Journal article
Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK
- Abstract:
- 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.
- Publication status:
- Published
- Peer review status:
- Peer reviewed
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(Preview, Version of record, 5.5MB, Terms of use)
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- Publisher copy:
- 10.1126/science.abf2946
Authors
- Publisher:
- American Association for the Advancement of Science
- Journal:
- Science More from this journal
- Volume:
- 371
- Issue:
- 6530
- Pages:
- 708-712
- Publication date:
- 2021-01-08
- Acceptance date:
- 2020-12-18
- DOI:
- EISSN:
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1095-9203
- ISSN:
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0036-8075
- Language:
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English
- Keywords:
- Pubs id:
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1150148
- Local pid:
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pubs:1150148
- Deposit date:
-
2020-12-18
Terms of use
- Copyright holder:
- du Plessis et al.
- Copyright date:
- 2021
- Rights statement:
- Copyright © 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution License 4.0 (CC BY). https://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- Licence:
- CC Attribution (CC BY)
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