Imperial College London
Portrait Picture

ProfessorWendyBarclay

Faculty of Medicine, Department of Infectious Disease

Action Medical Research Chair Virology. Head of Department
 
 
 
//

Contact

 

+44 (0)20 7594 5035w.barclay

 
 
//

Location

 

416Medical SchoolSt Mary's Campus

//

Summary

 

Publications

Citation

BibTex format

@article{Eales:2021:10.1101/2021.12.17.21267925,
author = {Eales, O and Page, AJ and de, Oliveira Martins L and Wang, H and Bodinier, B and Haw, D and Jonnerby, J and Atchison, C and Ashby, D and Barclay, W and Taylor, G and Cooke, G and Ward, H and Darzi, A and Riley, S and Chadeau-Hyam, M and Donnelly, CA and Elliott, P},
doi = {10.1101/2021.12.17.21267925},
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},
url = {http://dx.doi.org/10.1101/2021.12.17.21267925},
year = {2021}
}
Download

RIS format (EndNote, RefMan)

TY  - JOUR
AB  - <jats:title>Abstract</jats:title><jats:p>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 fou
AU  - Eales,O
AU  - Page,AJ
AU  - de,Oliveira Martins L
AU  - Wang,H
AU  - Bodinier,B
AU  - Haw,D
AU  - Jonnerby,J
AU  - Atchison,C
AU  - Ashby,D
AU  - Barclay,W
AU  - Taylor,G
AU  - Cooke,G
AU  - Ward,H
AU  - Darzi,A
AU  - Riley,S
AU  - Chadeau-Hyam,M
AU  - Donnelly,CA
AU  - Elliott,P
DO  - 10.1101/2021.12.17.21267925
PY  - 2021///
TI  - 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
UR  - http://dx.doi.org/10.1101/2021.12.17.21267925
ER  -
Download