The SARS-CoV-2 lineage B.1.1.7, designated variant of concern (VOC) 202012/01 by Public Health England¹, was first identified in the UK in late summer to early autumn 2020². 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.

SARS-CoV-2 谱系 B.1.1.7 被英国公共卫生部门指定为关注变体 (VOC) 202012/01 ¹，于 2020 年夏末至初秋首次在英国被发现²。从基于社区的 COVID-19 诊断测试中收集的全基因组 SARS-CoV-2 序列数据显示，B.1.1.7 谱系在 2020 年秋季期间急剧扩张，表明其具有选择性优势。在这里，我们表明，从遗传数据推断出的 VOC 频率变化与基于社区的诊断性 PCR 检测中S基因目标失败 (SGTF)推断出的变化密切相关。对英格兰各地 SGTF 和非 SGTF 病例数趋势的分析表明，B.1.1.7 比非 VOC 谱系具有更高的传播性，即使它具有不同的潜伏期或生成时间。SGTF 数据表明报告病例的年龄构成发生了短暂变化，B.1.1.7 病例中 20 岁以下的病例所占比例高于非 VOC 病例。我们使用 SGTF 和基因组数据估计了 B.1.1.7 和共循环谱系的随时间变化的繁殖数。支持最好的模型并未表明不同年龄组之间 VOC 传播率存在显着差异，但所有分析都一致认为，B.1.1.7 比其他谱系具有显着的传播优势，繁殖数高出 50% 至 100%。