SARS-CoV-2 lineage dynamics in England from September to November 2021:high diversity of Delta sub-lineages and increased transmissibility of AY.4.2

Eales, Oliver, Page, Andrew J., de Oliveira Martins, Leonardo, Wang, Haowei, Bodinier, Barbara, Haw, David, Jonnerby, Jakob, Atchison, Christina, The COVID-19 Genomics UK (COG-UK) Consortium, Ashby, Deborah, Barclay, Wendy, Taylor, Graham, Cooke, Graham, Ward, Helen, Darzi, Ara, Riley, Steven, Chadeau-Hyam, Marc, Donnelly, Christl A. and Elliott, Paul (2022) SARS-CoV-2 lineage dynamics in England from September to November 2021:high diversity of Delta sub-lineages and increased transmissibility of AY.4.2. BMC Infectious Diseases, 22 (1). ISSN 1471-2334

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Abstract

Background: Since the emergence of SARS-CoV-2, evolutionary pressure has driven large increases in the transmissibility of the virus. However, with increasing levels of immunity through vaccination and natural infection the evolutionary pressure will switch towards immune escape. Genomic surveillance in regions of high immunity is crucial in detecting emerging variants that can more successfully navigate the immune landscape. Methods: We present phylogenetic relationships and lineage dynamics within England (a country with high levels of immunity), as inferred from a random community sample of individuals who provided a self-administered throat and nose swab for rt-PCR testing as part of the REal-time Assessment of Community Transmission-1 (REACT-1) study. During round 14 (9 September–27 September 2021) and 15 (19 October–5 November 2021) lineages were determined for 1322 positive individuals, with 27.1% of those which reported their symptom status reporting no symptoms in the previous month. Results: We identified 44 unique lineages, all of which were Delta or Delta sub-lineages, and found a reduction in their mutation rate over the study period. The proportion of the Delta sub-lineage AY.4.2 was increasing, with a reproduction number 15% (95% CI 8–23%) greater than the most prevalent lineage, AY.4. Further, AY.4.2 was less associated with the most predictive COVID-19 symptoms (p = 0.029) and had a reduced mutation rate (p = 0.050). Both AY.4.2 and AY.4 were found to be geographically clustered in September but this was no longer the case by late October/early November, with only the lineage AY.6 exhibiting clustering towards the South of England. Conclusions: As SARS-CoV-2 moves towards endemicity and new variants emerge, genomic data obtained from random community samples can augment routine surveillance data without the potential biases introduced due to higher sampling rates of symptomatic individuals.

Item Type: Article
Additional Information: Funding Information: The study was funded by the Department of Health and Social Care in England. Sequencing was provided through the COVID-19 Genomics UK Consortium (COG-UK) which is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) [grant code: MC_PC_19027], and Genome Research Limited, operating as the Wellcome Sanger Institute. Publisher Copyright: © 2022, The Author(s).
Uncontrolled Keywords: covid-19,delta variant,genetic diversity,mutation,sars-cov-2,transmission advantage,infectious diseases,sdg 3 - good health and well-being ,/dk/atira/pure/subjectarea/asjc/2700/2725
Faculty \ School: Faculty of Science
Faculty of Medicine and Health Sciences > Norwich Medical School
Faculty of Science > School of Biological Sciences
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Depositing User: LivePure Connector
Date Deposited: 22 Sep 2022 09:31
Last Modified: 04 Oct 2022 00:28
URI: https://ueaeprints.uea.ac.uk/id/eprint/88583
DOI: 10.1186/s12879-022-07628-4

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