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

The Wellcome Sanger Institute Covid-19 Surveillance Team; The COVID-19 Genomics UK (COG-UK) consortium; Harald S. Vöhringer; Theo Sanderson; Matthew Sinnott; Nicola De Maio; Thuy Nguyen; Richard Goater; Frank Schwach; Ian Harrison; Joel Hellewell; Cristina V. Ariani; Sonia Gonçalves; David K. Jackson; Ian Johnston; Alexander W. Jung; Callum Saint; John Sillitoe; Maria Suciu; Nick Goldman; Jasmina Panovska-Griffiths; Ewan Birney; Erik Volz; Sebastian Funk; Dominic Kwiatkowski; Meera Chand; Inigo Martincorena; Jeffrey C. Barrett; Moritz Gerstung

doi:10.1038/s41586-021-04069-y

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

The Wellcome Sanger Institute Covid-19 Surveillance Team, The COVID-19 Genomics UK (COG-UK) consortium, Harald S. Vöhringer, Theo Sanderson, Matthew Sinnott, Nicola De Maio, Thuy Nguyen, Richard Goater, Frank Schwach, Ian Harrison, Joel Hellewell, Cristina V. Ariani, Sonia Gonçalves, David K. Jackson, Ian Johnston, Alexander W. Jung, Callum Saint, John Sillitoe, Maria Suciu, Nick GoldmanJasmina Panovska-Griffiths, Ewan Birney, Erik Volz, Sebastian Funk, Dominic Kwiatkowski, Meera Chand, Inigo Martincorena, Jeffrey C. Barrett, Moritz Gerstung^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

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Abstract

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.

Original language	English
Pages (from-to)	506-511
Number of pages	6
Journal	Nature
Volume	600
Issue number	7889
Early online date	14 Oct 2021
DOIs	https://doi.org/10.1038/s41586-021-04069-y
Publication status	Published - 16 Dec 2021

Bibliographical note

Funding Information: Open access funding provided by Deutsches Krebsforschungszentrum (DKFZ).

Open Access: This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

Publisher Copyright: © 2021, The Author(s), under exclusive licence to Springer Nature Limited.

Citation: Vöhringer, H.S., Sanderson, T., Sinnott, M. et al. Genomic reconstruction of the SARS-CoV-2 epidemic in England. Nature 600, 506–511 (2021). https://doi.org/10.1038/s41586-021-04069-y

DOI: https://doi.org/10.1038/s41586-021-04069-y

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Vöhringer2021GenomicReconstructionOfTheSARS-CoV-2EpidemicInEnglandNatureFinal published version, 12.7 MBLicence: CC BY

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The Wellcome Sanger Institute Covid-19 Surveillance Team, The COVID-19 Genomics UK (COG-UK) consortium, Vöhringer, H. S., Sanderson, T., Sinnott, M., De Maio, N., Nguyen, T., Goater, R., Schwach, F., Harrison, I., Hellewell, J., Ariani, C. V., Gonçalves, S., Jackson, D. K., Johnston, I., Jung, A. W., Saint, C., Sillitoe, J., Suciu, M., ... Gerstung, M. (2021). Genomic reconstruction of the SARS-CoV-2 epidemic in England. Nature, 600(7889), 506-511. https://doi.org/10.1038/s41586-021-04069-y

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abstract = "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.",

author = "{The Wellcome Sanger Institute Covid-19 Surveillance Team} and {The COVID-19 Genomics UK (COG-UK) consortium} and V{\"o}hringer, {Harald S.} and Theo Sanderson and Matthew Sinnott and {De Maio}, Nicola and Thuy Nguyen and Richard Goater and Frank Schwach and Ian Harrison and Joel Hellewell and Ariani, {Cristina V.} and Sonia Gon{\c c}alves and Jackson, {David K.} and Ian Johnston and Jung, {Alexander W.} and Callum Saint and John Sillitoe and Maria Suciu and Nick Goldman and Jasmina Panovska-Griffiths and Ewan Birney and Erik Volz and Sebastian Funk and Dominic Kwiatkowski and Meera Chand and Inigo Martincorena and Barrett, {Jeffrey C.} and Moritz Gerstung",

note = "Funding Information: Open access funding provided by Deutsches Krebsforschungszentrum (DKFZ). Open Access: This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article{\textquoteright}s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article{\textquoteright}s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. Publisher Copyright: {\textcopyright} 2021, The Author(s), under exclusive licence to Springer Nature Limited. Citation: V{\"o}hringer, H.S., Sanderson, T., Sinnott, M. et al. Genomic reconstruction of the SARS-CoV-2 epidemic in England. Nature 600, 506–511 (2021). https://doi.org/10.1038/s41586-021-04069-y DOI: https://doi.org/10.1038/s41586-021-04069-y",

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The Wellcome Sanger Institute Covid-19 Surveillance Team, The COVID-19 Genomics UK (COG-UK) consortium, Vöhringer, HS, Sanderson, T, Sinnott, M, De Maio, N, Nguyen, T, Goater, R, Schwach, F, Harrison, I, Hellewell, J, Ariani, CV, Gonçalves, S, Jackson, DK, Johnston, I, Jung, AW, Saint, C, Sillitoe, J, Suciu, M, Goldman, N, Panovska-Griffiths, J, Birney, E, Volz, E, Funk, S, Kwiatkowski, D, Chand, M, Martincorena, I, Barrett, JC & Gerstung, M 2021, 'Genomic reconstruction of the SARS-CoV-2 epidemic in England', Nature, vol. 600, no. 7889, pp. 506-511. https://doi.org/10.1038/s41586-021-04069-y

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AU - Sanderson, Theo

AU - Sinnott, Matthew

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N2 - 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.

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

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