Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: Insights from linking epidemiological and genetic data | medRxiv preprints (not peer reviewed)

Type Journal Article Author Erik Volz Author Swapnil Mishra Author Meera Chand Author Jeffrey C. Barrett Author Robert Johnson Author Lily Geidelberg Author Wes R. Hinsley Author Daniel J. Laydon Author Gavin Dabrera Author Áine O’Toole Author Roberto Amato Author Manon Ragonnet-Cronin Author Ian Harrison Author Ben Jackson Author Cristina V. Ariani Author Olivia Boyd Author Nicholas J. Loman Author John T. McCrone Author Sónia Gonçalves Author David Jorgensen Author Richard Myers Author Verity Hill Author David K. Jackson Author Katy Gaythorpe Author Natalie Groves Author John Sillitoe Author Dominic P. Kwiatkowski Author The COVID-19 Genomics UK (COG-UK) Consortium Author Seth Flaxman Author Oliver Ratmann Author Samir Bhatt Author Susan Hopkins Author Axel Gandy Author Andrew Rambaut Author Neil M. Ferguson URL https://www.medrxiv.org/content/10.1101/2020.12.30.20249034v2 Rights © 2021, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/ Pages 2020.12.30.20249034 Publication medRxiv Date 04/01/2021 Extra Publisher: Cold Spring Harbor Laboratory Press DOI 10.1101/2020.12.30.20249034 Library Catalog www.medrxiv.org Language en Abstract 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. Short Title Transmission of SARS-CoV-2 Lineage B.1.1.7 in England