Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: Insights from linking epidemiological and genetic data

Volz, Erik; Mishra, Swapnil; Chand, Meera; Barrett, Jeffrey C; Johnson, Robert; Geidelberg, Lily; Hinsley, Wes R; Laydon, Daniel J; Dabrera, Gavin; O039, Áine; Toole,; Amato, Roberto; Ragonnet-Cronin, Manon; Harrison, Ian; Jackson, Ben; Ariani, Cristina V; Boyd, Olivia; Loman, Nick; McCrone, John T; Gonçalves, Sonia; Jorgensen, David; Myers, Richard; Hill, Verity; Jackson, David K; Gaythorpe, Katy; Groves, Natalie; Sillitoe, John; Kwiatkowski, Dominic P; COG-UK, -; Flaxman, Seth; Ratman, Oliver; Bhatt, Samir; Hopkins, Susan; Gandy, Axel; Rambaut, Andrew; Ferguson, Neil M

The SARS-CoV-2 lineage B.1.1.7, now designated Variant of Concern 202012/01 (VOC) by Public Health England, originated in the UK in late Summer to early Autumn 2020. We examine epidemiological evidence for this VOC having a transmission advantage from several perspectives. First, whole genome sequence data collected from community-based diagnostic testing provides an indication of changing prevalence of different genetic variants through time. Phylodynamic modelling additionally indicates that genetic diversity of this lineage has changed in a manner consistent with exponential growth. Second, we find 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. Third, we examine growth trends in SGTF and non-SGTF case numbers at local area level across England, and show that the VOC has higher transmissibility than non-VOC lineages, even if the VOC has a different latent period or generation time. Available SGTF data indicate a shift in the age composition of reported cases, with a larger share of under 20 year olds among reported VOC than non-VOC cases. Fourth, we assess the association of VOC frequency with independent estimates of the overall SARS-CoV-2 reproduction number through time. Finally, we fit a semi-mechanistic model directly to local VOC and non-VOC case incidence to estimate the reproduction numbers over time for each. There is a consensus among all analyses that the VOC has a substantial transmission advantage, with the estimated difference in reproduction numbers between VOC and non-VOC ranging between 0.4 and 0.7, and the ratio of reproduction numbers varying between 1.4 and 1.8. We note that these estimates of transmission advantage apply to a period where high levels of social distancing were in place in England; extrapolation to other transmission contexts therefore requires caution.