Genomic reconstruction of the SARS-CoV-2 epidemic in England

被引:57
作者
Vohringer, Harald S. [1 ]
Sanderson, Theo [2 ,3 ]
Sinnott, Matthew [2 ]
De Maio, Nicola [1 ]
Thuy Nguyen [2 ]
Goater, Richard [2 ]
Schwach, Frank [2 ,4 ]
Harrison, Ian [4 ]
HeHowells, Joel [5 ]
Ariani, Cristina, V [2 ]
Goncalves, Sonia [2 ]
Jackson, David K. [2 ]
Johnstone, Ian [2 ]
Jung, Alexander W. [1 ]
Saint, Callum [2 ]
Sillitoe, John [2 ]
Suciu, Maria [2 ]
Goldman, Nick [1 ]
Panovska-Griffiths, Jasmine [6 ]
Birney, Ewan [1 ]
Volz, Erik [7 ]
Funk, Sebastian [5 ]
Kwiatkowski, Dominic [2 ]
Chand, Meera [4 ,8 ]
Martincorena, Inigo [2 ]
Barrett, Jeffrey C. [2 ]
Gerstung, Moritz [1 ,9 ]
机构
[1] European Bioinformat Inst EMBL EBI, European Mol Biol Lab, Hinxton, England
[2] Wellcome Sanger Inst, Hinxton, England
[3] Francis Crick Inst, London, England
[4] Publ Hlth England, London, England
[5] London Sch Hyg & Trop Med, London, England
[6] Univ Oxford, Big Data Inst, Nuffield Dept Med, Oxford, England
[7] Imperial Coll London, MRC Ctr Global Infect Dis Anal, Jameel Inst Dis & Emergency Analyt, London, England
[8] Guys & St Thomas NHS Fdn Trust, London, England
[9] German Canc Res Ctr, Div AI Oncol, Heidelberg, Germany
基金
英国惠康基金; 英国医学研究理事会;
关键词
RECEPTOR-BINDING DOMAIN; DYNAMICS; TRANSMISSION; MUTATIONS; COVID-19; REVEALS; B.1.1.7; MODEL;
D O I
10.1038/s41586-021-04069-y
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
The evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus leads to new variants that warrant timely epidemiological characterization. Here we use the dense genomic surveillance data generated by the COVID-19 Genomics UK Consortium to reconstruct the dynamics of 71 different lineages in each of 315 English local authorities between September 2020 and June 2021. This analysis reveals a series of subepidemics that peaked in early autumn 2020, followed by a jump in transmissibility of the B.1.1.7/Alpha lineage. The Alpha variant grew when other lineages declined during the second national lockdown and regionally tiered restrictions between November and December 2020. A third more stringent national lockdown suppressed the Alpha variant and eliminated nearly all other lineages in early 2021. Yet a series of variants (most of which contained the spike E484K mutation) defied these trends and persisted at moderately increasing proportions. However, by accounting for sustained introductions, we found that the transmissibility of these variants is unlikely to have exceeded the transmissibility of the Alpha variant. Finally, B.1.617.2/Delta was repeatedly introduced in England and grew rapidly in early summer 2021, constituting approximately 98% of sampled SARS-CoV-2 genomes on 26 June 2021.
引用
收藏
页码:506 / +
页数:23
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