Lineage replacement and evolution captured by three years of the United Kingdom Covid Infection Survey

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.