The UK's COVID-19 epidemic during early 2020 was one of world's largest and unusually well represented by virus genomic sampling. Here we reveal the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 SARS-CoV-2 genomes, including 26,181 from the UK sampled throughout the country's first wave of infection. Using large-scale phylogenetic analyses, combined with epidemiological and travel data, we quantify the size, spatio-temporal origins and persistence of genetically-distinct UK transmission lineages. Rapid fluctuations in virus importation rates resulted in >1000 lineages; those introduced prior to national lockdown tended to be larger and more dispersed. Lineage importation and regional lineage diversity declined after lockdown, while lineage elimination was size-dependent. We discuss the implications of our genetic perspective on transmission dynamics for COVID-19 epidemiology and control.

中文翻译：

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英国 SARS-CoV-2 流行病的建立和谱系动态

2020 年初，英国爆发的新冠肺炎 (COVID-19) 疫情是全球规模最大的疫情之一，病毒基因组采样的结果异常出色。在这里，我们通过分析 50,887 个 SARS-CoV-2 基因组（其中包括从英国在全国第一波感染中采样的 26,181 个基因组）揭示了这种流行病的精细遗传谱系结构。通过大规模系统发育分析，结合流行病学和旅行数据，我们量化了遗传上不同的英国传播谱系的规模、时空起源和持久性。病毒输入率的快速波动导致了超过 1000 个谱系；在全国封锁之前引入的措施往往规模更大、更分散。封锁后，谱系输入和区域谱系多样性下降，而谱系消除则取决于规模。我们讨论了我们的遗传观点对传播动力学对 COVID-19 流行病学和控制的影响。