Imperial College London
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ProfessorGrahamCooke

Faculty of Medicine, Department of Infectious Disease

Vice Dean (Research); Professor of Infectious Diseases
 
 
 
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Contact

 

g.cooke

 
 
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Location

 

Infectious Diseases SectionMedical SchoolSt Mary's Campus

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Summary

 

Publications

Citation

BibTex format

@article{Eales:2023:10.1099/mgen.0.000887,
author = {Eales, O and Page, AJ and Tang, SN and Walters, CE and Wang, H and Haw, D and Trotter, AJ and Le, Viet T and Foster-Nyarko, E and Prosolek, S and Atchison, C and Ashby, D and Cooke, G and Barclay, W and Donnelly, CA and O'Grady, J and Volz, E and The, Covid-Genomics Uk Cog-Uk Consortium and Darzi, A and Ward, H and Elliott, P and Riley, S},
doi = {10.1099/mgen.0.000887},
journal = {Microbial Genomics},
pages = {1--14},
title = {The use of representative community samples to assess SARS-CoV-2 lineage competition: Alpha outcompetes Beta and wild-type in England from January to March 2021.},
url = {http://dx.doi.org/10.1099/mgen.0.000887},
volume = {9},
year = {2023}
}
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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - Genomic surveillance for SARS-CoV-2 lineages informs our understanding of possible future changes in transmissibility and vaccine efficacy and will be a high priority for public health for the foreseeable future. However, small changes in the frequency of one lineage over another are often difficult to interpret because surveillance samples are obtained using a variety of methods all of which are known to contain biases. As a case study, using an approach which is largely free of biases, we here describe lineage dynamics and phylogenetic relationships of the Alpha and Beta variant in England during the first 3 months of 2021 using sequences obtained from a random community sample who provided a throat and nose swab for rt-PCR as part of the REal-time Assessment of Community Transmission-1 (REACT-1) study. Overall, diversity decreased during the first quarter of 2021, with the Alpha variant (first identified in Kent) becoming predominant, driven by a reproduction number 0.3 higher than for the prior wild-type. During January, positive samples were more likely to be Alpha in those aged 18 to 54 years old. Although individuals infected with the Alpha variant were no more likely to report one or more classic COVID-19 symptoms compared to those infected with wild-type, they were more likely to be antibody-positive 6 weeks after infection. Further, viral load was higher in those infected with the Alpha variant as measured by cycle threshold (Ct) values. The presence of infections with non-imported Beta variant (first identified in South Africa) during January, but not during February or March, suggests initial establishment in the community followed by fade-out. However, this occurred during a period of stringent social distancing. These results highlight how sequence data from representative community surveys such as REACT-1 can augment routine genomic surveillance during periods of lineage diversity.
AU  - Eales,O
AU  - Page,AJ
AU  - Tang,SN
AU  - Walters,CE
AU  - Wang,H
AU  - Haw,D
AU  - Trotter,AJ
AU  - Le,Viet T
AU  - Foster-Nyarko,E
AU  - Prosolek,S
AU  - Atchison,C
AU  - Ashby,D
AU  - Cooke,G
AU  - Barclay,W
AU  - Donnelly,CA
AU  - O'Grady,J
AU  - Volz,E
AU  - The,Covid-Genomics Uk Cog-Uk Consortium
AU  - Darzi,A
AU  - Ward,H
AU  - Elliott,P
AU  - Riley,S
DO  - 10.1099/mgen.0.000887
EP  - 14
PY  - 2023///
SN  - 2057-5858
SP  - 1
TI  - The use of representative community samples to assess SARS-CoV-2 lineage competition: Alpha outcompetes Beta and wild-type in England from January to March 2021.
T2  - Microbial Genomics
UR  - http://dx.doi.org/10.1099/mgen.0.000887
UR  - https://www.ncbi.nlm.nih.gov/pubmed/36745545
UR  - https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000887
UR  - http://hdl.handle.net/10044/1/103297
VL  - 9
ER  -
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