DOI: 10.5061/dryad.hx3ffbgm2
title: Lineage replacement and evolution captured by three years of the United Kingdom Covid Infection Survey

description: The Office for National Statistics 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 its
 predecessors. 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 characterised 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, particularly in the current
 phase of the pandemic with routine RT-PCR testing now ended in the
 community.
description: Samples collected as part of the ONS Covid Infection Survey and
 sequenced as part of the COG-UK consortium.
description: Lineage replacement and evolution captured by three years of the United
 Kingdom Covid Infection Survey --- Consensus sequences and associated
 metadata used in the above study. The Office for National Statistics
 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 its predecessors. 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 characterised 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, particularly in
 the current phase of the pandemic with routine RT-PCR testing now ended in
 the community. ## Description of the data and file structure
 consensus.fasta - a fasta file containing approximately 125,000 consensus
 sequences, each labelled by its COG-UK ID and collection data.
 SampleInfo.csv - a table giving key metadata for each consensus sequence,
 specifically collection date and Pango lineage TestingInfo.csv - a table
 giving number of swabs, positive swabs, positive swabs with Ct&lt;=30,
 and positive swab successfully sequenced (by week) ## Sharing/Access
 information The sequences have also been deposited in the European
 Nucleotide Archive (ENA) at EMBL-EBI as part of the COG-UK consortium,
 which has accession number PRJEB37886
 (https://www.ebi.ac.uk/ena/browser/view/PRJEB37886) ## Code/Software