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.
【초록키워드】 COVID-19, Epidemiology, lockdown, Genetic, Infection, Transmission, virus, Epidemic, persistence, Travel, Transmission dynamics, Lineage, Rapid, epidemiological, phylogenetic analyses, genomic, First wave, lineages, COVID-19 epidemic, Analysis, Perspective, SARS-CoV-2 genomes, National, implication, fluctuation, introduced, declined, 【제목키워드】 Epidemic, Lineage, the SARS-CoV-2,