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Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK.
du Plessis, Louis; McCrone, John T; Zarebski, Alexander E; Hill, Verity; Ruis, Christopher; Gutierrez, Bernardo; Raghwani, Jayna; Ashworth, Jordan; Colquhoun, Rachel; Connor, Thomas R; Faria, Nuno R; Jackson, Ben; Loman, Nicholas J; O'Toole, Áine; Nicholls, Samuel M; Parag, Kris V; Scher, Emily; Vasylyeva, Tetyana I; Volz, Erik M; Watts, Alexander; Bogoch, Isaac I; Khan, Kamran; Aanensen, David M; Kraemer, Moritz U G; Rambaut, Andrew; Pybus, Oliver G.
  • du Plessis L; Department of Zoology, University of Oxford, Oxford, UK.
  • McCrone JT; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
  • Zarebski AE; Department of Zoology, University of Oxford, Oxford, UK.
  • Hill V; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
  • Ruis C; Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK.
  • Gutierrez B; Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
  • Raghwani J; Department of Zoology, University of Oxford, Oxford, UK.
  • Ashworth J; School of Biological and Environmental Sciences, Universidad San Francisco de Quito, Quito, Ecuador.
  • Colquhoun R; Department of Zoology, University of Oxford, Oxford, UK.
  • Connor TR; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
  • Faria NR; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
  • Jackson B; School of Biosciences, Cardiff University, Cardiff, UK.
  • Loman NJ; Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK.
  • O'Toole Á; Department of Zoology, University of Oxford, Oxford, UK.
  • Nicholls SM; MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK.
  • Parag KV; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
  • Scher E; Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK.
  • Vasylyeva TI; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
  • Volz EM; Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK.
  • Watts A; MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK.
  • Bogoch II; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
  • Khan K; Department of Zoology, University of Oxford, Oxford, UK.
  • Aanensen DM; Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada.
  • Kraemer MUG; BlueDot, Toronto, Canada.
  • Rambaut A; Department of Medicine, University of Toronto, Toronto, Canada.
  • Pybus OG; Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada.
Science ; 371(6530): 708-712, 2021 02 12.
Article in English | MEDLINE | ID: covidwho-1066806
ABSTRACT
The United Kingdom's COVID-19 epidemic during early 2020 was one of world's largest and was unusually well represented by virus genomic sampling. We determined the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 severe acute respiratory syndrome coronavirus 2 (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 quantified the size, spatiotemporal 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, whereas lineage elimination was size-dependent. We discuss the implications of our genetic perspective on transmission dynamics for COVID-19 epidemiology and control.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Genome, Viral / SARS-CoV-2 / COVID-19 Type of study: Observational study / Randomized controlled trials Limits: Humans Country/Region as subject: Europa Language: English Journal: Science Year: 2021 Document Type: Article Affiliation country: Science.abf2946

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Genome, Viral / SARS-CoV-2 / COVID-19 Type of study: Observational study / Randomized controlled trials Limits: Humans Country/Region as subject: Europa Language: English Journal: Science Year: 2021 Document Type: Article Affiliation country: Science.abf2946