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.
Competing Interest Statement
The authors have declared no competing interest.
Funding Statement
COG-UK is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) and Genome Research Limited, operating as the Wellcome Sanger Institute. The Imperial College COVID-19 Research Fund, UKRI (MR/V038109/1), The Academy of Medical Sciences (SBF004/1080), Bill & Melinda Gates Foundation (OPP1197730, OPP1175094), the European Commission (CoroNAb 101003653), the NIHR BRC Imperial College NHS Trust Infection and COVID themes (RDA02), Amazon AWS and Microsoft AI for Health, the EPSRC, The Medical Research Council (MR/R015600/1), the NIHR Health Protection Research Unit for Modelling and Health Economics, NIHR VEEPD project funding. Wellcome core funding to the Wellcome Sanger Institute (206194).
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Footnotes
Version 1 had a figure 3 missing which has been added and in SI section a link to code and data is inserted.
↵1 We calculated this as the posterior mean and 2.5-97.5 quantiles of the set of 42×6 posterior medians of the distributions (R_{S-} - R_{S+}), one per STP-week
Data Availability
All aggregated data to reproduce analysis will be provided in the url below.
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