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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 and Pybus, Oliver G. 2021. Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK. Science 371 (6530) , pp. 708-712. 10.1126/science.abf2946

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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.

Item Type: Article
Date Type: Publication
Status: Published
Schools: Biosciences
Additional Information: This is an open-access article distributed under the terms of the Creative Commons Attribution license
Publisher: American Association for the Advancement of Science
ISSN: 0036-8075
Date of First Compliant Deposit: 15 March 2021
Date of Acceptance: 18 December 2020
Last Modified: 16 Mar 2021 10:15
URI: http://orca.cardiff.ac.uk/id/eprint/139786

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