Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence

The COVID-19 Genomics UK (COG-UK) Consortium, Moritz U. G. Kraemer*, Verity Hill, Christopher Ruis, Simon Dellicour, Sumali Bajaj, John T. McCrone, Guy Baele, Kris V. Parag, Anya Lindström Battle, Bernardo Gutierrez, Ben Jackson, Rachel M. Colquhoun, Áine O'Toole, Brennan Klein, Alessandro Vespignani, Erik Volz, Nuno R. Faria, David Aanensen, Nicholas J. LomanLouis Du Plessis, Simon Cauchemez, Andrew Rambaut, Samuel V. Scarpino*, Oliver G. Pybus*, Matthew Bashton, Andrew Nelson, Greg Young, Darren Smith, Clare McCann

*Corresponding author for this work

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Abstract

Understanding the causes and consequences of the emergence of SARS-CoV-2 variants of concern is crucial to pandemic control yet difficult to achieve, as they arise in the context of variable human behavior and immunity. We investigate the spatial invasion dynamics of lineage B.1.1.7 by jointly analyzing UK human mobility, virus genomes, and community-based PCR data. We identify a multi-stage spatial invasion process in which early B.1.1.7 growth rates were associated with mobility and asymmetric lineage export from a dominant source location, enhancing the effects of B.1.1.7’s increased intrinsic transmissibility. We further explore how B.1.1.7 spread was shaped by non-pharmaceutical interventions and spatial variation in previous attack rates. Our findings show that careful accounting of the behavioral and epidemiological context within which variants of concern emerge is necessary to interpret correctly their observed relative growth rates.
Original languageEnglish
Article numbereabj0113
JournalScience
Early online date22 Jul 2021
DOIs
Publication statusE-pub ahead of print - 22 Jul 2021

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