Establishment & 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 & 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 WattsIsaac I. Bogoch, Kamran Khan, David M Aanensen, Moritz U G Kraemer, Andrew Rambaut, Oliver G. Pybus

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

Abstract

The UK’s COVID-19 epidemic during early 2020 was one of world’s largest and unusually well represented by virus genomic sampling. Here we reveal the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 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 quantify the size, spatio-temporal 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, whilst 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
Early online date	8 Jan 2021
DOIs	https://doi.org/10.1126/science.abf2946
Publication status	Published - 12 Feb 2021

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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 & lineage dynamics of the SARS-CoV-2 epidemic in the UK. Science, 371(6530), 708-712. https://doi.org/10.1126/science.abf2946

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

abstract = "The UK{\textquoteright}s COVID-19 epidemic during early 2020 was one of world{\textquoteright}s largest and unusually well represented by virus genomic sampling. Here we reveal the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 SARS-CoV-2 genomes, including 26,181 from the UK sampled throughout the country{\textquoteright}s first wave of infection. Using large-scale phylogenetic analyses, combined with epidemiological and travel data, we quantify the size, spatio-temporal 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, whilst 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.}",

year = "2021",

month = feb,

day = "12",

doi = "10.1126/science.abf2946",

language = "English",

volume = "371",

pages = "708--712",

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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 & 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 & 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 UK’s COVID-19 epidemic during early 2020 was one of world’s largest and unusually well represented by virus genomic sampling. Here we reveal the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 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 quantify the size, spatio-temporal 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, whilst lineage elimination was size-dependent. We discuss the implications of our genetic perspective on transmission dynamics for COVID-19 epidemiology and control.

AB - The UK’s COVID-19 epidemic during early 2020 was one of world’s largest and unusually well represented by virus genomic sampling. Here we reveal the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 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 quantify the size, spatio-temporal 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, whilst 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.ebi.ac.uk/ena/browser/view/PRJEB37886

U2 - 10.1126/science.abf2946

DO - 10.1126/science.abf2946

M3 - Article

VL - 371

SP - 708

EP - 712

JO - Science

JF - Science

SN - 0036-8075

IS - 6530

ER -

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

Abstract

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Putting genomic surveillance at the heart of viral epidemic response.

The evolutionary dynamics of pathogen emergence and establishment: from Reservoir Detection to Outbreak Control

Andrew Rambaut

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

Abstract

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Putting genomic surveillance at the heart of viral epidemic response.

The evolutionary dynamics of pathogen emergence and establishment: from Reservoir Detection to Outbreak Control

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Andrew Rambaut

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