Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England.
Volz E., Mishra S., Chand M., Barrett JC., Johnson R., Geidelberg L., Hinsley WR., Laydon DJ., Dabrera G., O'Toole Á., Amato R., Ragonnet-Cronin M., Harrison I., Jackson B., Ariani CV., Boyd O., Loman NJ., McCrone JT., Gonçalves S., Jorgensen D., Myers R., Hill V., Jackson DK., Gaythorpe K., Groves N., Sillitoe J., Kwiatkowski DP., COVID-19 Genomics UK (COG-UK) consortium None., Flaxman S., Ratmann O., Bhatt S., Hopkins S., Gandy A., Rambaut A., Ferguson NM.
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.