TY - JOUR
AU - Lythgoe, Katrina A.
AU - Golubchik, Tanya
AU - Hall, Matthew
AU - House, Thomas
AU - MacIntyre-Cockett, George
AU - Fryer, Helen
AU - Thomson, Laura
AU - Nurtay, Anel
AU - Buck, David
AU - Green, Angie
AU - Trebes, Amy
AU - Piazza, Paolo
AU - Lonie, Lorne J.
AU - Studley, Ruth
AU - Rourke, Emma
AU - Cook, Duncan
AU - Smith, Darren
AU - Bashton, Matthew
AU - Nelson, Andrew
AU - Crown, Matthew R.
AU - McCann, Clare M.
AU - Young, Gregory R.
AU - dos Santos, Rui Andre Nunes
AU - Richards, Zack
AU - Tariq, Adnan
AU - Wellcome Sanger Institute COVID-19 Surveillance Team
AU - COVID-19 Infection Survey Group
AU - The COVID-19 Genomics UK (COG-UK) Consortium
AU - Fraser, Christophe
AU - Diamond, Ian
AU - Barrett, Jeffrey C.
AU - Walker, Sarah A
AU - Bonsall, David
PY - 2022
DA - January
TI - Lineage replacement and evolution captured by the United Kingdom Covid Infection Survey
JO - MedRxiv
DO - https://doi.org/10.1101/2022.01.05.21268323
AB - 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.
PB - medRxiv
UR - https://publichealthscotland.scot/id/83241
KW - Coronavirus (COVID-19)
ER