Hannah Jones, Sara Kumziene-Summerhayes, Caoimhe McKerr, Catherine Moore, Mari Morgan, Nicole Pacchiarini, Malorie Perry, Jessica Powell, Georgia Pugh, Sara Rey, Sarah Taylor, Joanne Watkins, Chris Williams & Catryn Williams
Cardiff and Vale University Health Board, Cardiff, UK
Safiah Afifi, Robert Beer, Michaela John, Joshua Maksimovic, Kathryn McCluggage, Sian Morgan & Karla Spellman
Department of Medicine, University of Cambridge, Cambridge, UK
Dinesh Aggarwal, Beth Blane, Ellena Brooks, Alessandro M. Carabelli, Carol M. Churcher, MacGregor Cox, Theresa Feltwell, Mireille Fragakis, Katerina Galai, Andrew Jermy, Sarah Judges, Catherine Ludden, Patrick Maxwell, Georgina M. McManus, Sharon J. Peacock, Ken Smith, Kim S. Smith & Elaine Westwick
Manchester University NHS Foundation Trust, Manchester, UK
Shazaad S. Y. Ahmad, Ryan P. George & Nicholas W. Machin
Wellcome Sanger Institute, Manchester, UK
Louise Aigrain, Roberto Amato, Cristina V. Ariani, Jeffrey C. Barrett, Andrew R. Bassett, Charlotte Beaver, Katherine L. Bellis, Emma Betteridge, James Bonfield, Iraad F. Bronner, Robert M. Davies, Matthew J. Dorman, Jillian Durham, Ben W. Farr, Luke Foulser, Sónia Gonçalves, Scott Goodwin, Marina Gourtovaia, Ewan M. Harrison, David K. Jackson, Keith James, Ian Johnston, Sally Kay, Jon-Paul Keatley, Dominic Kwiatkowski, Cordelia F. Langford, Stefanie V. Lensing, Steven Leonard, Kevin Lewis, Jennifier Liddle, Rich Livett, Stephanie Lo, Inigo Martincorena, Shane A. McCarthy, Robin J. Moll, Karen Oliver, Naomi R. Park, Liam Prestwood, Michael A. Quail, Diana Rajan, Shavanthi Rajatileka, Nicholas M. Redshaw, Theo Sanderson, Carol Scott, Lesley Shirley, John Sillitoe, Michael H. Spencer Chapman, Scott A. J. Thurston, Gerry Tonkin-Hill, Jaime M. Tovar-Corona, Danni Weldon & Andrew Whitwham
Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
Adela Alcolea-Medina, Natasha Ohemeng-Kumi, John Ramble, Jasveen Sehmi & Perminder Smith
Quadram Institute Bioscience, Norwich, UK
Nabil-Fareed Alikhan, Alp Aydin, David J. Baker, Leonardo de Oliveira Martins, Ebenezer Foster-Nyarko, Gemma L. Kay, Thanh Le-Viet, Alison E. Mather, Lizzie Meadows, Justin O’Grady, Andrew J. Page, Sophie J. Prosolek, Steven Rudder & Alexander J. Trotter
Public Health England, London, UK
Elias Allara, Andrew Bosworth, Richard Hopes, Stephanie Hutchings, Peter Muir, Husam Osman, Clare Pearson, Hannah M. Pymont, Esther Robinson & Barry B. Vipond
University of Sheffield, Sheffield, UK
Adrienn Angyal, Thushan I. de Silva, Benjamin H. Foulkes, Timothy M. Freeman, Marta Gallis, Luke R. Green, Samantha E. Hansford, Hailey R. Hornsby, Sharon N. Hsu, Alexander J. Keeley, Benjamin B. Lindsey, Stavroula F. Louka, Matthew D. Parker, Manoj Pohare, Nikki Smith, Dennis Wang, Max Whiteley, Paige Wolverson & Peijun Zhang
University Hospital Southampton NHS Foundation Trust, Southampton, UK
Stephen Aplin, Matthew Harvey, Sarah Jeremiah, Adhyana I. K. Mahanama, Emanuela Pelosi, Jacqui A. Prieto, Kordo Saeed, Buddhini Samaraweera, Thea Sass, Siona Silviera, Helen Umpleby, Helen Wheeler & Eleri Wilson-Davies
Barking, Havering and Redbridge University Hospitals NHS Trust, Romford, UK
Amy Ash & Cherian Koshy
The Royal Wolverhampton NHS Trust, Wolverhampton, UK
Paula Ashfield & Donald Dobie
Turnkey Laboratory, University of Birmingham, Birmingham, UK
Fiona Ashford, Angus Best, Liam Crawford, Nicola Cumley, Megan Mayhew, Oliver Megram, Jeremy Mirza, Emma Moles-Garcia & Benita Percival
Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
Laura Atkinson, Julianne R. Brown, Kathryn A. Harris, Jack C. D. Lee, Divya Shah & Nathaniel Storey
Department of Zoology, University of Oxford, Oxford, UK
Stephen W. Attwood, Louis du Plessis, Marina Escalera Zamudio, Sarah Francois, Bernardo Gutierrez, Moritz U. G. Kraemer, Oliver G. Pybus, Jayna Raghwani, Tetyana I. Vasylyeva & Alex E. Zarebski
Royal Devon and Exeter NHS Foundation Trust, Wonford, UK
Cressida Auckland, Christopher R. Jones, Bridget A. Knight, Helen Morcrette & Jennifer Poyner
South Tees Hospitals NHS Foundation Trust, Middlesbrough, UK
Paul Baker, Stephen Bonner, Sarah Essex, Steven Liggett, Craig Mower, Leanne J. Murray & Louisa K. Watson
University of Edinburgh, Edinburgh, UK
Carlos E. Balcazar, Rachel Colquhoun, Michael D. Gallagher, Verity Hill, Ben Jackson, Daniel Maloney, J. T. McCrone, Nathan Medd, Áine O’Toole, Andrew Rambaut, Emily Scher, Thomas D. Stanton, Thomas Williams & Kathleen A. Williamson
Virology, School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, UK
Jonathan Ball, Timothy Byaruhanga, Joseph G. Chappell, Jayasree Dey, Jack D. Hill, Patrick C. McClure & Emily J. Park
Bournemouth University, Poole, UK
Magdalena Barrow, Sarah L. Buchan & Anna Mantzouratou
North Cumbria Integrated Care NHS Foundation Trust, Cumbria, UK
Edward Barton, Clive Graham, Debra Padgett & Garren Scott
Hub for Biotechnology in the Built Environment, Northumbria University, Newcastle upon Tyne, UK
Matthew Bashton, Darren L. Smith & Gregory R. Young
Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, UK
Rahul Batra, Themoula Charalampous, Jonathan Edgeworth, Gaia Nebbia, Amita Patel, Bindi Patel & Luke B. Snell
Queen’s University Belfast, Belfast, UK
Chris Baxter, Stephen Bridgett, Sílvia F. Carvalho, Marc Fuchs, Deborah Lavin, Arun Mariappan, Julia Miskelly, Zoltan Molnar, Clara Radulescu, Fiona Rogan, David A. Simpson, Aditi Singh, Timofey Skvortsov & Miao Tang
University College London Hospitals NHS Foundation Trust, London, UK
Nadua Bayzid, Judith Breuer, Marius Cotic, Megan Driscoll, Leah Ensell, John A. Hartley, Catherine Houlihan, Helen L. Lowe, Laurentiu Maftei, Matteo Mondani, Eleni Nastouli, Sunando Roy, Charlotte A. Williams & Rachel J. Williams
Centre for Enzyme Innovation, University of Portsmouth, Portsmouth, UK
Angela H. Beckett, Samuel C. Robson & Ekaterina Shelest
Blackpool Teaching Hospitals NHS Foundation Trust, Blackpool, UK
Shaun M. Beckwith, Abigail Murray & Dawn Singleton
East Suffolk and North Essex NHS Foundation Trust, Colchester, UK
Luke Bedford
University of Birmingham, Birmingham, UK
Andrew Beggs & Alex Richter
Clinical Microbiology Department, Queens Medical Centre, Nottingham University Hospitals NHS Trust, Nottingham, UK
Louise Berry, Tim Boswell, Gemma Clark, Vicki M. Fleming, Hannah C. Howson-Wells, Amelia Joseph, Manjinder Khakh & Michelle M. Lister
Hampshire Hospitals NHS Foundation Trust, Basingstoke, UK
Beatrice Bertolusso, Nicholas Cortes, Stephen P. Kidd, Jessica Lynch, Nathan Moore, Claire Thomas, Gabrielle Vernet & Rebecca Williams
Public Health England, Colindale, UK
David Bibby, Chloe Bishop, Vicki Chalker, Meera Chand, Gavin Dabrera, Nicholas Ellaby, Eileen Gallagher, Ian Harrison, Jonathan Hubb, Angie Lackenby, David Lee, Nikos Manesis, Tamyo Mbisa, Richard Myers, Steven Platt, Alicia Thornton & Katherine A. Twohig
Portsmouth Hospitals University NHS Trust, Portsmouth, UK
Kelly Bicknell, Scott Elliott, Sharon Glaysher, Robert Impey & Sarah Wyllie
Microbiology Department, Buckinghamshire Healthcare NHS Trust, Amersham, UK
Debbie Binns, Victoria James, David T. Pritchard & Nick Wong
Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester, UK
Paul W. Bird, Karlie Fallon, Thomas Helmer, Christopher W. Holmes, Claire L. McMurray, Mina Odedra, Jessica Shaw, Julian W. Tang & Nicholas J. Willford
NHS Greater Glasgow and Clyde, Glasgow, UK
Rachel Blacow, Rory N. Gunson & Jon Perkins
County Durham and Darlington NHS Foundation Trust, Darlington, UK
Victoria Blakey, Sharon Campbell, Veena Raviprakash, Nicola Sheriff & Lesley-Anne Williams
Imperial College Healthcare NHS Trust, London, UK
Frances Bolt, Alison Cox, Alison H. Holmes, Pinglawathee Madona, Siddharth Mookerjee, Marcus Pond, James R. Price & Paul A. Randell
Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
David Bonsall, Christophe Fraser, Helen Fryer, Tanya Golubchik, Katrina Lythgoe & Laura Thomson
School of Biological Sciences, University of Portsmouth, Portsmouth, UK
Yann Bourgeois
Imperial College London, London, UK
Olivia Boyd, Lily Geidelberg, Rob Johnson, Manon Ragonnet-Cronin & Erik M. Volz
Public Health Agency, Northern Ireland, Belfast, UK
Declan T. Bradley & Tim Wyatt
Liverpool Clinical Laboratories, Liverpool, UK
Cassie Breen
Cardiff University, Cardiff, UK
Catherine Bresner, Thomas R. Connor, William Fuller, Martyn Guest, Owen Jones, Christine Kitchen, Andrew Mack, Angela Marchbank, Ian Merrick, Arthur Morriss, Robert Munn, Anna Price, Joel Southgate, Thomas Whalley & Trudy Workman
MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
Alice Broos, Ana da Silva Filipe, William T. Harvey, Joseph Hughes, Daniel Mair, Afrida Mukaddas, Jenna Nichols, Kyriaki Nomikou, Richard J. Orton, David L. Robertson, James G. Shepherd, Igor Starinskij, Emma C. Thomson, Lily Tong, Ioulia Tsatsani, Sreenu Vattipally & Derek W. Wright
University of Brighton, Brighton, UK
Giselda Bucca, Andrew R. Hesketh & Colin P. Smith
Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
David Buck, Angie Green, George MacIntyre-Cockett, John A. Todd & Amy Trebes
Hull University Teaching Hospitals NHS Trust, Hull, UK
Phillipa J. Burns, Kirstine Eastick, William Everson, Kavitha Gajee, Katie Kitchman & Patrick J. Lillie
The Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
Shirelle Burton-Fanning, Jennifer Collins, Gary Eltringham, Brendan A. I. Payne, Yusri Taha & Sheila Waugh
University College London Hospital Advanced Pathogen Diagnostics Unit, London, UK
Matthew Byott & Judith Heaney
East Sussex Healthcare NHS Trust, Seaford, UK
James S. Cargill & Warwick Hughes
Deep Seq, School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, UK
Matthew Carlile, Johnny Debebe, Nadine Holmes, Matthew W. Loose, Christopher Moore, Fei Sang & Victoria Wright
Queen Elizabeth Hospital, Birmingham, Birmingham, UK
Anna Casey & Liz Ratcliffe
Isle of Wight NHS Trust, Newport, UK
Anibolina Castigador & Emily Macnaughton
Whittington Health NHS Trust, London, UK
Jana Catalan & Neil Jones
University Hospitals Sussex NHS Foundation Trust, Southampton, UK
Nicola J. Chaloner, Benjamin J. Cogger, Lisa J. Easton, Michelle J. Erkiert, Mohammed O. Hassan-Ibrahim, Hannah Huckson, Jonathan Lewis, Sarah Lowdon, Cassandra S. Malone, Florence Munemo, Manasa Mutingwende, Roberto Nicodemi, Olga Podplomyk, Paul Randell & Thomas Somassa
Health Services Laboratories, London, UK
Wendy Chatterton, Paul R. Grant, Stuart Kirk, Lisa J. Levett & Monika Pusok
Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
Yasmin Chaudhry, Iliana Georgana, Ian G. Goodfellow, Myra Hosmillo, Rhys Izuagbe, Aminu S. Jahun & Malte L. Pinckert
Path Links, Northern Lincolnshire and Goole NHS Foundation Trust, London, UK
Phillip Clarke, Nichola Duckworth, Tim J. Sloan & Sarah Walsh
Northumbria Healthcare NHS Foundation Trust, Newcastle upon Tyne, UK
Kevin Cole & Giles Idle
School of Pharmacy & Biomedical Sciences, University of Portsmouth, Portsmouth, UK
Kate F. Cook, Christopher Fearn, Salman Goudarzi & Katie F. Loveson
University of Cambridge, Cambridge, UK
Claire Cormie, Joana Dias, Sally Forrest, Sophia T. Girgis, Ravi K. Gupta, Ellen E. Higginson, Leanne M. Kermack, Mailis Maes, Chris Ruis & Jamie Young
NHS Lothian, Edinburgh, UK
Seb Cotton, Rebecca Dewar, Abbie Gallagher, Martin P. McHugh, Kate E. Templeton & Elizabeth Wastnedge
Norfolk and Norwich University Hospitals NHS Foundation Trust, Norwich, UK
Lindsay Coupland, Samir Dervisevic & Rachael Stanley
North Middlesex University Hospital NHS Trust, London, UK
Aidan Cross & Mariyam Mirfenderesky
Northumbria University, Newcastle upon Tyne, UK
Matthew R. Crown, John H. Henderson, Amy Hollis, Clare M. McCann, Andrew Nelson, William Stanley & Wen C. Yew
University Hospitals Dorset NHS Foundation Trust, London, UK
Dorian Crudgington, Ben Macklin & Liz A. Sheridan
Belfast Health & Social Care Trust, Belfast, UK
Tanya Curran, Derek J. Fairley & James P. McKenna
Public Health England, Cambridge, Cambridge, UK
Martin D. Curran & Surendra Parmar
University of Liverpool, Liverpool, UK
Alistair C. Darby, Richard Eccles, Matthew Gemmell, Richard Gregory, Sam T. Haldenby, Margaret Hughes, Miren Iturriza-Gomara, Kathryn A. Jackson, Anita O. Lucaci, Charlotte Nelson, Steve Paterson, Lucille Rainbow, Lance Turtle, Edith E. Vamos, Hermione J. Webster, Mark Whitehead & Claudia Wierzbicki
University of East Anglia, Norwich, UK
Rose K. Davidson
Department of Microbiology, Kettering General Hospital, Kettering, UK
Thomas Davis, Sahar Eldirdiri & Anita Kenyon
MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
Daniela de Angelis, Chris J. Illingworth, Chris Jackson & David Pascall
North Tees and Hartlepool NHS Foundation Trust, Durham, UK
Rebecca Denton-Smith, Jane Greenaway, Emma Swindells & Robyn Turnbull
King’s College Hospital NHS Foundation Trust, London, UK
Kate El Bouzidi, Temi Lampejo & Malur Sudhanva
Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
Cariad Evans, Kate Johnson, David G. Partridge, Mohammad Raza & Mehmet Yavus
Watford General Hospital, Watford, UK
Arezou Fanaie, Rachel A. Hilson & Geraldine Yaze
West of Scotland Specialist Virology Centre, NHS Greater Glasgow and Clyde, Glasgow, UK
Lynne Ferguson, Emily J. Goldstein, Alasdair Maclean & Rachael Tomb
Guy’s and St. Thomas’ Biomedical Research Centre, London, UK
Flavia Flaviani
Division of Infection and Immunity, University College London, London, UK
Dan Frampton
The Royal Marsden NHS Foundation Trust, London, UK
Andrea N. Gomes, Maimuna Kimuli & Darren R. Murray
Department of Infectious Diseases and Microbiology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
William L. Hamilton & M. Estee Torok
Royal Free London NHS Foundation Trust, London, UK
Tanzina Haque, Jennifer Hart, Dianne Irish-Tavares, Tabitha W. Mahungu & Eric Witele
Public Health Scotland, London, UK
Matthew T. G. Holden, Stefan Rooke, Sharif Shaaban & Gonzalo Yebra
University of Exeter, Exeter, UK
Leigh M. Jackson, Aaron R. Jeffries, Robin Manley, Stephen L. Michell, Michelle L. Michelsen, Christine M. Sambles, David J. Studholme, Ben Temperton & Joanna Warwick-Dugdale
The Queen Elizabeth Hospital King’s Lynn NHS Foundation Trust, King’s Lynn, UK
Christopher Jeanes
Institute for Infection and Immunity, St George’s University of London, London, UK
Kenneth G. Laing, Irene M. Monahan & Adam A. Witney
Southwest Pathology Services, Taunton, UK
Andrew I. Lawton
Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
Nicholas J. Loman, Claire McMurray, Alan McNally, Sam Nicholls, Radoslaw Poplawski, Joshua Quick, Will Rowe & Joanne Stockton
East Kent Hospitals University NHS Foundation Trust, London, UK
Hannah Lowe, Samuel Moses & Felicity Ryan
Swansea University, Swansea, UK
Ronan A. Lyons
King’s College London, London, UK
Rocio T. Martinez Nunez
Gateshead Health NHS Foundation Trust, Gateshead, UK
Jonathan Moore & Susanne Stonehouse
University of Southampton, Southampton, UK
Matilde Mori
Newcastle University, Newcastle upon Tyne, UK
Sarah O’Brien, Steven Rushton & Roy Sanderson
Infection Care Group, St George’s University Hospitals NHS Foundation Trust, London, UK
Cassie F. Pope
Royal Brompton and Harefield Hospitals, Harefield, UK
Newara A. Ramadan
Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
Nicola Reynolds
Maidstone and Tunbridge Wells NHS Trust, Royal Tunbridge Wells, UK
Graciela Sluga & Karen T. Withell
Norfolk County Council, Norfolk, UK
Louise Smith & Lewis G. Spurgin
Institute of Biodiversity, Animal Health & Comparative Medicine, Glasgow, UK
Katherine L. Smollett
Great Ormond Street Institute of Child Health (GOS ICH), University College London (UCL), London, UK
Moira J. Spyer
Department of Microbiology, South West London Pathology, London, UK
Ngee Keong Tan & Joshua F. Taylor
Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
Ben Warne
Microbiology, Royal Oldham Hospital, Oldham, UK
Cheryl Williams
Heartlands Hospital, Birmingham, Birmingham, UK
Li Xu-McCrae
K.K., C.H.S., M.S.G., S.O., T.D.S., C.J.S., and E.L.D. contributed to study concept and design. C.H.S., A.M., B.M., J.C., The COG-UK Consortium, JW, TDS, CJS, and SO contributed to acquisition of data. K.K., C.H.S., M.S.G., A.M. and E.L.D. contributed to data analysis and verified the underlying data. K.K., E.M., M.S.G., CHS and E.L.D. contributed to initial drafting of the manuscript. All authors contributed to interpretation of data and critical revision of the manuscript. C.J.S., T.D.S., S.O. and E.L.D. contributed to study supervision. All authors had full access to all the data in the study and had final responsibility for the decision to submit for publication.
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