Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK.
du Plessis L., McCrone JT., Zarebski AE., Hill V., Ruis C., Gutierrez B., Raghwani J., Ashworth J., Colquhoun R., Connor TR., Faria NR., Jackson B., Loman NJ., O'Toole Á., Nicholls SM., Parag KV., Scher E., Vasylyeva TI., Volz EM., Watts A., Bogoch II., Khan K., COVID-19 Genomics UK (COG-UK) Consortium None., Aanensen DM., Kraemer MUG., Rambaut A., Pybus OG.
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.