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

du Plessis, Louis, McCrone, John T., Zarebski, Alexander E., Hill, Verity, Ruis, Christopher, Gutierrez, Bernardo, Raghwani, Jayna, Ashworth, Jordan, Colquhoun, Rachel, Connor, Thomas R., Faria, Nuno R., Jackson, Ben, Loman, Nicholas J., O’Toole, Áine, Nicholls, Samuel M., Parag, Kris V., Scher, Emily, Vasylyeva, Tetyana I., Volz, Erik M., Watts, Alexander, Bogoch, Isaac I., Khan, Kamran, Aanensen, David M., Kraemer, Moritz U. G., Rambaut, Andrew, Pybus, Oliver G., COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, Smith, Darren, Young, Greg and Nelson, Andrew (2021) Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK. Science. eabf2946. ISSN 0036-8075 (In Press)

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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, while lineage elimination was size-dependent. We discuss the implications of our genetic perspective on transmission dynamics for COVID-19 epidemiology and control.

Item Type: Article
Additional Information: Matthew Bashton, Darren L Smith, Gregory R Young and Andrew Nelson are member of the COVID-19 Genomics UK (COG-UK) Consortium. 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 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.
Subjects: C700 Molecular Biology, Biophysics and Biochemistry
Department: Faculties > Health and Life Sciences > Applied Sciences
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Depositing User: John Coen
Date Deposited: 12 Jan 2021 10:45
Last Modified: 15 Jan 2021 11:00

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