Genomic reconstruction of the SARS-CoV-2 epidemic in England

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 diffe...

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Bibliographic Details
Published in:	Nature (London) Vol. 600; no. 7889; pp. 506 - 511
Main Authors:	Vöhringer, Harald S., Sanderson, Theo, Sinnott, Matthew, De Maio, Nicola, Nguyen, Thuy, Goater, Richard, Schwach, Frank, Harrison, Ian, Hellewell, Joel, Ariani, Cristina V., Gonçalves, Sonia, Jackson, David K., Johnston, Ian, Jung, Alexander W., Saint, Callum, Sillitoe, John, Suciu, Maria, Goldman, Nick, Panovska-Griffiths, Jasmina, Birney, Ewan, Volz, Erik, Funk, Sebastian, Kwiatkowski, Dominic, Chand, Meera, Martincorena, Inigo, Barrett, Jeffrey C., Gerstung, Moritz
Format:	Journal Article
Language:	English
Published:	London Nature Publishing Group UK 16-12-2021 Nature Publishing Group
Subjects:	45 631/181/2474 631/326/596/4130 692/308/174 692/699/255/2514 Amino Acid Substitution Consortia Coronaviruses COVID-19 COVID-19 - epidemiology COVID-19 - transmission COVID-19 - virology Disease transmission Distribution England - epidemiology Epidemics Epidemiological Monitoring Epidemiology Forecasts and trends Genetic aspects Genome, Viral - genetics Genomes Genomics Humanities and Social Sciences Humans International travel Molecular Epidemiology multidisciplinary Mutation Quarantine - statistics & numerical data SARS-CoV-2 - classification SARS-CoV-2 - genetics Science Science (multidisciplinary) Severe acute respiratory syndrome coronavirus 2 Spatio-Temporal Analysis Spike Glycoprotein, Coronavirus - genetics United Kingdom Viral diseases England United Kingdom United Kingdom > UK Europe
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Summary:	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. A study of the evolution of the SARS-CoV-2 virus in England between September 2020 and June 2021 finds that interventions capable of containing previous variants were insufficient to stop the more transmissible Alpha and Delta variants.
ISSN:	0028-0836 1476-4687
DOI:	10.1038/s41586-021-04069-y