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.
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du Plessis, L., McCrone, J., Zarebski, A., Hill, V., Ruis, C., Gutierrez, B., Raghwani, J., Ashworth, J., Colquhoun, R., Connor, T., Faria, N., Jackson, B., Loman, N., O’toole, Á., Nicholls, S., Parag, K., Scher, E., Vasylyeva, T., Volz, E., Watts, A., Bogoch, I., Khan, K., Aanensen, D., Kraemer, M., Rambaut, A. & Pybus, O. 2021, 'Establishment & lineage dynamics of the SARS-CoV-2 epidemic in the UK', Science, 371(6530), pp. 708-712. http://dx.doi.org/10.1126/science.abf2946