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

The COVID-19 Genomics UK (COG-UK) Consortium; 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; Matthew Bashton; Darren Smith; Greg Young; Andrew Nelson

doi:10.1126/science.abf2946

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

The COVID-19 Genomics UK (COG-UK) Consortium, 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. VolzAlexander Watts, Isaac I. Bogoch, Kamran Khan, David M. Aanensen, Moritz U. G. Kraemer, Andrew Rambaut^*, Oliver G. Pybus^*, Matthew Bashton, Darren Smith, Greg Young, Andrew Nelson

^*Corresponding author for this work

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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
Article number	eabf2946
Pages (from-to)	708-712
Number of pages	6
Journal	Science
Volume	371
Issue number	6530
Early online date	8 Jan 2021
DOIs	https://doi.org/10.1126/science.abf2946
Publication status	Published - 12 Feb 2021

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https://science.sciencemag.org/content/suppl/2021/01/07/science.abf2946.DC1

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The COVID-19 Genomics UK (COG-UK) Consortium, 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., ... Nelson, A. (2021). Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK. Science, 371(6530), 708-712. Article eabf2946. https://doi.org/10.1126/science.abf2946

@article{cf2fa854822745e281b8f593f6a6bb89,

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 = "{The COVID-19 Genomics UK (COG-UK) Consortium} and {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{\textquoteright}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.} and Matthew Bashton and Darren Smith and Greg Young and Andrew Nelson",

note = "Matthew Bashton, Darren L Smith, Gregory R Young and Andrew Nelson are member of the COVID-19 Genomics UK (COG-UK) Consortium. 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. Distributed under a Creative Commons Attribution License 4.0 (CC BY). https://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/. This license does not apply to figures/photos/artwork or other content included in the article that is credited to a third party; obtain authorization from the rights holder before using such material.",

year = "2021",

month = feb,

day = "12",

doi = "10.1126/science.abf2946",

language = "English",

volume = "371",

pages = "708--712",

journal = "Science",

issn = "0036-8075",

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

number = "6530",

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The COVID-19 Genomics UK (COG-UK) Consortium, 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, Bashton, M , Smith, D, Young, G & Nelson, A 2021, 'Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK', Science, vol. 371, no. 6530, eabf2946, pp. 708-712. https://doi.org/10.1126/science.abf2946

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

AU - The COVID-19 Genomics UK (COG-UK) Consortium

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.

AU - Bashton, Matthew

AU - Smith, Darren

AU - Young, Greg

AU - Nelson, Andrew

N1 - Matthew Bashton, Darren L Smith, Gregory R Young and Andrew Nelson are member of the COVID-19 Genomics UK (COG-UK) Consortium. Copyright © 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution License 4.0 (CC BY). https://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/. This license does not apply to figures/photos/artwork or other content included in the article that is credited to a third party; obtain authorization from the rights holder before using such material.

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.

U2 - 10.1126/science.abf2946

DO - 10.1126/science.abf2946

M3 - Article

C2 - 33419936

SN - 0036-8075

VL - 371

SP - 708

EP - 712

JO - Science

JF - Science

IS - 6530

M1 - eabf2946

ER -

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

Abstract

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