• Erik Volz, Swapnil Mishra, Meera Chand, Jeffrey C Barrett, Robert Johnson, Lily Geidelberg, Wes R Hinsley, Daniel J Laydon, Gavin Dabrera, Áine O'Toole, Robert Amato, Manon Ragonnet-Cronin, Ian Harrison, Ben Jackson, Cristina V Ariani, Olivia Boyd, Nicholas J Loman, John T McCrone, Sónia Gonçalves, David Jorgensen, Richard Myers, Verity Hill, David K Jackson, Katy Gaythorpe, Natalie Groves, John Sillitoe, Dominic P Kwiatkowski, COVID-19 Genomics UK (COG-UK) consortium, Seth Flaxman, Oliver Ratmann, Samir Bhatt, Susan Hopkins, Axel Gandy, Andrew Rambaut, and Neil M Ferguson.
• MRC Centre for Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK. e.volz@imperial.ac.uk.
• Nature. 2021 May 1; 593 (7858): 266-269.

AbstractThe SARS-CoV-2 lineage B.1.1.7, designated variant of concern (VOC) 202012/01 by Public Health England1, was first identified in the UK in late summer to early autumn 20202. Whole-genome SARS-CoV-2 sequence data collected from community-based diagnostic testing for COVID-19 show an extremely rapid expansion of the B.1.1.7 lineage during autumn 2020, suggesting that it has a selective advantage. Here we show that changes in VOC frequency inferred from genetic data correspond closely to changes inferred by S gene target failures (SGTF) in community-based diagnostic PCR testing. Analysis of trends in SGTF and non-SGTF case numbers in local areas across England shows that B.1.1.7 has higher transmissibility than non-VOC lineages, even if it has a different latent period or generation time. The SGTF data indicate a transient shift in the age composition of reported cases, with cases of B.1.1.7 including a larger share of under 20-year-olds than non-VOC cases. We estimated time-varying reproduction numbers for B.1.1.7 and co-circulating lineages using SGTF and genomic data. The best-supported models did not indicate a substantial difference in VOC transmissibility among different age groups, but all analyses agreed that B.1.1.7 has a substantial transmission advantage over other lineages, with a 50% to 100% higher reproduction number.

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