Establishment & lineage dynamics of the SARS-CoV-2 epidemic in the UK
Louis Raymond du Plessis,
John T. McCrone,
Alexander E. Zarebski,
Thomas Richard Connor,
Nuno R. Faria,
Nicholas J. Loman,
Samuel M. Nicholls,
Kris V. Parag,
Tetyana I. Vasylyeva,
the COVID-19 Genomics UK (COG-UK) Consortium,
David M. Aanensen,
Moritz U. G. Kraemer,
Oliver G. Pybus
Posted 27 Oct 2020
medRxiv DOI: 10.1101/2020.10.23.20218446
Posted 27 Oct 2020
The UKs COVID-19 epidemic during early 2020 was one of worlds 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 countrys 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 were 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.
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