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., Elliott, Paul, Smith, Darren, Bashton, Matthew, McCann, Clare, Nelson, Andrew, Crown, Matthew, Henderson, John, Hollis, Amy, Stanley, William and Yew, Wen Chyin (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). p. 647. ISSN 1471-233

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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: MC-H acknowledges support from the H2020-EXPANSE project (Horizon 2020 Grant No 874627). MC-H and BB acknowledge support from Cancer Research UK, Population Research Committee Project grant 'Mechanomics’ (Grant No 22184 to MC-H). CAD acknowledges support from the MRC Centre for Global Infectious Disease Analysis and National Institute for Health Research (NIHR) Health Protection Research Unit (HPRU). GC is supported by an NIHR Professorship. HW acknowledges support from an NIHR Senior Investigator Award and the Wellcome Trust (205456/Z/16/Z). PE is Director of the Medical Research Council (MRC) Centre for Environment and Health (MR/L01341X/1, MR/S019669/1). PE acknowledges support from Health Data Research UK (HDR UK); the NIHR Imperial Biomedical Research Centre; NIHR Health Protection Research Units in Chemical and Radiation Threats and Hazards, and Environmental Exposures and Health; the British Heart Foundation Centre for Research Excellence at Imperial College London (RE/18/4/34215); and the UK Dementia Research Institute at Imperial College London (MCPC17114). AJP acknowledges the support of the Biotechnology and Biological Sciences Research Council (BB/R012504/1). We thank The Huo Family Foundation for their support of our work on COVID-19.
Uncontrolled Keywords: COVID-19, Delta variant, Genetic diversity, Mutation, SARS-CoV-2, Transmission advantage
Subjects: B900 Others in Subjects allied to Medicine
C500 Microbiology
Department: Faculties > Health and Life Sciences > Applied Sciences
Depositing User: John Coen
Date Deposited: 27 Sep 2022 11:59
Last Modified: 27 Sep 2022 12:00

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