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Genomic reconstruction of the SARS-CoV-2 epidemic in England.
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.
  • Vöhringer HS; European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK.
  • Sanderson T; Wellcome Sanger Institute, Hinxton, UK.
  • Sinnott M; The Francis Crick Institute, London, UK.
  • De Maio N; Wellcome Sanger Institute, Hinxton, UK.
  • Nguyen T; European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK.
  • Goater R; Wellcome Sanger Institute, Hinxton, UK.
  • Schwach F; Wellcome Sanger Institute, Hinxton, UK.
  • Harrison I; Wellcome Sanger Institute, Hinxton, UK.
  • Hellewell J; Public Health England, London, UK.
  • Ariani CV; Public Health England, London, UK.
  • Gonçalves S; London School of Hygiene & Tropical Medicine, London, UK.
  • Jackson DK; Wellcome Sanger Institute, Hinxton, UK.
  • Johnston I; Wellcome Sanger Institute, Hinxton, UK.
  • Jung AW; Wellcome Sanger Institute, Hinxton, UK.
  • Saint C; Wellcome Sanger Institute, Hinxton, UK.
  • Sillitoe J; European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK.
  • Suciu M; Wellcome Sanger Institute, Hinxton, UK.
  • Goldman N; Wellcome Sanger Institute, Hinxton, UK.
  • Panovska-Griffiths J; Wellcome Sanger Institute, Hinxton, UK.
  • Funk S; European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK.
  • Kwiatkowski D; MRC Centre for Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK.
  • Chand M; London School of Hygiene & Tropical Medicine, London, UK.
  • Martincorena I; Wellcome Sanger Institute, Hinxton, UK.
  • Barrett JC; Public Health England, London, UK.
  • Gerstung M; Guy's and St Thomas' NHS Foundation Trust, London, UK.
Nature ; 600(7889): 506-511, 2021 12.
Article in English | MEDLINE | ID: covidwho-1467111
Preprint
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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.
Subject(s)

Full text: Available Collection: International databases Database: MEDLINE Main subject: Genome, Viral / Genomics / SARS-CoV-2 / COVID-19 Type of study: Observational study Topics: Variants Limits: Humans Country/Region as subject: Europa Language: English Journal: Nature Year: 2021 Document Type: Article Affiliation country: S41586-021-04069-y

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Genome, Viral / Genomics / SARS-CoV-2 / COVID-19 Type of study: Observational study Topics: Variants Limits: Humans Country/Region as subject: Europa Language: English Journal: Nature Year: 2021 Document Type: Article Affiliation country: S41586-021-04069-y