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

谱系(遗传) 传输(电信) 生物 基本再生数 严重急性呼吸综合征冠状病毒2型(SARS-CoV-2) 流行病学 人口学 进化生物学 2019年冠状病毒病(COVID-19) 遗传学 基因 医学 疾病 计算机科学 传染病(医学专业) 社会学 病理 人口 内科学 电信
作者
Erik Volz,Swapnil Mishra,Meera Chand,Jeffrey C. Barrett,Robert A. Johnson,Lily Geidelberg,Wes Hinsley,Daniel J. Laydon,Gavin Dabrera,Áine O’Toole,Roberto Amato,Manon Ragonnet‐Cronin,Ian Harrison,Ben Jackson,Cristina V. Ariani,Olivia Boyd,Nicholas J. Loman,John McCrone,Sónia Gonçalves,David A. Jorgensen,Richard Myers,Verity Hill,David Jackson,Katy A. M. Gaythorpe,Natalie Groves,John Sillitoe,Dominic Kwiatkowski,Cog-Uk,Seth Flaxman,Oliver Ratman,Samir Bhatt,Susan Hopkins,Axel Gandy,Andrew Rambaut,Neil Ferguson
出处
期刊:Cold Spring Harbor Laboratory - medRxiv 被引量:394
标识
DOI:10.1101/2020.12.30.20249034
摘要

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.
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