Journal article
Lineage replacement and evolution captured by 3 years of the United Kingdom Coronavirus (COVID-19) Infection Survey
- Abstract:
- The Office for National Statistics Coronavirus (COVID-19) Infection Survey (ONS-CIS) is the largest surveillance study of SARS-CoV-2 positivity in the community, and collected data on the United Kingdom (UK) epidemic from April 2020 until March 2023 before being paused. Here, we report on the epidemiological and evolutionary dynamics of SARS-CoV-2 determined by analysing the sequenced samples collected by the ONS-CIS during this period. We observed a series of sweeps or partial sweeps, with each sweeping lineage having a distinct growth advantage compared to their predecessors, although this was also accompanied by a gradual fall in average viral burdens from June 2021 to March 2023. The sweeps also generated an alternating pattern in which most samples had either S-gene target failure (SGTF) or non-SGTF over time. Evolution was characterized by steadily increasing divergence and diversity within lineages, but with step increases in divergence associated with each sweeping major lineage. This led to a faster overall rate of evolution when measured at the between-lineage level compared to within lineages, and fluctuating levels of diversity. These observations highlight the value of viral sequencing integrated into community surveillance studies to monitor the viral epidemiology and evolution of SARS-CoV-2, and potentially other pathogens.
- Publication status:
- Published
- Peer review status:
- Peer reviewed
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- Files:
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(Preview, Version of record, pdf, 802.8KB, Terms of use)
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- Publisher copy:
- 10.1098/rspb.2023.1284
Authors
Contributors
+ Wellcome Sanger Institute COVID-19 Surveillance Team
- Role:
- Contributor
+ COVID-19 Infection Survey Group
- Role:
- Contributor
+ The COVID-19 Genomics UK (COG-UK) Consortium
- Role:
- Contributor
- Publisher:
- Royal Society
- Journal:
- Proceedings of the Royal Society B: Biological Sciences More from this journal
- Volume:
- 290
- Article number:
- 20231284
- Publication date:
- 2023-10-18
- Acceptance date:
- 2023-09-08
- DOI:
- EISSN:
-
1471-2954
- ISSN:
-
0962-8452
- Pmid:
-
37848057
- Language:
-
English
- Keywords:
- Pubs id:
-
1546066
- Local pid:
-
pubs:1546066
- Deposit date:
-
2023-11-02
Terms of use
- Copyright holder:
- Lythgoe et al.
- Copyright date:
- 2023
- Rights statement:
- © 2023 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.
- Licence:
- CC Attribution (CC BY)
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