L. du Plessis, J. T. McCrone, A. Zarebski, V. Hill, C. Ruis, B. Gutiérrez, J. Raghwani, J. Ashworth, R. Colquhoun, T. Connor, Nuno R. Faria, B. Jackson, N. Loman, Á. O'toole, S. Nicholls, K. Parag, E. Scher, T. Vasylyeva, E. Volz, A. Watts, I. Bogoch, K. Khan, COG-UK consortium, D. Aanensen, M. Kraemer, A. Rambaut, O. Pybus
medRxiv, 2020
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 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.
Cited by 13 publications.
Field of study: Medicine