Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK

doi:10.1126/science.abf2946

GSTDTAP > 气候变化

DOI	10.1126/science.abf2946
	Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK
	Louis du Plessis; John T. McCrone; Alexander E. Zarebski; Verity Hill; Christopher Ruis; Bernardo Gutierrez; Jayna Raghwani; Jordan Ashworth; Rachel Colquhoun; Thomas R. Connor; Nuno R. Faria; Ben Jackson; Nicholas J. Loman; Áine O’Toole; Samuel M. Nicholls; Kris V. Parag; Emily Scher; Tetyana I. Vasylyeva; Erik M. Volz; Alexander Watts; Isaac I. Bogoch; Kamran Khan; COVID-19 Genomics UK Consortium†; David M. Aanensen; Moritz U. G. Kraemer; Andrew Rambaut; Oliver G. Pybus
	2021-02-12
发表期刊	Science
出版年	2021
英文摘要	The scale of genome-sequencing efforts for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is unprecedented. The United Kingdom has contributed more than 26,000 sequences to this effort. This volume of data allowed du Plessis et al. to develop a detailed picture of the influxes of virus reaching U.K. shores as the pandemic developed during the first months of 2020 (see the Perspective by Nelson). Before lockdown, high travel volumes and few restrictions on international travel allowed more than 1000 lineages to become established. This accelerated local epidemic growth and exceeded contact tracing capacity. The authors were able to quantify the abundance, size distribution, and spatial range of the lineages that were transmitted. Transmission was highly heterogeneous, favoring some lineages that became widespread and subsequently harder to eliminate. This dire history indicates that rapid or even preemptive responses should have been used as they were elsewhere where containment was successful. Science , this issue p. [708][1]; see also p. [680][2] The United Kingdom’s COVID-19 epidemic during early 2020 was one of world’s largest and was unusually well represented by virus genomic sampling. We determined the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 severe acute respiratory syndrome coronavirus 2 (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 quantified the size, spatiotemporal 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, whereas lineage elimination was size-dependent. We discuss the implications of our genetic perspective on transmission dynamics for COVID-19 epidemiology and control. [1]: /lookup/doi/10.1126/science.abf2946 [2]: /lookup/doi/10.1126/science.abg2297
领域	气候变化 ; 资源环境
URL	查看原文
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文献类型	期刊论文
条目标识符	http://119.78.100.173/C666/handle/2XK7JSWQ/314086
专题	气候变化资源环境科学
推荐引用方式 GB/T 7714	Louis du Plessis,John T. McCrone,Alexander E. Zarebski,et al. Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK[J]. Science,2021.
APA	Louis du Plessis.,John T. McCrone.,Alexander E. Zarebski.,Verity Hill.,Christopher Ruis.,...&Oliver G. Pybus.(2021).Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK.Science.
MLA	Louis du Plessis,et al."Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK".Science (2021).