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

Wellcome Sanger Institute COVID-19 Surveillance Team, Katrina A Lythgoe, Tanya Golubchik, Matthew Hall, Thomas House, Roberto Cahuantzi, George MacIntyre-Cockett, Helen Fryer, Laura Thomson, Anel Nurtay, Mahan Ghafani, David Buck, Angie Green, Amy Trebes, Paolo Piazza, Lorne J Lonie, Ruth Studley, Emma Rourke, Darren Smith, Matthew BashtonAndrew Nelson, Matthew Crown, Clare McCann, Gregory R Young, Rui Andre Nunes Dos Santos, Zack Richards, Adnan Tariq, Christophe Fraser, Ian Diamond, Jeff Barrett, Ann Sarah Walker, David Bonsall

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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.

Original languageEnglish
Article number20231284
Number of pages10
JournalProceedings of the Royal Society B: Biological Sciences
Issue number2009
Early online date18 Oct 2023
Publication statusPublished - 25 Oct 2023

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