Research Article
Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK
- View ORCID ProfileLouis du Plessis1,*,
- View ORCID ProfileJohn T. McCrone2,*,
- View ORCID ProfileAlexander E. Zarebski1,*,
- View ORCID ProfileVerity Hill2,*,
- View ORCID ProfileChristopher Ruis3,4,*,
- View ORCID ProfileBernardo Gutierrez1,5,
- View ORCID ProfileJayna Raghwani1,
- View ORCID ProfileJordan Ashworth2,
- View ORCID ProfileRachel Colquhoun2,
- View ORCID ProfileThomas R. Connor6,7,
- View ORCID ProfileNuno R. Faria1,8,
- View ORCID ProfileBen Jackson2,
- View ORCID ProfileNicholas J. Loman9,
- View ORCID ProfileÁine O’Toole2,
- View ORCID ProfileSamuel M. Nicholls9,
- View ORCID ProfileKris V. Parag8,
- View ORCID ProfileEmily Scher2,
- Tetyana I. Vasylyeva1,
- View ORCID ProfileErik M. Volz8,
- View ORCID ProfileAlexander Watts10,11,
- Isaac I. Bogoch12,13,
- View ORCID ProfileKamran Khan10,11,12,
- COVID-19 Genomics UK (COG-UK) Consortium†,
- David M. Aanensen14,15,
- Moritz U. G. Kraemer1,‡,
- Andrew Rambaut2,‡,§,
- Oliver G. Pybus1,16,‡,§
- 1Department of Zoology, University of Oxford, Oxford, UK.
- 2Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
- 3Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK.
- 4Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
- 5School of Biological and Environmental Sciences, Universidad San Francisco de Quito, Quito, Ecuador.
- 6School of Biosciences, Cardiff University, Cardiff, UK.
- 7Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK.
- 8MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK.
- 9Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK.
- 10Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, Canada.
- 11BlueDot, Toronto, Canada.
- 12Department of Medicine, University of Toronto, Toronto, Canada.
- 13Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada.
- 14Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK.
- 15Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- 16Department of Pathobiology and Population Sciences, Royal Veterinary College London, London, UK.
- ↵§Corresponding author. Email: a.rambaut{at}ed.ac.uk (A.R.); oliver.pybus{at}zoo.ox.ac.uk (O.G.P.)
↵* These authors contributed equally to this work.
↵‡ These authors contributed equally to this work.
↵† See supplementary materials for list of consortium members and affiliations.
See allHide authors and affiliations
Science 12 Feb 2021:
Vol. 371, Issue 6530, pp. 708-712
DOI: 10.1126/science.abf2946
Vol. 371, Issue 6530, pp. 708-712
DOI: 10.1126/science.abf2946
Louis du Plessis
1Department of Zoology, University of Oxford, Oxford, UK.
John T. McCrone
2Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
Alexander E. Zarebski
1Department of Zoology, University of Oxford, Oxford, UK.
Verity Hill
2Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
Christopher Ruis
3Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK.
4Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
Bernardo Gutierrez
1Department of Zoology, University of Oxford, Oxford, UK.
5School of Biological and Environmental Sciences, Universidad San Francisco de Quito, Quito, Ecuador.
Jayna Raghwani
1Department of Zoology, University of Oxford, Oxford, UK.
Jordan Ashworth
2Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
Rachel Colquhoun
2Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
Thomas R. Connor
6School of Biosciences, Cardiff University, Cardiff, UK.
7Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK.
Nuno R. Faria
1Department of Zoology, University of Oxford, Oxford, UK.
8MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK.
Ben Jackson
2Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
Nicholas J. Loman
9Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK.
Áine O’Toole
2Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
Samuel M. Nicholls
9Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK.
Kris V. Parag
8MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK.
Emily Scher
2Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
Tetyana I. Vasylyeva
1Department of Zoology, University of Oxford, Oxford, UK.
Erik M. Volz
8MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK.
Alexander Watts
10Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, Canada.
11BlueDot, Toronto, Canada.
Isaac I. Bogoch
12Department of Medicine, University of Toronto, Toronto, Canada.
13Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada.
Kamran Khan
10Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, Canada.
11BlueDot, Toronto, Canada.
12Department of Medicine, University of Toronto, Toronto, Canada.
David M. Aanensen
14Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK.
15Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
Moritz U. G. Kraemer
1Department of Zoology, University of Oxford, Oxford, UK.
Andrew Rambaut
2Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
Oliver G. Pybus
1Department of Zoology, University of Oxford, Oxford, UK.
16Department of Pathobiology and Population Sciences, Royal Veterinary College London, London, UK.
