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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
Oliver Eales; Andrew Page; Leonardo de Oliveira Martins; Haowei Wang; Barbara Bodinier; David Haw; Jakob Jonnerby; Christina Atchison; - The COVID-19 Genomics UK (COG-UK) Consortium; Deborah Ashby; Wendy Barclay; Graham Taylor; Graham Cooke; Helen Ward; Ara Darzi; Steven Riley; Marc Chadeau-Hyam; Christl A Donnelly; Paul Elliott.
Affiliation
  • Oliver Eales; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc
  • Andrew Page; Quadram Institute, Norwich, UK
  • Leonardo de Oliveira Martins; Quadram Institute, Norwich, UK
  • Haowei Wang; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc
  • Barbara Bodinier; School of Public Health, Imperial College London, UK MRC Centre for Environment and Health, School of Public Health, Imperial College London, UK
  • David Haw; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc
  • Jakob Jonnerby; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc
  • Christina Atchison; School of Public Health, Imperial College London, UK
  • - The COVID-19 Genomics UK (COG-UK) Consortium;
  • Deborah Ashby; School of Public Health, Imperial College London, UK
  • Wendy Barclay; Department of Infectious Disease, Imperial College London, UK
  • Graham Taylor; Department of Infectious Disease, Imperial College London, UK
  • Graham Cooke; Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic
  • Helen Ward; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear
  • Ara Darzi; Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a
  • Steven Riley; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc
  • Marc Chadeau-Hyam; School of Public Health, Imperial College London, UK MRC Centre for Environment and Health, School of Public Health, Imperial College London, UK
  • Christl A Donnelly; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc
  • Paul Elliott; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear
Preprint in English | medRxiv | ID: ppmedrxiv-21267925
ABSTRACT
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. Here 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. From 9 to 27 September 2021 (round 14) and 19 October to 5 November 2021 (round 15), all lineages sequenced within REACT-1 were Delta or a Delta sub-lineage with 44 unique lineages identified. The proportion of the original Delta variant (B.1.617.2) was found to be increasing between September and November 2021, which may reflect an increasing number of sub-lineages which have yet to be identified. The proportion of B.1.617.2 was greatest in London, which was further identified as a region with an increased level of genetic diversity. The Delta sub-lineage AY.4.2 was found to be robustly increasing in proportion, with a reproduction number 15% (8%, 23%) greater than its parent and most prevalent lineage, AY.4. 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. Though no difference in the viral load based on cycle threshold (Ct) values was identified, a lower proportion of those infected with AY.4.2 had symptoms for which testing is usually recommend (loss or change of sense of taste, loss or change of sense of smell, new persistent cough, fever), compared to AY.4 (p = 0.026). The evolutionary rate of SARS-CoV-2, as measured by the mutation rate, was found to be slowing down during the study period, with AY.4.2 further found to have a reduced mutation rate relative to AY.4. 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.
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Full text: Available Collection: Preprints Database: medRxiv Type of study: Rct Language: English Year: 2021 Document type: Preprint
Full text: Available Collection: Preprints Database: medRxiv Type of study: Rct Language: English Year: 2021 Document type: Preprint
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