• 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, COVID-19 Genomics UK (COG-UK) Consortium, David M Aanensen, Kraemer Moritz U G MUG 0000-0001-8838-7147 Department of Zoology, University of Oxford, Oxford, UK., Andrew Rambaut, and Oliver G Pybus.
• Department of Zoology, University of Oxford, Oxford, UK.
• Science. 2021 Feb 12; 371 (6530): 708-712.

AbstractThe 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.Copyright © 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

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