Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England
Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England
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DOI：
10.1038/s41586-021-03470-x
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发表时间：
2021-03-25
期刊：
影响因子：
64.8
通讯作者：
Ferguson, Neil M.
中科院分区：
文献类型：
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作者：
Volz, Erik;Mishra, Swapnil;Ferguson, Neil M.
来自英格兰的遗传和检测数据表明，关注的B.1.1.7的SARS-CoV-2变体比其他谱系具有传播优势。SARS-CoV-2谱系B.1.1.7，被英格兰公共卫生部指定为关注变体（VOC） 2012012 /01(1)，于2020年夏末至秋初在英国首次发现(2)。从基于社区的COVID-19诊断检测中收集的全基因组SARS-CoV-2序列数据显示，2020年秋季，B.1.1.7谱系的扩张速度极快，这表明它具有选择优势。本研究表明，从遗传数据推断的VOC频率变化与社区诊断PCR检测中S基因靶失败（SGTF）推断的变化密切相关。对英格兰地区SGTF和非SGTF病例数趋势的分析表明，B.1.1.7比非voc谱系具有更高的传性，即使它具有不同的潜伏期或世代时间。SGTF数据表明，报告病例的年龄构成发生了短暂变化，与非voc病例相比，B.1.1.7病例中20岁以下的比例更大。我们使用SGTF和基因组数据估计了B.1.1.7和共循环谱系随时间变化的繁殖数。最受支持的模型并没有显示VOC在不同年龄组之间的传播率有实质性的差异，但所有的分析都一致认为，B.1.1.7比其他血统具有明显的传播优势，其繁殖数量高出50%至100%。
Genetic and testing data from England show that the SARS-CoV-2 variant of concern B.1.1.7 has a transmission advantage over other lineages.The SARS-CoV-2 lineage B.1.1.7, designated variant of concern (VOC) 202012/01 by Public Health England(1), was first identified in the UK in late summer to early autumn 2020(2). 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.