Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England

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 JorgensenRichard Myers, Verity Hill, David K. Jackson, Katy Gaythorpe, Natalie Groves, John Sillitoe, Dominic P. Kwiatkowski, Cherian Koshy, Amy Ash, Emma Wise, Nathan Moore, Matilde Mori, Nick Cortes, Jessica Lynch, Stephen Kidd, Derek J. Fairley, Tanya Curran, James P. McKenna, Helen Adams, Christophe Fraser, The COVID-19 Genomics UK (COG-UK) Consortium, Darren L. Smith, Matthew Bashton, Gregory R. Young, Andrew Nelson, Clare M. McCann, Wen C. Yew, Hannah Jones, Seth Flaxman, Oliver Ratmann, Samir Bhatt, Susan Hopkins, Axel Gandy, Andrew Rambaut, Neil M. Ferguson*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

81 Citations (Scopus)

Abstract

The 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.

Original languageEnglish
Pages (from-to)266-269
Number of pages4
JournalNature
Volume593
Issue number7858
Early online date25 Mar 2021
DOIs
Publication statusPublished - 13 May 2021

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