Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK

Louis du Plessis; John T. McCrone; Alexander E. Zarebski; Verity Hill; Christopher Ruis; Bernardo Gutierrez; Jayna Raghwani; Jordan Ashworth; Rachel Colquhoun; Thomas R. Connor; Nuno R. Faria; Ben Jackson; Nicholas J. Loman; Áine O'Toole; Samuel M. Nicholls; Kris V. Parag; Emily Scher; Tetyana I. Vasylyeva; Erik M. Volz; Alexander Watts; Isaac I. Bogoch; Kamran Khan; David M. Aanensen; Moritz U.G. Kraemer; Andrew Rambaut; Oliver G. Pybus

doi:10.1126/science.abf2946

Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK

Louis du Plessis
, John T. McCrone
, Alexander E. Zarebski
, Verity Hill
, Christopher Ruis
, Bernardo Gutierrez
, Jayna Raghwani
, Jordan Ashworth
, Rachel Colquhoun
, Thomas R. Connor
, Nuno R. Faria
, Ben Jackson
, Nicholas J. Loman
, Áine O'Toole
, Samuel M. Nicholls
, Kris V. Parag
, Emily Scher
, Tetyana I. Vasylyeva
, Erik M. Volz
, Alexander Watts

Isaac I. Bogoch, Kamran Khan, David M. Aanensen, Moritz U.G. Kraemer, Andrew Rambaut^*, Oliver G. Pybus^*

^*Corresponding author for this work

University of Oxford
EaStCHEM School of Chemistry, University of Edinburgh
University of Cambridge
Universidad San Francisco de Quito
Cardiff University
Public Health Wales
Medical Research Council
University of Birmingham
University of Toronto
BlueDot Inc.
University of Toronto Faculty of Medicine
University Health Network and Mount Sinai Hospital
Centre for Genomic Pathogen Surveillance
Nuffield Department of Medicine
Royal Veterinary College University of London

Research output: Contribution to journal › Article › peer-review

285 Scopus citations

Abstract

The United Kingdom's COVID-19 epidemic during early 2020 was one of world's largest and was unusually well represented by virus genomic sampling. We determined the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes, including 26,181 from the UK sampled throughout the country's first wave of infection. Using large-scale phylogenetic analyses combined with epidemiological and travel data, we quantified the size, spatiotemporal origins, and persistence of genetically distinct UK transmission lineages. Rapid fluctuations in virus importation rates resulted in >1000 lineages; those introduced prior to national lockdown tended to be larger and more dispersed. Lineage importation and regional lineage diversity declined after lockdown, whereas lineage elimination was size-dependent. We discuss the implications of our genetic perspective on transmission dynamics for COVID-19 epidemiology and control.

Original language	English
Pages (from-to)	708-712
Number of pages	5
Journal	Science
Volume	371
Issue number	6530
DOIs	https://doi.org/10.1126/science.abf2946
State	Published - 12 Feb 2021
Externally published	Yes

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du Plessis, L., McCrone, J. T., Zarebski, A. E., Hill, V., Ruis, C., Gutierrez, B., Raghwani, J., Ashworth, J., Colquhoun, R., Connor, T. R., Faria, N. R., Jackson, B., Loman, N. J., O'Toole, Á., Nicholls, S. M., Parag, K. V., Scher, E., Vasylyeva, T. I., Volz, E. M., ... Pybus, O. G. (2021). Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK. Science, 371(6530), 708-712. https://doi.org/10.1126/science.abf2946

@article{0384216898514cb99f2b14db6bbdffa6,

title = "Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK",

abstract = "The United Kingdom's COVID-19 epidemic during early 2020 was one of world's largest and was unusually well represented by virus genomic sampling. We determined the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes, including 26,181 from the UK sampled throughout the country's first wave of infection. Using large-scale phylogenetic analyses combined with epidemiological and travel data, we quantified the size, spatiotemporal origins, and persistence of genetically distinct UK transmission lineages. Rapid fluctuations in virus importation rates resulted in >1000 lineages; those introduced prior to national lockdown tended to be larger and more dispersed. Lineage importation and regional lineage diversity declined after lockdown, whereas lineage elimination was size-dependent. We discuss the implications of our genetic perspective on transmission dynamics for COVID-19 epidemiology and control.",

author = "\{du Plessis\}, Louis and McCrone, \{John T.\} and Zarebski, \{Alexander E.\} and Verity Hill and Christopher Ruis and Bernardo Gutierrez and Jayna Raghwani and Jordan Ashworth and Rachel Colquhoun and Connor, \{Thomas R.\} and Faria, \{Nuno R.\} and Ben Jackson and Loman, \{Nicholas J.\} and {\'A}ine O'Toole and Nicholls, \{Samuel M.\} and Parag, \{Kris V.\} and Emily Scher and Vasylyeva, \{Tetyana I.\} and Volz, \{Erik M.\} and Alexander Watts and Bogoch, \{Isaac I.\} and Kamran Khan and Aanensen, \{David M.\} and Kraemer, \{Moritz U.G.\} and Andrew Rambaut and Pybus, \{Oliver G.\}",

note = "Publisher Copyright: Copyright {\textcopyright} 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works",

year = "2021",

month = feb,

day = "12",

doi = "10.1126/science.abf2946",

language = "Ingl{\'e}s",

volume = "371",

pages = "708--712",

journal = "Science",

issn = "0036-8075",

publisher = "American Association for the Advancement of Science",

number = "6530",

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du Plessis, L, McCrone, JT, Zarebski, AE, Hill, V, Ruis, C, Gutierrez, B, Raghwani, J, Ashworth, J, Colquhoun, R, Connor, TR, Faria, NR, Jackson, B, Loman, NJ, O'Toole, Á, Nicholls, SM, Parag, KV, Scher, E, Vasylyeva, TI, Volz, EM, Watts, A, Bogoch, II, Khan, K, Aanensen, DM, Kraemer, MUG, Rambaut, A & Pybus, OG 2021, 'Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK', Science, vol. 371, no. 6530, pp. 708-712. https://doi.org/10.1126/science.abf2946

TY - JOUR

T1 - Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK

AU - du Plessis, Louis

AU - McCrone, John T.

AU - Zarebski, Alexander E.

AU - Hill, Verity

AU - Ruis, Christopher

AU - Gutierrez, Bernardo

AU - Raghwani, Jayna

AU - Ashworth, Jordan

AU - Colquhoun, Rachel

AU - Connor, Thomas R.

AU - Faria, Nuno R.

AU - Jackson, Ben

AU - Loman, Nicholas J.

AU - O'Toole, Áine

AU - Nicholls, Samuel M.

AU - Parag, Kris V.

AU - Scher, Emily

AU - Vasylyeva, Tetyana I.

AU - Volz, Erik M.

AU - Watts, Alexander

AU - Bogoch, Isaac I.

AU - Khan, Kamran

AU - Aanensen, David M.

AU - Kraemer, Moritz U.G.

AU - Rambaut, Andrew

AU - Pybus, Oliver G.

PY - 2021/2/12

Y1 - 2021/2/12

N2 - The United Kingdom's COVID-19 epidemic during early 2020 was one of world's largest and was unusually well represented by virus genomic sampling. We determined the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes, including 26,181 from the UK sampled throughout the country's first wave of infection. Using large-scale phylogenetic analyses combined with epidemiological and travel data, we quantified the size, spatiotemporal origins, and persistence of genetically distinct UK transmission lineages. Rapid fluctuations in virus importation rates resulted in >1000 lineages; those introduced prior to national lockdown tended to be larger and more dispersed. Lineage importation and regional lineage diversity declined after lockdown, whereas lineage elimination was size-dependent. We discuss the implications of our genetic perspective on transmission dynamics for COVID-19 epidemiology and control.

AB - The United Kingdom's COVID-19 epidemic during early 2020 was one of world's largest and was unusually well represented by virus genomic sampling. We determined the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes, including 26,181 from the UK sampled throughout the country's first wave of infection. Using large-scale phylogenetic analyses combined with epidemiological and travel data, we quantified the size, spatiotemporal origins, and persistence of genetically distinct UK transmission lineages. Rapid fluctuations in virus importation rates resulted in >1000 lineages; those introduced prior to national lockdown tended to be larger and more dispersed. Lineage importation and regional lineage diversity declined after lockdown, whereas lineage elimination was size-dependent. We discuss the implications of our genetic perspective on transmission dynamics for COVID-19 epidemiology and control.

UR - https://www.scopus.com/pages/publications/85101031256

U2 - 10.1126/science.abf2946

DO - 10.1126/science.abf2946

M3 - Artículo

C2 - 33419936

AN - SCOPUS:85101031256

SN - 0036-8075

VL - 371

SP - 708

EP - 712

JO - Science

JF - Science

IS - 6530

ER -

Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK

Abstract

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