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

Volz, Erik, Mishra, Swapnil, Chand, Meera, Barrett, Jeffrey C, Johnson, Robert and Geidelberg, Lily , COVID-19 Genomics UK (COG-UK) consortium (2021) Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England. Nature, 593 (7858), 266-269. (doi:10.1038/s41586-021-03470-x).

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.

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Contributors

Author: Kordo Saeed

Author: Jacqui Prieto

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