The coronavirus pandemic that gripped the UK between September 2020 and June 2021 can be seen as a series of overlapping epidemics, rather than a single event, researchers have said.
Over this time the country saw several variants of the virus that had different properties which required a reassessment of the public health response.
The new study describes the scientific story of the pandemic, and researchers highlight the importance of quick surveillance of the virus to understand and respond to outbreaks.
We will continue to monitor the SARS-CoV-2 virus to ensure that we can use the most effective vaccines, treatments and public health measures against current and future variantsDr Meera Chand, UK Health Security Agency
The Covid-19 Genomics UK (Cog-UK) consortium was set up in March 2020 – as the UK was preparing to enter lockdown – to monitor the spread and evolution of the virus by sequencing its genome.
Cog-UK has since identified and monitored numerous variants, including the Alpha and Delta variants, which both changed the course of the pandemic in the UK.
In the new study, scientists analysed data from England collected between September 2020 and June 2021.
They characterised the growth rates and geographic spread of 71 lineages and reconstructed how newly emerging variants changed the course of the epidemic.
Researchers found that when tiered restrictions were in place last December, infection rates were higher in areas with fewer restrictions.
Time has proven how ingenious an idea it was to set up the Covid-19 Genomics UK (Cog-UK) consortium at the beginning of the pandemicDr Moritz Gerstung, senior author
Alpha was brought under control in a third national lockdown between January and March 2021.
This measure simultaneously eliminated most variants that had been dominant in September and October 2020, the study found.
In March 2021, the first samples of Delta began appearing in sequence data, and by June 26 it accounted for 98% of viral genomes sequenced.
Delta variant cases continued to rise in the first two weeks of July 2021, as restrictions were relaxed, even though more than 90% of adults in England had Covid-19 antibodies, and close to 70% had received two doses of vaccine.
Dr Meera Chand, Covid-19 incident director at the UK Health Security Agency (UKHSA) and one of the authors of the paper, said: “We will continue to monitor the SARS-CoV-2 virus to ensure that we can use the most effective vaccines, treatments and public health measures against current and future variants.”
Dr Moritz Gerstung, a senior author of the paper from EMBL-EBI and The German Cancer Research Centre (Deutsches Krebsforschungszentrum, DKFZ), said: “Time has proven how ingenious an idea it was to set up the Covid-19 Genomics UK (Cog-UK) consortium at the beginning of the pandemic.
“Being able to see lineages side-by-side, mapped to specific locations, has been incredibly informative in terms of understanding how this series of epidemics has unfolded.
“To see Alpha growing faster in nearly 250 out of 315 local authorities was a clear signal that we were dealing with something very different.
“At the same time, we’ve learned that the genetics of SARS-CoV-2 are incredibly complex.
“Even though we knew all of Delta’s mutations, it wasn’t immediately clear that it would become the dominant lineage, for example.”
Analysis of Delta suggests its growth rate was 59% higher than that of Alpha, the greatest growth advantage observed in any other variant to date.
Overall, the researchers estimate that the spread of more transmissible variants between August 2020 and the early summer of 2021 more than doubled the average growth rate of the virus in England.
The study, published in Nature, was conducted by researchers at the Wellcome Sanger Institute, EMBL’s European Bioinformatics Institute (EMBL-EBI) and their collaborators.