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, Meera
AU - Gandy, Axel
AU - Martin, Javier
AU - Volz, Erik
AU - Ferguson, Neil M.
AU - Bhatt, Samir
AU - Brauner, Jan M.
AU - Flaxman, Seth
AU - Bashton, Matthew
AU - Smith, Darren
AU - Nelson, Andrew
AU - Young, Greg
AU - McCann, Clare
N1 - Funding information:
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.
Matthew Bashton, Andrew Nelson, Darren Smith, Greg Young are members of the COVID-19 Genomics UK (COG-UK) consortium.
PY - 2021/9/1
Y1 - 2021/9/1
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
UR - http://www.scopus.com/inward/record.url?scp=85111520377&partnerID=8YFLogxK
U2 - 10.1016/j.eclinm.2021.101064
DO - 10.1016/j.eclinm.2021.101064
M3 - Article
AN - SCOPUS:85111520377
SN - 2589-5370
VL - 39
JO - EClinicalMedicine
JF - EClinicalMedicine
M1 - 101064
ER -