Rxivist logo

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.

Download data

  • Downloaded 1,828 times
  • Download rankings, all-time:
    • Site-wide: 10,732
    • In epidemiology: 812
  • Year to date:
    • Site-wide: 8,368
  • Since beginning of last month:
    • Site-wide: 23,283

Altmetric data


Downloads over time

Distribution of downloads per paper, site-wide


PanLingua

News