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Context-specific emergence and growth of the SARS-CoV-2 Delta variant
John T. McCrone; Verity Hill; Sumali Bajaj; Rosario Evans Pena; Ben C. Lambert; Rhys Inward; Samir Bhatt; Erik Volz; Christopher Ruis; Simon Dellicour; Guy Baele; Alexander E. Zarebski; Adam Sadilek; Neo Wu; Aaron Schneider; Xiang Ji; Jayna Raghwani; Ben Jackson; Rachel Colquhoun; Áine O'Toole; Thomas P. Peacock; Kate Twohig; Simon Thelwall; Gavin Dabrera; Richard Myers; - The COVID-19 genomics UK (COG-UK) consortium; Nuno R. Faria; Carmen Huber; Isaac I. Bogoch; Kamran Khan; Louis du Plessis; Jeffrey C. Barrett; David M. Aanensen; Wendy S. Barclay; Meera Chand; Thomas Connor; Nicholas J. Loman; Marc A. Suchard; Oliver G. Pybus; Andrew Rambaut; Moritz U.G. Kraemer.
  • John T. McCrone; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
  • Verity Hill; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
  • Sumali Bajaj; Department of Zoology, University of Oxford, Oxford, UK
  • Rosario Evans Pena; Department of Zoology, University of Oxford, Oxford, UK
  • Ben C. Lambert; Department of Computer Science, University of Oxford, Oxford, UK
  • Rhys Inward; Department of Zoology, University of Oxford, Oxford, UK & MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics
  • Samir Bhatt; MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK & 5. Section of Epid
  • Erik Volz; MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
  • Christopher Ruis; Molecular Immunity Unit, Department of Medicine, Cambridge University, Cambridge, UK
  • Simon Dellicour; Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium & Department of Microbiology, Immunology and Transplantation, Rega Institute
  • Guy Baele; Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
  • Alexander E. Zarebski; Department of Zoology, University of Oxford, Oxford, UK
  • Adam Sadilek; Google, Mountain View, CA, USA
  • Neo Wu; Google, Mountain View, CA, USA
  • Aaron Schneider; Google, Mountain View, CA, USA
  • Xiang Ji; Department of Mathematics, School of Science & Engineering, Tulane University, New Orleans, LA, USA
  • Jayna Raghwani; Department of Zoology, University of Oxford, Oxford, UK
  • Ben Jackson; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
  • Rachel Colquhoun; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
  • Áine O'Toole; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
  • Thomas P. Peacock; Department of Infectious Disease, Imperial College London, London, UK & UK Health Security Agency, London, UK
  • Kate Twohig; UK Health Security Agency, London, UK
  • Simon Thelwall; UK Health Security Agency, London, UK
  • Gavin Dabrera; UK Health Security Agency, London, UK
  • Richard Myers; UK Health Security Agency, London, UK
  • - The COVID-19 genomics UK (COG-UK) consortium;
  • Nuno R. Faria; Department of Zoology, University of Oxford, Oxford, UK & MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics
  • Carmen Huber; BlueDot, Toronto, Canada
  • Isaac I. Bogoch; Divisions of Internal Medicine & Infectious Diseases, Toronto General Hospital, University Health Network, Toronto, Canada & 16. Department of Medicine, Divisio
  • Kamran Khan; BlueDot, Toronto, Canada & Divisions of Internal Medicine & Infectious Diseases, Toronto General Hospital, University Health Network, Toronto, Canada & Departme
  • Louis du Plessis; Department of Zoology, University of Oxford, Oxford, UK
  • Jeffrey C. Barrett; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
  • David M. Aanensen; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK & Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Departmen
  • Wendy S. Barclay; Department of Infectious Disease, Imperial College London, London, UK
  • Meera Chand; UK Health Security Agency, London, UK
  • Thomas Connor; Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK & School of Biosciences, The Sir Martin Evans Building, Cardiff University, Cardiff, UK & Qu
  • Nicholas J. Loman; Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
  • Marc A. Suchard; Departments of Biostatistics, Biomathematics and Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
  • Oliver G. Pybus; Department of Zoology, University of Oxford, Oxford, UK & Department of Pathobiology and Population Sciences, Royal Veterinary College London, London, UK
  • Andrew Rambaut; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
  • Moritz U.G. Kraemer; Department of Zoology, University of Oxford, Oxford, UK
Preprint in English | medRxiv | ID: ppmedrxiv-21267606
ABSTRACT
The Delta variant of concern of SARS-CoV-2 has spread globally causing large outbreaks and resurgences of COVID-19 cases1-3. The emergence of Delta in the UK occurred on the background of a heterogeneous landscape of immunity and relaxation of non-pharmaceutical interventions4,5. Here we analyse 52,992 Delta genomes from England in combination with 93,649 global genomes to reconstruct the emergence of Delta, and quantify its introduction to and regional dissemination across England, in the context of changing travel and social restrictions. Through analysis of human movement, contact tracing, and virus genomic data, we find that the focus of geographic expansion of Delta shifted from India to a more global pattern in early May 2021. In England, Delta lineages were introduced >1,000 times and spread nationally as non-pharmaceutical interventions were relaxed. We find that hotel quarantine for travellers from India reduced onward transmission from importations; however the transmission chains that later dominated the Delta wave in England had been already seeded before restrictions were introduced. In England, increasing inter-regional travel drove Deltas nationwide dissemination, with some cities receiving >2,000 observable lineage introductions from other regions. Subsequently, increased levels of local population mixing, not the number of importations, was associated with faster relative growth of Delta. Among US states, we find that regions that previously experienced large waves also had faster Delta growth rates, and a model including interactions between immunity and human behaviour could accurately predict the rise of Delta there. Deltas invasion dynamics depended on fine scale spatial heterogeneity in immunity and contact patterns and our findings will inform optimal spatial interventions to reduce transmission of current and future VOCs such as Omicron.
Full text: Available Collection: Preprints Database: medRxiv Type of study: Prognostic study Topics: Variants Language: English Year: 2021 Document Type: Preprint

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Full text: Available Collection: Preprints Database: medRxiv Type of study: Prognostic study Topics: Variants Language: English Year: 2021 Document Type: Preprint