@article{Lythgoe_K-2022_83241,
title = {Lineage replacement and evolution captured by the United Kingdom Covid Infection Survey},
author = {Lythgoe, K. and Golubchik, T. and Hall, M. and House, T. and MacIntyre-Cockett, G. and Fryer, H. and Thomson, L. and Nurtay, A. and Buck, D. and Green, A. and Trebes, A. and Piazza, P. and Lonie, L. and Studley, R. and Rourke, E. and Cook, D. and Smith, D. and Bashton, M. and Nelson, A. and Crown, M. and McCann, C. and Young, G. and dos Santos, R. and Richards, Z. and Tariq, A. and Team, W. and COVID-19 Infection Survey Group and The COVID-19 Genomics UK (COG-UK) Consortium and Fraser, C. and Diamond, I. and Barrett, J. and Walker, S. and Bonsall, D.},
month = {jan},
year = {2022},
abstract = {The Office for National Statistics COVID-19 Infection Survey is a large household-based surveillance study based in the United Kingdom. Here, we report on the epidemiological and evolutionary dynamics of SARS-CoV-2 determined by analysing sequenced samples collected up until 13th November 2021. We observed four distinct sweeps or partial-sweeps, by lineages B.1.177, B.1.1.7/Alpha, B.1.617.2/Delta, and finally AY.4.2, a sublineage of B.1.617.2, with each sweeping lineage having a distinct growth advantage compared to their predecessors. Evolution was characterised by steady rates of evolution and increasing diversity within lineages, but with step increases in divergence associated with each sweeping major lineage, leading to a faster overall rate of evolution 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, particularly as routine PCR testing is phased out or in settings where large-scale sequencing is not feasible.},
journal = {MedRxiv},
publisher = {medRxiv},
url = {https://doi.org/10.1101/2022.01.05.21268323},
}
