@article{2ca79132902a48a7937913bb819ed6b9,
title = "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",
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.",
keywords = "COVID-19, Delta variant, Genetic diversity, Mutation, SARS-CoV-2, Transmission advantage",
author = "Oliver Eales and Page, {Andrew J.} and {de Oliveira Martins}, Leonardo and Haowei Wang and Barbara Bodinier and David Haw and Jakob Jonnerby and Christina Atchison and {The COVID-19 Genomics UK (COG-UK) Consortium} and Deborah Ashby and Wendy Barclay and Graham Taylor and Graham Cooke and Helen Ward and Ara Darzi and Steven Riley and Marc Chadeau-Hyam and Donnelly, {Christl A} and Paul Elliott and Smith, {Darren L.} and Matthew Bashton and Young, {Gregory R.} and McCann, {Clare M.} and Andrew Nelson and Crown, {Matthew R.} and Henderson, {John H.} and Amy Hollis and William Stanley and Yew, {Wen C.}",
note = "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{\textquoteright} (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 (MC_PC_17114). 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.",
year = "2022",
month = dec,
doi = "10.1186/s12879-022-07628-4",
language = "English",
volume = "22",
journal = "BMC Infectious Diseases",
issn = "1471-2334",
publisher = "BioMed Central",
number = "1",
}