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

Harald S. Vöhringer, Theo Sanderson, Matthew Sinnott, Nicola Maio, Thuy Nguyen, Richard Goater, Frank Schwach, Ian Harrison, Joel Hellewell, Cristina V. Ariani, Sonia Gonçalves, David K. Jackson, Ian Johnston, Alexander W. Jung, Callum Saint, John Sillitoe, Maria Suciu, Nick Goldman, Jasmina Panovska-Griffiths, Ewan Birney, Erik Volz, Sebastian Funk, Dominic Kwiatkowski, Meera Chand, Inigo Martincorena, Jeffrey C. Barrett () and Moritz Gerstung ()
Additional contact information
Harald S. Vöhringer: European Bioinformatics Institute EMBL-EBI
Theo Sanderson: Wellcome Sanger Institute
Matthew Sinnott: Wellcome Sanger Institute
Nicola Maio: European Bioinformatics Institute EMBL-EBI
Thuy Nguyen: Wellcome Sanger Institute
Richard Goater: Wellcome Sanger Institute
Frank Schwach: Wellcome Sanger Institute
Ian Harrison: Public Health England
Joel Hellewell: London School of Hygiene & Tropical Medicine
Cristina V. Ariani: Wellcome Sanger Institute
Sonia Gonçalves: Wellcome Sanger Institute
David K. Jackson: Wellcome Sanger Institute
Ian Johnston: Wellcome Sanger Institute
Alexander W. Jung: European Bioinformatics Institute EMBL-EBI
Callum Saint: Wellcome Sanger Institute
John Sillitoe: Wellcome Sanger Institute
Maria Suciu: Wellcome Sanger Institute
Nick Goldman: European Bioinformatics Institute EMBL-EBI
Jasmina Panovska-Griffiths: University of Oxford
Ewan Birney: European Bioinformatics Institute EMBL-EBI
Erik Volz: Imperial College London
Sebastian Funk: London School of Hygiene & Tropical Medicine
Dominic Kwiatkowski: Wellcome Sanger Institute
Meera Chand: Public Health England
Inigo Martincorena: Wellcome Sanger Institute
Jeffrey C. Barrett: Wellcome Sanger Institute
Moritz Gerstung: European Bioinformatics Institute EMBL-EBI

Nature, 2021, vol. 600, issue 7889, 506-511

Abstract: 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.

Date: 2021
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DOI: 10.1038/s41586-021-04069-y

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