Lineage replacement and evolution captured by 3 years of the United Kingdom Coronavirus (COVID-19) Infection Survey.

Lythgoe, Katrina A, Golubchik, Tanya, Hall, Matthew, House, Thomas, Cahuantzi, Roberto, MacIntyre-Cockett, George, Fryer, Helen, Thomson, Laura, Nurtay, Anel, Ghafani, Mahan
et al (show 23 more authors) (2023) Lineage replacement and evolution captured by 3 years of the United Kingdom Coronavirus (COVID-19) Infection Survey. Proceedings. Biological sciences, 290 (2009). p. 20231284.

Access the full-text of this item by clicking on the Open Access link.


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.

Item Type: Article
Uncontrolled Keywords: COVID-19 Infection Survey Group, The COVID-19 Genomics UK (COG-UK) Consortium, Wellcome Sanger Institute COVID-19 Surveillance Team
Divisions: Faculty of Health and Life Sciences
Faculty of Health and Life Sciences > Institute of Infection, Veterinary and Ecological Sciences
Depositing User: Symplectic Admin
Date Deposited: 01 Feb 2024 09:38
Last Modified: 01 Feb 2024 09:38
DOI: 10.1098/rspb.2023.1284
Open Access URL:
Related URLs: