Abstract
The evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus leads to new variants that warrant timely epidemiological characterization. Here we use the dense genomic surveillance data generated by the COVID-19 Genomics UK Consortium to reconstruct the dynamics of 71 different lineages in each of 315 English local authorities between September 2020 and June 2021. This analysis reveals a series of subepidemics that peaked in early autumn 2020, followed by a jump in transmissibility of the B.1.1.7/Alpha lineage. The Alpha variant grew when other lineages declined during the second national lockdown and regionally tiered restrictions between November and December 2020. A third more stringent national lockdown suppressed the Alpha variant and eliminated nearly all other lineages in early 2021. Yet a series of variants (most of which contained the spike E484K mutation) defied these trends and persisted at moderately increasing proportions. However, by accounting for sustained introductions, we found that the transmissibility of these variants is unlikely to have exceeded the transmissibility of the Alpha variant. Finally, B.1.617.2/Delta was repeatedly introduced in England and grew rapidly in early summer 2021, constituting approximately 98% of sampled SARS-CoV-2 genomes on 26 June 2021.
Original language | English |
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Pages (from-to) | 506-511 |
Number of pages | 6 |
Journal | Nature |
Volume | 600 |
Issue number | 7889 |
Early online date | 14 Oct 2021 |
DOIs | |
Publication status | Published - 16 Dec 2021 |
Bibliographical note
Funding Information:Acknowledgements We thank E. Allara (Cambridge) and G. Whitton (Sanger) for providing outer postcodes to LTLA mappings; R. Beale for comments and J. McCrone for setting up Thorney Beast analysis; all of the contributors who submitted genome sequences to GISAID (acknowledgement tables for individual sequences are provided at GitHub; https://github. com/NicolaDM/phylogeographySARS-CoV-2); and our colleagues at EMBL-EBI, the Wellcome Sanger Institute and COG-UK for discussions and comments on this manuscript. COG-UK is supported by funding from the Medical Research Council (MRC), part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) and Genome Research Limited, operating as the Wellcome Sanger Institute. Additional sequence generation was funded by the Department of Health and Social Care. H.S.V., J.P.G. and M.G. are supported by a grant from the Department of Health and Social Care. A.W.J., E.B. and M.G. are beneficiaries from grant NNF17OC0027594 from the Novo Nordisk Foundation. E.V. is supported by Wellcome Trust grant 220885/Z/20/Z. T.S. is supported by grant 210918/Z/18/Z, and J.H. and S.F. by grant 210758/Z/18/Z from the Wellcome Trust. H.S.V., N.D.M., A.W.J., N.G., E.B. and M.G. are supported by EMBL.
Publisher Copyright:
© 2021, The Author(s).
ASJC Scopus subject areas
- General