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, Nuno R. Faria, Carmen Huber, Isaac I. Bogoch, Kamran Khan, Louis 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 () and Moritz U. G. Kraemer ()
Additional contact information
John T. McCrone: University of Edinburgh
Verity Hill: University of Edinburgh
Sumali Bajaj: University of Oxford
Rosario Evans Pena: University of Oxford
Ben C. Lambert: University of Exeter
Rhys Inward: University of Oxford
Samir Bhatt: MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London
Erik Volz: MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London
Christopher Ruis: Cambridge University
Simon Dellicour: Université Libre de Bruxelles
Guy Baele: Rega Institute, KU Leuven
Alexander E. Zarebski: University of Oxford
Adam Sadilek: Google
Neo Wu: Google
Aaron Schneider: Google
Xiang Ji: Tulane University
Jayna Raghwani: University of Oxford
Ben Jackson: University of Edinburgh
Rachel Colquhoun: University of Edinburgh
Áine O’Toole: University of Edinburgh
Thomas P. Peacock: Imperial College London
Kate Twohig: UK Health Security Agency
Simon Thelwall: UK Health Security Agency
Gavin Dabrera: UK Health Security Agency
Richard Myers: UK Health Security Agency
Nuno R. Faria: University of Oxford
Carmen Huber: BlueDot
Isaac I. Bogoch: University Health Network
Kamran Khan: BlueDot
Louis Plessis: University of Oxford
Jeffrey C. Barrett: Wellcome Genome Campus
David M. Aanensen: University of Oxford
Wendy S. Barclay: Imperial College London
Meera Chand: UK Health Security Agency
Thomas Connor: Public Health Wales NHS Trust
Nicholas J. Loman: University of Birmingham
Marc A. Suchard: University of California, Los Angeles
Oliver G. Pybus: University of Oxford
Andrew Rambaut: University of Edinburgh
Moritz U. G. Kraemer: University of Oxford

Nature, 2022, vol. 610, issue 7930, 154-160

Abstract: Abstract The SARS-CoV-2 Delta (Pango lineage B.1.617.2) variant of concern spread globally, causing resurgences of COVID-19 worldwide1,2. The emergence of the Delta variant in the UK occurred on the background of a heterogeneous landscape of immunity and relaxation of non-pharmaceutical interventions. Here we analyse 52,992 SARS-CoV-2 genomes from England together with 93,649 genomes from the rest of the world 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. Using analysis of human movement, contact tracing and virus genomic data, we find that the geographic focus of the expansion of Delta shifted from India to a more global pattern in early May 2021. In England, Delta lineages were introduced more than 1,000 times and spread nationally as non-pharmaceutical interventions were relaxed. We find that hotel quarantine for travellers reduced onward transmission from importations; however, the transmission chains that later dominated the Delta wave in England were seeded before travel restrictions were introduced. Increasing inter-regional travel within England drove the nationwide dissemination of Delta, with some cities receiving more than 2,000 observable lineage introductions from elsewhere. Subsequently, increased levels of local population mixing—and not the number of importations—were associated with the faster relative spread of Delta. The invasion dynamics of Delta depended on spatial heterogeneity in contact patterns, and our findings will inform optimal spatial interventions to reduce the transmission of current and future variants of concern, such as Omicron (Pango lineage B.1.1.529).

Date: 2022
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DOI: 10.1038/s41586-022-05200-3

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