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.
Bibliographical noteFunding 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.
- Genomic surveillance
- Public health
- Variants of concern
- Waste water monitoring