Cookies on this website

We use cookies to ensure that we give you the best experience on our website. If you click 'Accept all cookies' we'll assume that you are happy to receive all cookies and you won't see this message again. If you click 'Reject all non-essential cookies' only necessary cookies providing core functionality such as security, network management, and accessibility will be enabled. Click 'Find out more' for information on how to change your cookie settings.

The United Kingdom's COVID-19 epidemic during early 2020 was one of world's largest and was unusually well represented by virus genomic sampling. We determined the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 severe acute respiratory syndrome coronavirus 2 (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 quantified the size, spatiotemporal 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, whereas lineage elimination was size-dependent. We discuss the implications of our genetic perspective on transmission dynamics for COVID-19 epidemiology and control.

Original publication

DOI

10.1126/science.abf2946

Type

Journal article

Journal

Science (New York, N.Y.)

Publication Date

02/2021

Volume

371

Pages

708 - 712

Addresses

Department of Zoology, University of Oxford, Oxford, UK.

Keywords

COVID-19 Genomics UK (COG-UK) Consortium, Humans, Communicable Disease Control, Phylogeny, Genome, Viral, Travel, Epidemics, United Kingdom, Communicable Diseases, Imported, COVID-19, SARS-CoV-2, Chain of Infection