Changing composition of SARS-CoV-2 lineages and rise of Delta variant in England

The COVID-19 Genomics UK (COG-UK) consortium

doi:10.1016/j.eclinm.2021.101064

Changing composition of SARS-CoV-2 lineages and rise of Delta variant in England

The COVID-19 Genomics UK (COG-UK) consortium

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

86 Citations (Scopus)

31 Downloads (Pure)

Abstract

Background: Since its emergence in Autumn 2020, the SARS-CoV-2 Variant of Concern (VOC) B.1.1.7 (WHO label Alpha) rapidly became the dominant lineage across much of Europe. Simultaneously, several other VOCs were identified globally. Unlike B.1.1.7, some of these VOCs possess mutations thought to confer partial immune escape. Understanding when and how these additional VOCs pose a threat in settings where B.1.1.7 is currently dominant is vital.

Methods: We examine trends in the prevalence of non-B.1.1.7 lineages in London and other English regions using passive-case detection PCR data, cross-sectional community infection surveys, genomic surveillance, and wastewater monitoring. The study period spans from 31st January 2021 to 15th May 2021.

Findings: Across data sources, the percentage of non-B.1.1.7 variants has been increasing since late March 2021. This increase was initially driven by a variety of lineages with immune escape. From mid-April, B.1.617.2 (WHO label Delta) spread rapidly, becoming the dominant variant in England by late May.

Interpretation: The outcome of competition between variants depends on a wide range of factors such as intrinsic transmissibility, evasion of prior immunity, demographic specificities and interactions with non-pharmaceutical interventions. The presence and rise of non-B.1.1.7 variants in March likely was driven by importations and some community transmission. There was competition between non-B.1.17 variants which resulted in B.1.617.2 becoming dominant in April and May with considerable community transmission. Our results underscore that early detection of new variants requires a diverse array of data sources in community surveillance. Continued real-time information on the highly dynamic composition and trajectory of different SARS-CoV-2 lineages is essential to future control efforts

Funding: National Institute for Health Research, Medicines and Healthcare products Regulatory Agency, DeepMind, EPSRC, EA Funds programme, Open Philanthropy, Academy of Medical Sciences Bill,Melinda Gates Foundation, Imperial College Healthcare NHS Trust, The Novo Nordisk Foundation, MRC Centre for Global Infectious Disease Analysis, Community Jameel, Cancer Research UK, Imperial College COVID-19 Research Fund, Medical Research Council, Wellcome Sanger Institute.

Original language	English
Article number	101064
Journal	EClinicalMedicine
Volume	39
Early online date	31 Jul 2021
DOIs	https://doi.org/10.1016/j.eclinm.2021.101064
Publication status	Published - Sept 2021

Bibliographical note

Funding Information: M. Sharma reports grants from EPSRC Centre for Doctoral Training in Autonomous Intelligent Machines and Systems (EP/S024050/1) and a grant from the EA Funds programme, during the conduct of the study.

Dr. Ferguson reports grants from UK Medical Research Council, grants from UK National Institute of Health Research, grants from Community Jameel, during the conduct of the study; grants from NIH NIGMS, grants from Janssen Pharmaceuticals, grants from Bill and Melinda Gates Foundation, grants from Gavi, the Vaccine Alliance, outside the submitted work.

Dr. Gal reports grants from research grant (studentship) from GlaxoSmithKline, outside the submitted work;

National Institute for Health Research, Medicines and Healthcare products Regulatory Agency, DeepMind, EPSRC, EA Funds programme, Open Philanthropy, Academy of Medical Sciences Bill,Melinda Gates Foundation, Imperial College Healthcare NHS Trust, The Novo Nordisk Foundation, MRC Centre for Global Infectious Disease Analysis, Community Jameel, Cancer Research UK, Imperial College COVID-19 Research Fund, Medical Research Council, Wellcome Sanger Institute.

Open Access: This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/)

Publisher Copyright: © 2021 The Authors

Citation: Swapnil Mishra, Sören Mindermann, Mrinank Sharma, Charles Whittaker, Thomas A Mellan, Thomas Wilton, Dimitra Klapsa, Ryan Mate, Martin Fritzsche, Maria Zambon, Janvi Ahuja, Adam Howes, Xenia Miscouridou, Guy P Nason, Oliver Ratmann, Elizaveta Semenova, Gavin Leech, Julia Fabienne Sandkühler, Charlie Rogers-Smith, Michaela Vollmer, H Juliette T Unwin, Yarin Gal, Meera Chand, Axel Gandy, Javier Martin, Erik Volz, Neil M Ferguson, Samir Bhatt, Jan M Brauner, Seth Flaxman, Changing composition of SARS-CoV-2 lineages and rise of Delta variant in England, EClinicalMedicine, Volume 39, 2021, 101064, ISSN 2589-5370.

DOI: https://doi.org/10.1016/j.eclinm.2021.101064.

Keywords

Epidemiology
Genomic surveillance
Public health
SARS-CoV-2
Variants of concern
Waste water monitoring

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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Cite this

@article{a3bef6b9440b40d98a92a0628d71d4b3,

title = "Changing composition of SARS-CoV-2 lineages and rise of Delta variant in England",

abstract = "Background: Since its emergence in Autumn 2020, the SARS-CoV-2 Variant of Concern (VOC) B.1.1.7 (WHO label Alpha) rapidly became the dominant lineage across much of Europe. Simultaneously, several other VOCs were identified globally. Unlike B.1.1.7, some of these VOCs possess mutations thought to confer partial immune escape. Understanding when and how these additional VOCs pose a threat in settings where B.1.1.7 is currently dominant is vital. Methods: We examine trends in the prevalence of non-B.1.1.7 lineages in London and other English regions using passive-case detection PCR data, cross-sectional community infection surveys, genomic surveillance, and wastewater monitoring. The study period spans from 31st January 2021 to 15th May 2021. Findings: Across data sources, the percentage of non-B.1.1.7 variants has been increasing since late March 2021. This increase was initially driven by a variety of lineages with immune escape. From mid-April, B.1.617.2 (WHO label Delta) spread rapidly, becoming the dominant variant in England by late May. Interpretation: The outcome of competition between variants depends on a wide range of factors such as intrinsic transmissibility, evasion of prior immunity, demographic specificities and interactions with non-pharmaceutical interventions. The presence and rise of non-B.1.1.7 variants in March likely was driven by importations and some community transmission. There was competition between non-B.1.17 variants which resulted in B.1.617.2 becoming dominant in April and May with considerable community transmission. Our results underscore that early detection of new variants requires a diverse array of data sources in community surveillance. Continued real-time information on the highly dynamic composition and trajectory of different SARS-CoV-2 lineages is essential to future control efforts Funding: National Institute for Health Research, Medicines and Healthcare products Regulatory Agency, DeepMind, EPSRC, EA Funds programme, Open Philanthropy, Academy of Medical Sciences Bill,Melinda Gates Foundation, Imperial College Healthcare NHS Trust, The Novo Nordisk Foundation, MRC Centre for Global Infectious Disease Analysis, Community Jameel, Cancer Research UK, Imperial College COVID-19 Research Fund, Medical Research Council, Wellcome Sanger Institute.",

keywords = "Epidemiology, Genomic surveillance, Public health, SARS-CoV-2, Variants of concern, Waste water monitoring",

author = "{The COVID-19 Genomics UK (COG-UK) consortium} and Swapnil Mishra and S{\"o}ren Mindermann and Mrinank Sharma and Charles Whittaker and Mellan, {Thomas A.} and Thomas Wilton and Dimitra Klapsa and Ryan Mate and Martin Fritzsche and Maria Zambon and Janvi Ahuja and Adam Howes and Xenia Miscouridou and Nason, {Guy P.} and Oliver Ratmann and Elizaveta Semenova and Gavin Leech and Sandk{\"u}hler, {Julia Fabienne} and Charlie Rogers-Smith and Michaela Vollmer and Unwin, {H. Juliette T.} and Yarin Gal and Meera Chand-Kumar and Axel Gandy and Javier Martin and Erik Volz and Ferguson, {Neil M.} and Samir Bhatt and Brauner, {Jan M.} and Seth Flaxman",

note = "Funding Information: M. Sharma reports grants from EPSRC Centre for Doctoral Training in Autonomous Intelligent Machines and Systems (EP/S024050/1) and a grant from the EA Funds programme, during the conduct of the study. Dr. Ferguson reports grants from UK Medical Research Council, grants from UK National Institute of Health Research, grants from Community Jameel, during the conduct of the study; grants from NIH NIGMS, grants from Janssen Pharmaceuticals, grants from Bill and Melinda Gates Foundation, grants from Gavi, the Vaccine Alliance, outside the submitted work. Dr. Gal reports grants from research grant (studentship) from GlaxoSmithKline, outside the submitted work; National Institute for Health Research, Medicines and Healthcare products Regulatory Agency, DeepMind, EPSRC, EA Funds programme, Open Philanthropy, Academy of Medical Sciences Bill,Melinda Gates Foundation, Imperial College Healthcare NHS Trust, The Novo Nordisk Foundation, MRC Centre for Global Infectious Disease Analysis, Community Jameel, Cancer Research UK, Imperial College COVID-19 Research Fund, Medical Research Council, Wellcome Sanger Institute. Open Access: This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/) Publisher Copyright: {\textcopyright} 2021 The Authors Citation: Swapnil Mishra, S{\"o}ren Mindermann, Mrinank Sharma, Charles Whittaker, Thomas A Mellan, Thomas Wilton, Dimitra Klapsa, Ryan Mate, Martin Fritzsche, Maria Zambon, Janvi Ahuja, Adam Howes, Xenia Miscouridou, Guy P Nason, Oliver Ratmann, Elizaveta Semenova, Gavin Leech, Julia Fabienne Sandk{\"u}hler, Charlie Rogers-Smith, Michaela Vollmer, H Juliette T Unwin, Yarin Gal, Meera Chand, Axel Gandy, Javier Martin, Erik Volz, Neil M Ferguson, Samir Bhatt, Jan M Brauner, Seth Flaxman, Changing composition of SARS-CoV-2 lineages and rise of Delta variant in England, EClinicalMedicine, Volume 39, 2021, 101064, ISSN 2589-5370. DOI: https://doi.org/10.1016/j.eclinm.2021.101064.",

year = "2021",

month = sep,

doi = "10.1016/j.eclinm.2021.101064",

language = "English",

volume = "39",

journal = "EClinicalMedicine",

issn = "2589-5370",

publisher = "Elsevier",

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TY - JOUR

T1 - Changing composition of SARS-CoV-2 lineages and rise of Delta variant in England

AU - The COVID-19 Genomics UK (COG-UK) consortium

AU - Mishra, Swapnil

AU - Mindermann, Sören

AU - Sharma, Mrinank

AU - Whittaker, Charles

AU - Mellan, Thomas A.

AU - Wilton, Thomas

AU - Klapsa, Dimitra

AU - Mate, Ryan

AU - Fritzsche, Martin

AU - Zambon, Maria

AU - Ahuja, Janvi

AU - Howes, Adam

AU - Miscouridou, Xenia

AU - Nason, Guy P.

AU - Ratmann, Oliver

AU - Semenova, Elizaveta

AU - Leech, Gavin

AU - Sandkühler, Julia Fabienne

AU - Rogers-Smith, Charlie

AU - Vollmer, Michaela

AU - Unwin, H. Juliette T.

AU - Gal, Yarin

AU - Chand-Kumar, Meera

AU - Gandy, Axel

AU - Martin, Javier

AU - Volz, Erik

AU - Ferguson, Neil M.

AU - Bhatt, Samir

AU - Brauner, Jan M.

AU - Flaxman, Seth

N1 - Funding Information: M. Sharma reports grants from EPSRC Centre for Doctoral Training in Autonomous Intelligent Machines and Systems (EP/S024050/1) and a grant from the EA Funds programme, during the conduct of the study. Dr. Ferguson reports grants from UK Medical Research Council, grants from UK National Institute of Health Research, grants from Community Jameel, during the conduct of the study; grants from NIH NIGMS, grants from Janssen Pharmaceuticals, grants from Bill and Melinda Gates Foundation, grants from Gavi, the Vaccine Alliance, outside the submitted work. Dr. Gal reports grants from research grant (studentship) from GlaxoSmithKline, outside the submitted work; National Institute for Health Research, Medicines and Healthcare products Regulatory Agency, DeepMind, EPSRC, EA Funds programme, Open Philanthropy, Academy of Medical Sciences Bill,Melinda Gates Foundation, Imperial College Healthcare NHS Trust, The Novo Nordisk Foundation, MRC Centre for Global Infectious Disease Analysis, Community Jameel, Cancer Research UK, Imperial College COVID-19 Research Fund, Medical Research Council, Wellcome Sanger Institute. Open Access: This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/) Publisher Copyright: © 2021 The Authors Citation: Swapnil Mishra, Sören Mindermann, Mrinank Sharma, Charles Whittaker, Thomas A Mellan, Thomas Wilton, Dimitra Klapsa, Ryan Mate, Martin Fritzsche, Maria Zambon, Janvi Ahuja, Adam Howes, Xenia Miscouridou, Guy P Nason, Oliver Ratmann, Elizaveta Semenova, Gavin Leech, Julia Fabienne Sandkühler, Charlie Rogers-Smith, Michaela Vollmer, H Juliette T Unwin, Yarin Gal, Meera Chand, Axel Gandy, Javier Martin, Erik Volz, Neil M Ferguson, Samir Bhatt, Jan M Brauner, Seth Flaxman, Changing composition of SARS-CoV-2 lineages and rise of Delta variant in England, EClinicalMedicine, Volume 39, 2021, 101064, ISSN 2589-5370. DOI: https://doi.org/10.1016/j.eclinm.2021.101064.

PY - 2021/9

Y1 - 2021/9

N2 - Background: Since its emergence in Autumn 2020, the SARS-CoV-2 Variant of Concern (VOC) B.1.1.7 (WHO label Alpha) rapidly became the dominant lineage across much of Europe. Simultaneously, several other VOCs were identified globally. Unlike B.1.1.7, some of these VOCs possess mutations thought to confer partial immune escape. Understanding when and how these additional VOCs pose a threat in settings where B.1.1.7 is currently dominant is vital. Methods: We examine trends in the prevalence of non-B.1.1.7 lineages in London and other English regions using passive-case detection PCR data, cross-sectional community infection surveys, genomic surveillance, and wastewater monitoring. The study period spans from 31st January 2021 to 15th May 2021. Findings: Across data sources, the percentage of non-B.1.1.7 variants has been increasing since late March 2021. This increase was initially driven by a variety of lineages with immune escape. From mid-April, B.1.617.2 (WHO label Delta) spread rapidly, becoming the dominant variant in England by late May. Interpretation: The outcome of competition between variants depends on a wide range of factors such as intrinsic transmissibility, evasion of prior immunity, demographic specificities and interactions with non-pharmaceutical interventions. The presence and rise of non-B.1.1.7 variants in March likely was driven by importations and some community transmission. There was competition between non-B.1.17 variants which resulted in B.1.617.2 becoming dominant in April and May with considerable community transmission. Our results underscore that early detection of new variants requires a diverse array of data sources in community surveillance. Continued real-time information on the highly dynamic composition and trajectory of different SARS-CoV-2 lineages is essential to future control efforts Funding: National Institute for Health Research, Medicines and Healthcare products Regulatory Agency, DeepMind, EPSRC, EA Funds programme, Open Philanthropy, Academy of Medical Sciences Bill,Melinda Gates Foundation, Imperial College Healthcare NHS Trust, The Novo Nordisk Foundation, MRC Centre for Global Infectious Disease Analysis, Community Jameel, Cancer Research UK, Imperial College COVID-19 Research Fund, Medical Research Council, Wellcome Sanger Institute.

AB - Background: Since its emergence in Autumn 2020, the SARS-CoV-2 Variant of Concern (VOC) B.1.1.7 (WHO label Alpha) rapidly became the dominant lineage across much of Europe. Simultaneously, several other VOCs were identified globally. Unlike B.1.1.7, some of these VOCs possess mutations thought to confer partial immune escape. Understanding when and how these additional VOCs pose a threat in settings where B.1.1.7 is currently dominant is vital. Methods: We examine trends in the prevalence of non-B.1.1.7 lineages in London and other English regions using passive-case detection PCR data, cross-sectional community infection surveys, genomic surveillance, and wastewater monitoring. The study period spans from 31st January 2021 to 15th May 2021. Findings: Across data sources, the percentage of non-B.1.1.7 variants has been increasing since late March 2021. This increase was initially driven by a variety of lineages with immune escape. From mid-April, B.1.617.2 (WHO label Delta) spread rapidly, becoming the dominant variant in England by late May. Interpretation: The outcome of competition between variants depends on a wide range of factors such as intrinsic transmissibility, evasion of prior immunity, demographic specificities and interactions with non-pharmaceutical interventions. The presence and rise of non-B.1.1.7 variants in March likely was driven by importations and some community transmission. There was competition between non-B.1.17 variants which resulted in B.1.617.2 becoming dominant in April and May with considerable community transmission. Our results underscore that early detection of new variants requires a diverse array of data sources in community surveillance. Continued real-time information on the highly dynamic composition and trajectory of different SARS-CoV-2 lineages is essential to future control efforts Funding: National Institute for Health Research, Medicines and Healthcare products Regulatory Agency, DeepMind, EPSRC, EA Funds programme, Open Philanthropy, Academy of Medical Sciences Bill,Melinda Gates Foundation, Imperial College Healthcare NHS Trust, The Novo Nordisk Foundation, MRC Centre for Global Infectious Disease Analysis, Community Jameel, Cancer Research UK, Imperial College COVID-19 Research Fund, Medical Research Council, Wellcome Sanger Institute.

KW - Epidemiology

KW - Genomic surveillance

KW - Public health

KW - SARS-CoV-2

KW - Variants of concern

KW - Waste water monitoring

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DO - 10.1016/j.eclinm.2021.101064

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SN - 2589-5370

VL - 39

JO - EClinicalMedicine

JF - EClinicalMedicine

M1 - 101064

ER -

Changing composition of SARS-CoV-2 lineages and rise of Delta variant in England

Abstract

Bibliographical note

Keywords

UN SDGs

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