Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England (original) (raw)

Data availability

All data used in this study, including SGTF and genome counts aggregated by region and week and multiple sequence alignments, have been deposited in Zenodo at https://doi.org/10.5281/zenodo.4593885.

Code availability

The Zenodo repository https://doi.org/10.5281/zenodo.4593885 includes code to reproduce all figures and results presented here.

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Acknowledgements

We thank all partners and contributors to the COG-UK consortium who are listed at https://www.cogconsortium.uk/about/. We thank the Sanger Covid Team (https://www.sanger.ac.uk/covid-team) for data preparation and feedback on the manuscript. COG-UK is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) and Genome Research Limited, operating as the Wellcome Sanger Institute. N.M.F., E.V., M.R. and S.B. acknowledge support from the MRC Centre for Global Infectious Disease Analysis (MR/R015600/1). R.J. and E.V. acknowledge funding from the European Commission (CoroNAb 101003653). D.J.L. and N.M.F. were supported by the NIHR VEEPED (PR-OD-1017-20002). S.B. received support from the NIHR BRC Imperial College NHS Trust Infection and COVID themes. S.B and N.M.F were supported by the UK Research and Innovation Fund MR/V038109/1. S.B. is supported by the Academy of Medical Sciences Springboard Award SBF004/1080. S.B. is supported by the Novo Nordisk Foundation Young Investigator Award NNF20OC0059309. O.R. and S.B. were supported by the Bill & Melinda Gates Foundation (OPP1175094, OPP1084362). Computational resources were provided by Amazon AWS and Microsoft AI for Health.

Author information

Author notes

  1. These authors contributed equally: Erik Volz, Swapnil Mishra, Meera Chand, Jeffrey C. Barrett, Robert Johnson, Axel Gandy, Andrew Rambaut, Neil M. Ferguson

Authors and Affiliations

  1. MRC Centre for Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
    Erik Volz, Swapnil Mishra, Robert Johnson, Lily Geidelberg, Wes R. Hinsley, Daniel J. Laydon, Manon Ragonnet-Cronin, Olivia Boyd, David Jorgensen, Katy Gaythorpe, Samir Bhatt & Neil M. Ferguson
  2. Public Health England, London, UK
    Meera Chand, Gavin Dabrera, Ian Harrison, Nicholas J. Loman, Richard Myers, Natalie Groves, Elias Allara, Clare Pearson, Husam Osman, Andrew Bosworth, Esther Robinson, Peter Muir, Ian B. Vipond, Richard Hopes, Hannah M. Pymont, Stephanie Hutchings, Angie Lackenby, Tamyo Mbisa, Steven Platt, Shahjahan Miah, David Bibby, Carmen Manso, Jonathan Hubb, Mary Ramsay, Daniel Bradshaw, Alicia Thornton, Ulf Schaefer, Eileen Gallagher, David Lee, David Williams, Nicholas Ellaby, Hassan Hartman, Nikos Manesis, Vineet Patel, Chloe Bishop, Vicki Chalker, Juan Ledesma, Katherine A. Twohig & Susan Hopkins
  3. Wellcome Sanger Institute, Cambridge, UK
    Jeffrey C. Barrett, Robert Amato, Cristina V. Ariani, Sónia Gonçalves, David K. Jackson, John Sillitoe, Dominic P. Kwiatkowski, Alex Alderton, Roberto Amato, Mathew A. Beale, Charlotte Beaver, Katherine L. Bellis, Emma Betteridge, James Bonfield, John Danesh, Matthew J. Dorman, Eleanor Drury, Ben W. Farr, Luke Foulser, Sonia Goncalves, Scott Goodwin, Marina Gourtovaia, Ewan M. Harrison, Dorota Jamrozy, Ian Johnston, Leanne Kane, Sally Kay, Jon-Paul Keatley, Dominic Kwiatkowski, Cordelia F. Langford, Mara Lawniczak, Laura Letchford, Rich Livett, Stephanie Lo, Inigo Martincorena, Samantha McGuigan, Rachel Nelson, Steve Palmer, Naomi R. Park, Minal Patel, Liam Prestwood, Christoph Puethe, Michael A. Quail, Shavanthi Rajatileka, Carol Scott, Lesley Shirley, Michael H. Spencer Chapman, Scott A. J. Thurston, Gerry Tonkin-Hill, Danni Weldon, Diana Rajan, Iraad F. Bronner, Louise Aigrain, Nicholas M. Redshaw, Stefanie V. Lensing, Robert Davies, Andrew Whitwham, Jennifier Liddle, Kevin Lewis, Jaime M. Tovar-Corona, Steven Leonard, Jillian Durham, Andrew R. Bassett, Shane McCarthy, Robin J. Moll, Keith James, Karen Oliver, Alex Makunin & Jeff Barrett
  4. Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
    Áine O’Toole, Ben Jackson, John T. McCrone, Verity Hill & Andrew Rambaut
  5. Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
    Nicholas J. Loman, Nicholas J. Loman, Joshua Quick, Claire McMurray, Joanne Stockton, Sam Nicholls, Will Rowe, Radoslaw Poplawski & Alan McNally
  6. Department of Mathematics, Imperial College London, London, UK
    Seth Flaxman, Oliver Ratmann & Axel Gandy
  7. Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
    Samir Bhatt
  8. Barking, Havering and Redbridge University Hospitals NHS Trust, Barking, UK
    Cherian Koshy & Amy Ash
  9. Basingstoke Hospital, Basingstoke, UK
    Emma Wise, Nathan Moore, Matilde Mori, Nick Cortes, Jessica Lynch & Stephen Kidd
  10. Belfast Health and Social Care Trust, Belfast, UK
    Derek J. Fairley, Tanya Curran & James P. McKenna
  11. Betsi Cadwaladr University Health Board, Betsi Cadwaladr, UK
    Helen Adams
  12. Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
    Christophe Fraser, Tanya Golubchik & David Bonsall
  13. Brighton and Sussex University Hospitals NHS Trust, Brighton, UK
    Mohammed O. Hassan-Ibrahim, Cassandra S. Malone & Benjamin J. Cogger
  14. Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
    Michelle Wantoch & Nicola Reynolds
  15. Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
    Ben Warne
  16. Cardiff and Vale University Health Board, Cardiff, UK
    Joshua Maksimovic, Karla Spellman, Kathryn McCluggage, Michaela John, Robert Beer, Safiah Afifi & Sian Morgan
  17. Cardiff University, Cardiff, UK
    Angela Marchbank, Anna Price, Christine Kitchen, Huw Gulliver, Ian Merrick, Joel Southgate, Martyn Guest, Robert Munn, Trudy Workman, Thomas R. Connor, William Fuller & Catherine Bresner
  18. Centre for Clinical Infection and Diagnostics Research, St. Thomas’ Hospital and Kings College London, London, UK
    Luke B. Snell & Amita Patel
  19. Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust, London, UK
    Themoula Charalampous, Gaia Nebbia, Rahul Batra & Jonathan Edgeworth
  20. Centre for Enzyme Innovation, University of Portsmouth (PORT), Portsmouth, UK
    Samuel C. Robson & Angela H. Beckett
  21. Centre for Genomic Pathogen Surveillance, University of Oxford, Oxford, UK
    David M. Aanensen, Anthony P. Underwood, Corin A. Yeats, Khalil Abudahab, Ben E. W. Taylor & Mirko Menegazzo
  22. Clinical Microbiology Department, Queens Medical Centre, Nottingham, UK
    Gemma Clark, Wendy Smith, Manjinder Khakh, Vicki M. Fleming, Michelle M. Lister, Hannah C. Howson-Wells, Louise Berry, Tim Boswell, Amelia Joseph, Iona Willingham & Carl Jones
  23. Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester, UK
    Christopher Holmes, Paul Bird, Thomas Helmer, Karlie Fallon & Julian Tang
  24. County Durham and Darlington NHS Foundation Trust, Durham, UK
    Veena Raviprakash, Sharon Campbell, Nicola Sheriff, Victoria Blakey & Lesley-Anne Williams
  25. Deep Seq, School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, UK
    Matthew W. Loose, Nadine Holmes, Christopher Moore, Matthew Carlile, Victoria Wright, Fei Sang & Johnny Debebe
  26. Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
    Francesc Coll
  27. Department of Infectious Diseases, King’s College London, London, UK
    Adrian W. Signell, Gilberto Betancor & Harry D. Wilson
  28. Department of Microbiology, Kettering General Hospital, Kettering, UK
    Sahar Eldirdiri, Anita Kenyon & Thomas Davis
  29. Department of Zoology, University of Oxford, Oxford, UK
    Oliver G. Pybus, Louis du Plessis, Alex E. Zarebski, Jayna Raghwani, Moritz U. G. Kraemer, Sarah Francois, Stephen W. Attwood, Tetyana I. Vasylyeva, Marina Escalera Zamudio & Bernardo Gutierrez
  30. Departments of Infectious Diseases and Microbiology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
    M. Estee Torok & William L. Hamilton
  31. Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
    Ian G. Goodfellow, Grant Hall, Aminu S. Jahun, Yasmin Chaudhry, Myra Hosmillo, Malte L. Pinckert & Iliana Georgana
  32. East Kent Hospitals University NHS Foundation Trust, Canterbury, UK
    Samuel Moses & Hannah Lowe
  33. East Suffolk and North Essex NHS Foundation Trust, Ipswich, UK
    Luke Bedford
  34. Gateshead Health NHS Foundation Trust, Gateshead, UK
    Jonathan Moore & Susanne Stonehouse
  35. Genomics Innovation Unit, Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
    Chloe L. Fisher & Ali R. Awan
  36. Gloucestershire Hospitals NHS Foundation Trust, Gloucester, UK
    John BoYes
  37. Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
    Judith Breuer, Kathryn Ann Harris, Julianne Rose Brown, Divya Shah, Laura Atkinson, Jack C. D. Lee & Nathaniel Storey
  38. Guy’s and St. Thomas’ BRC, London, UK
    Flavia Flaviani
  39. Guy’s and St. Thomas’ Hospitals, London, UK
    Adela Alcolea-Medina
  40. Hampshire Hospitals NHS Foundation Trust, Winchester, UK
    Rebecca Williams & Gabrielle Vernet
  41. Health Data Research UK Cambridge, Cambridge, UK
    Michael R. Chapman
  42. Health Services Laboratories, London, UK
    Lisa J. Levett, Judith Heaney, Wendy Chatterton & Monika Pusok
  43. Heartlands Hospital, Birmingham, UK
    Li Xu-McCrae
  44. Hub for Biotechnology in the Built Environment, Northumbria University, Newcastle-upon-Tyne, UK
    Darren L. Smith, Matthew Bashton & Gregory R. Young
  45. Imperial College Hospitals NHS Trust, London, UK
    Alison Holmes, Paul Anthony Randell, Alison Cox, Pinglawathee Madona, Frances Bolt, James Price & Siddharth Mookerjee
  46. Imperial College London, London, UK
    Manon Ragonnet-Cronin, Fabricia F. Nascimento, David Jorgensen, Igor Siveroni, Rob Johnson, Olivia Boyd, Lily Geidelberg, Erik M. Volz, Aileen Rowan & Graham P. Taylor
  47. Institute of Biodiversity, Animal Health and Comparative Medicine, Glasgow, UK
    Katherine L. Smollett
  48. King’s College London, London, UK
    Rocio T. Martinez Nunez
  49. Liverpool Clinical Laboratories, Liverpool, UK
    Jenifer Mason, Trevor I. Robinson, Elaine O’Toole, Joanne Watts, Cassie Breen & Angela Cowell
  50. Maidstone and Tunbridge Wells NHS Trust, Maidstone, UK
    Graciela Sluga
  51. Manchester University NHS Foundation Trust, Manchester, UK
    Nicholas W. Machin, Shazaad S. Y. Ahmad & Ryan P. George
  52. Microbiology Department, Wye Valley NHS Trust, Hereford, UK
    Fenella Halstead, Venkat Sivaprakasam & Wendy Hogsden
  53. MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
    Chris J. Illingworth & Chris Jackson
  54. MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
    Emma C. Thomson, James G. Shepherd, Patawee Asamaphan, Marc O. Niebel, Kathy K. Li, Rajiv N. Shah, Natasha G. Jesudason, Lily Tong, Alice Broos, Daniel Mair, Jenna Nichols, Stephen N. Carmichael, Kyriaki Nomikou, Elihu Aranday-Cortes, Natasha Johnson, Igor Starinskij, Ana da Silva Filipe, David L. Robertson, Richard J. Orton, Joseph Hughes, Sreenu Vattipally, Joshua B. Singer & Seema Nickbakhsh
  55. National Infection Service, PHE and Leeds Teaching Hospitals Trust, Leeds, UK
    Antony D. Hale, Louissa R. Macfarlane-Smith, Katherine L. Harper & Holli Carden
  56. Newcastle Hospitals NHS Foundation Trust, Newcastle, UK
    Yusri Taha, Brendan A. I. Payne, Shirelle Burton-Fanning, Sheila Waugh, Jennifer Collins & Gary Eltringham
  57. Newcastle University, Newcastle, UK
    Steven Rushton & Sarah O’Brien
  58. NHS Greater Glasgow and Clyde, Glasgow, UK
    Amanda Bradley, Alasdair Maclean, Guy Mollett & Rachel Blacow
  59. NHS Lothian, Edinburgh, UK
    Kate E. Templeton, Martin P. McHugh, Rebecca Dewar & Elizabeth Wastenge
  60. Norfolk and Norwich University Hospital, Norwich, UK
    Samir Dervisevic, Rachael Stanley, Emma J. Meader & Lindsay Coupland
  61. Norfolk County Council, Norwich, UK
    Louise Smith
  62. North Cumbria Integrated Care NHS Foundation Trust, Carlisle, UK
    Clive Graham, Edward Barton, Debra Padgett & Garren Scott
  63. North Tees and Hartlepool NHS Foundation Trust, Stockton-on-Tees, UK
    Emma Swindells & Jane Greenaway
  64. Northumbria University, Newcastle-upon-Tyne, UK
    Andrew Nelson, Clare M. McCann & Wen C. Yew
  65. Oxford University Hospitals NHS Foundation Trust, Oxford, UK
    Monique Andersson, Timothy Peto, Anita Justice, David Eyre & Derrick Crook
  66. PathLinks, Northern Lincolnshire & Goole NHS Foundation Trust, Scunthorpe, UK
    Tim J. Sloan, Nichola Duckworth & Sarah Walsh
  67. Portsmouth Hospitals University NHS Trust, Portsmouth, UK
    Anoop J. Chauhan, Sharon Glaysher, Kelly Bicknell, Sarah Wyllie, Scott Elliott, Allyson Lloyd & Robert Impey
  68. Princess Alexandra Hospital Microbiology Department, Harlow, UK
    Nick Levene & Lynn Monaghan
  69. Public Health Agency, Belfast, UK
    Declan T. Bradley & Tim Wyatt
  70. Public Health England, Clinical Microbiology and Public Health Laboratory, Cambridge, UK
    Martin D. Curran & Surendra Parmar
  71. Public Health Scotland, Glasgow, UK
    Matthew T. G. Holden & Sharif Shaaban
  72. Public Health Wales NHS Trust, Cardiff, UK
    Alec Birchley, Alexander Adams, Alisha Davies, Amy Gaskin, Amy Plimmer, Bree Gatica-Wilcox, Caoimhe McKerr, Catherine Moore, Chris Williams, David Heyburn, Elen De Lacy, Ember Hilvers, Fatima Downing, Giri Shankar, Hannah Jones, Hibo Asad, Jason Coombes, Joanne Watkins, Johnathan M. Evans, Laia Fina, Laura Gifford, Lauren Gilbert, Lee Graham, Malorie Perry, Mari Morgan, Matthew Bull, Michelle Cronin, Nicole Pacchiarini, Noel Craine, Rachel Jones, Robin Howe, Sally Corden, Sara Rey, Sara Kumziene-Summerhayes, Sarah Taylor, Simon Cottrell, Sophie Jones & Sue Edwards
  73. Quadram Institute Bioscience, Norwich, UK
    Justin O’Grady, Andrew J. Page, Alison E. Mather, David J. Baker, Steven Rudder, Alp Aydin, Gemma L. Kay, Alexander J. Trotter, Nabil-Fareed Alikhan, Leonardo de Oliveira Martins, Thanh Le-Viet & Lizzie Meadows
  74. Queen Elizabeth Hospital, Birmingham, UK
    Anna Casey & Liz Ratcliffe
  75. Queen’s University Belfast, Belfast, UK
    David A. Simpson, Zoltan Molnar, Thomas Thompson & Erwan Acheson
  76. Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
    Jane A. H. Masoli, Bridget A. Knight, Sian Ellard, Cressida Auckland & Christopher R. Jones
  77. Royal Free NHS Trust, London, UK
    Tabitha W. Mahungu, Dianne Irish-Tavares, Tanzina Haque, Jennifer Hart & Eric Witele
  78. Sandwell and West Birmingham NHS Trust, Birmingham, UK
    Melisa Louise Fenton, Ashok Dadrah, Amanda Symmonds & Tranprit Saluja
  79. School of Biological Sciences, University of Portsmouth (PORT), Portsmouth, UK
    Yann Bourgeois & Garry P. Scarlett
  80. School of Pharmacy and Biomedical Sciences, University of Portsmouth (PORT), Portsmouth, UK
    Katie F. Loveson, Salman Goudarzi, Christopher Fearn, Kate Cook, Hannah Dent & Hannah Paul
  81. Sheffield Teaching Hospitals, Sheffield, UK
    David G. Partridge, Mohammad Raza, Cariad Evans & Kate Johnson
  82. South Tees Hospitals NHS Foundation Trust, Newcastle, UK
    Steven Liggett, Paul Baker, Stephen Bonner & Sarah Essex
  83. Swansea University, Swansea, UK
    Ronan A. Lyons
  84. University Hospitals Southampton NHS Foundation Trust, Southampton, UK
    Kordo Saeed, Adhyana I. K. Mahanama, Buddhini Samaraweera, Siona Silveira, Emanuela Pelosi, Eleri Wilson-Davies, Jacqui A. Prieto & Sarah Jeremiah
  85. University College London, London, UK
    Rachel J. Williams, Mark Kristiansen, Sunando Roy, Charlotte A. Williams, Marius Cotic, Nadua Bayzid, Adam P. Westhorpe, John A. Hartley, Riaz Jannoo, Helen L. Lowe, Angeliki Karamani & Leah Ensell
  86. University Hospitals Coventry and Warwickshire, Coventry, UK
    Dimitris Grammatopoulos, Sarojini Pandey, Lisa Berry & Katie Jones
  87. University of Birmingham, Birmingham, UK
    Alex Richter & Andrew Beggs
  88. University of Birmingham Turnkey Laboratory, Birmingham, UK
    Angus Best, Benita Percival, Jeremy Mirza, Oliver Megram, Megan Mayhew, Liam Crawford, Fiona Ashcroft, Emma Moles-Garcia & Nicola Cumley
  89. University of Brighton, Brighton, UK
    Colin P. Smith, Giselda Bucca & Andrew R. Hesketh
  90. University of Cambridge, Cambridge, UK
    Beth Blane, Sophia T. Girgis, Danielle Leek, Sushmita Sridhar, Sally Forrest, Claire Cormie, Harmeet K. Gill, Joana Dias, Ellen E. Higginson, Mailis Maes, Jamie Young, Leanne M. Kermack, Ravi Kumar Gupta, Catherine Ludden, Sharon J. Peacock, Sophie Palmer, Carol M. Churcher, Nazreen F. Hadjirin, Alessandro M. Carabelli, Ellena Brooks, Kim S. Smith, Katerina Galai, Georgina M. McManus & Chris Ruis
  91. University of East Anglia, Norwich, UK
    Rose K. Davidson
  92. University of Edinburgh, Edinburgh, UK
    Andrew Rambaut, Thomas Williams, Carlos E. Balcazar, Michael D. Gallagher, Áine O’Toole, Stefan Rooke, Verity Hill, Kathleen A. Williamson & Thomas D. Stanton
  93. University of Exeter, Exeter, UK
    Stephen L. Michell, Claire M. Bewshea, Ben Temperton, Michelle L. Michelsen, Joanna Warwick-Dugdale, Robin Manley, Audrey Farbos, James W. Harrison, Christine M. Sambles, David J. Studholme & Aaron R. Jeffries
  94. University of Liverpool, Liverpool, UK
    Alistair C. Darby, Julian A. Hiscox, Steve Paterson, Miren Iturriza-Gomara, Kathryn A. Jackson, Anita O. Lucaci, Edith E. Vamos, Margaret Hughes, Lucille Rainbow, Richard Eccles, Charlotte Nelson, Mark Whitehead, Lance Turtle, Sam T. Haldenby, Richard Gregory, Matthew Gemmell, Claudia Wierzbicki & Hermione J. Webster
  95. University of Sheffield, Sheffield, UK
    Thushan I. de Silva, Nikki Smith, Adrienn Angyal, Benjamin B. Lindsey, Danielle C. Groves, Luke R. Green, Dennis Wang, Timothy M. Freeman, Matthew D. Parker, Alexander J. Keeley, Paul J. Parsons, Rachel M. Tucker, Rebecca Brown, Matthew Wyles, Max Whiteley, Peijun Zhang, Marta Gallis & Stavroula F. Louka
  96. University of Warwick, Warwick, UK
    Chrystala Constantinidou, Meera Unnikrishnan, Sascha Ott, Jeffrey K. J. Cheng, Hannah E. Bridgewater, Lucy R. Frost, Grace Taylor-Joyce, Richard Stark, Laura Baxter, Mohammad T. Alam & Paul E. Brown
  97. University of Cambridge, Cambridge, UK
    Dinesh Aggarwal
  98. Viapath, London, UK
    Alberto C. Cerda, Tammy V. Merrill & Rebekah E. Wilson
  99. Guy’s and St Thomas’ NHS Foundation Trust, London, UK
    Alberto C. Cerda, Tammy V. Merrill & Rebekah E. Wilson
  100. King’s College Hospital NHS Foundation Trust, London, UK
    Alberto C. Cerda, Tammy V. Merrill & Rebekah E. Wilson
  101. Virology, School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, UK
    Patrick C. McClure, Joseph G. Chappell, Theocharis Tsoleridis & Jonathan Ball
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Authors

  1. Erik Volz
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  2. Swapnil Mishra
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  3. Meera Chand
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  4. Jeffrey C. Barrett
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  5. Robert Johnson
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  6. Lily Geidelberg
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  7. Wes R. Hinsley
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  8. Daniel J. Laydon
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  9. Gavin Dabrera
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  10. Áine O’Toole
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  11. Robert Amato
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  12. Manon Ragonnet-Cronin
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  13. Ian Harrison
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  14. Ben Jackson
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  15. Cristina V. Ariani
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  16. Olivia Boyd
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  17. Nicholas J. Loman
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  18. John T. McCrone
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  19. Sónia Gonçalves
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  20. David Jorgensen
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  21. Richard Myers
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  22. Verity Hill
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  23. David K. Jackson
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  24. Katy Gaythorpe
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  25. Natalie Groves
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  26. John Sillitoe
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  27. Dominic P. Kwiatkowski
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  28. Seth Flaxman
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  29. Oliver Ratmann
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  30. Samir Bhatt
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  31. Susan Hopkins
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  33. Andrew Rambaut
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  34. Neil M. Ferguson
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Consortia

The COVID-19 Genomics UK (COG-UK) consortium

Contributions

Conceptualization: E.V., S.B., A.G., S.M., N.M.F., M.C., S.H., J.C.B., D.P.K., A.R.; writing (first draft): E.V., S.F., S.B., A.G., O.R., S.M., R.J., A.R., N.M.F.; writing (review and editing): E.V., S.F., S.B., A.G., O.R., S.M., R.J., N.M.F., M.R.-C., D.J.L., M.C., S.H., J.C.B., K.G., C.V.A., J.T.M., V.H., B.J., Á.O’T.; analysis: E.V., S.F., S.B., A.G., O.R., S.M., R.J., N.M.F., L.G., D.J., M.C., R.M., N.G., J.C.B., J.S., A.R.; methodology: E.V., S.F., S.B., A.G., O.R., S.M., R.J., N.M.F., A.R.; data generation: S.H., S.M., R.J., O.B., M.C., R.M., N.G., I.H., G.D., N.J.L., J.C.B., D.P.K., R.A., C.V.A., S.G., W.R.H.,D.K.J., J.S., O.B., K.G., J.T.M., V.H., B.J., Á.O’T., A.R.; software: E.V., S.F., A.G., S.M., R.J., N.M.F., R.A., S.G., K.G.; validation: E.V., S.B., S.M., N.M.F.; visualization: E.V., S.F., S.B., O.R., S.M., M.R.-C.; supervision: E.V., S.B., O.R., N.M.F., A.R.; funding acquisition: E.V., S.F., S.B., A.G., N.M.F., N.J.L., A.R.

Corresponding authors

Correspondence toErik Volz or Neil M. Ferguson.

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The authors declare no competing interests.

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Peer review information Nature thanks Alexei Drummond and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available.

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Extended data figures and tables

Extended Data Fig. 1 Weekly growth rate of the VOC relative to other variants and relationship of VOC growth rate with VOC frequency.

a, The additive difference in growth rate between VOC and other lineages inferred from observed frequency of VOC genomes over time (Supplementary Methods section 2). b, The additive difference in growth rates plotted against estimated frequency of the VOC for different NHS regions. The difference in growth rate correlates more strongly with VOC frequency than with time (data not shown). Estimates are presented for weeks 44–56 for each region.

Extended Data Fig. 3 Weekly numbers of _S_-gene-positive samples with TPP correction plotted against the effective population size of the VOC.

Point labels indicate week of data collection. Effective sample size is taken on the final day of the corresponding epidemiological week. Error bars, 95% bootstrap CIs.

Extended Data Fig. 4 Empirical data analysis of the advantage in weekly growth factors (cases in week t + 1 divided by cases in week t) for the VOC and non-VOC lineages (Supplementary Methods section 5).

Each point represents either the ratio (left) or difference (right) of weekly growth factors for the VOC versus the non-VOC for an NHS England STP area and week, using the raw SGTF data shown in Fig. 2 (not adjusting for TPP). Colours and shapes differentiate epidemiological weeks. Numbers above 1 on the left plot and above 0 on the right plot show a transmission advantage. The blue line represents the mean advantage for a particular proportion of VOC among all cases, and the grey shading the 95% asymptotic CrI (±2_σ_). Scatter at low frequencies largely reflects statistical noise resulting from low counts.

Extended Data Fig. 5 Sensitivity of reproduction number estimates at regional level to differences in the mean generation time in the VOC (0–25% reduction in the mean, while holding coefficient of variation constant).

Top, scatter plots of estimated ratio of _S_− to _S_+ reproduction numbers plotted against the reproduction number of _S_-gene-positive cases over time and among STP regions. Grey lines, linear regression—if changes in the generation time were able to completely explain temporal variation in the ratio, we would expect the slope to be zero. Bottom, ratio of reproduction number over time for each assumption about the mean generation time of the VOC. Shaded region, 95% CrI.

Extended Data Fig. 6 Proportion of all cases in individuals over 10 years of age that were in 11–18-year-olds, stratified by SGTF status, NHS regions and week of testing.

Top, data; middle, predicted trends from a semi-mechanistic model (Supplementary Methods section 7) fitting a time- and region-varying transmission advantage, but no age variation in transmission advantage; bottom, predicted trends from the model fitting a transmission that which varies by week, region and age group. Shaded region, 95% CrI.

Extended Data Fig. 7 The overall multiplicative transmission advantage of the VOC over time estimated using a semi-mechanistic model with a VOC transmission advantage that varies by week and region, but not with age (Supplementary Methods section 7).

The model fitted one transmission advantage parameter per week and per NHS region to SGTF (STP-level) counts by NHS STP area (left; finer scale than region) and SGTF counts by STP area and VOC genome counts by NHS region (right). Solid lines, medians; shading, 95% CrI pooled over all regions.

Extended Data Table 1 Tabulation of parameter estimates and model assessment using Pareto-smoothed importance sampling leave-one-out cross validation (PSIS-LOO CV) and widely applicable information criterion (WAIC)

Full size table

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Volz, E., Mishra, S., Chand, M. et al. Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England.Nature 593, 266–269 (2021). https://doi.org/10.1038/s41586-021-03470-x

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