Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK.


du Plessis, Louis ORCID: 0000-0003-0352-6289, McCrone, John T ORCID: 0000-0002-9846-8917, Zarebski, Alexander E ORCID: 0000-0003-1824-7653, Hill, Verity ORCID: 0000-0002-3509-8146, Ruis, Christopher ORCID: 0000-0003-0977-5534, Gutierrez, Bernardo ORCID: 0000-0002-9220-2739, Raghwani, Jayna ORCID: 0000-0001-8538-4995, Ashworth, Jordan ORCID: 0000-0003-1740-7475, Colquhoun, Rachel ORCID: 0000-0002-5577-9897, Connor, Thomas R ORCID: 0000-0003-2394-6504 et al (show 17 more authors) (2021) Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK. Science (New York, N.Y.), 371 (6530). pp. 708-712.

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Abstract

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.

Item Type: Article
Uncontrolled 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
Divisions: Faculty of Health and Life Sciences
Faculty of Health and Life Sciences > Institute of Infection, Veterinary and Ecological Sciences
Depositing User: Symplectic Admin
Date Deposited: 09 May 2022 08:37
Last Modified: 16 Dec 2023 03:36
DOI: 10.1126/science.abf2946
Open Access URL: https://doi.org/10.1126/science.abf2946
Related URLs:
URI: https://livrepository.liverpool.ac.uk/id/eprint/3154479
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