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COVID-19 genomic surveillance data tells story of pandemic in England

18 October 2021
Appeared in BioNews 1117

Genomic surveillance of the COVID-19 epidemic in England has cast light how different variants of the SARS-CoV-2 virus spread in the population since autumn 2020.

It showed that while the second and third lockdowns in the UK from 5 November to 1 December 2020 and from 6 January to 7 March 2021 reduced infection rates in England, Alpha and Delta variants of SARS-CoV-2, the virus that causes COVID-19, overtook other variants to become the dominant strain. Lower overall infection rates meant this was not immediately obvious, demonstrating the need for greater genomic surveillance, authors from the Wellcome Sanger Institute and European Molecular Biology Laboratory's European Bioinformatics Institute argued.

Dr Jeffrey Barrett senior author of the paper and director of the COVID-19 Genomics Initiative launched at the start of the pandemic at the Wellcome Sanger Institute said: 'These genomic surveillance data have given us a totally new way of watching an outbreak unfold, which has taught us a lot about how a new infectious agent spreads and evolves. My hope is that similar genomic surveillance programmes will be developed across the world, so that we are as well-prepared as we can be to respond to future infectious disease outbreaks – whether they be familiar pathogens or new ones.'

By sequencing genomes from 281,178 samples supplied by the government's Lighthouse Laboratories taken from people with positive PCR tests, researchers discovered there were 71 lineages of SARS-CoV-2 that had been present in England between 1 September 2020 and 26 June 2021. Samples from recent travelers were excluded from the analysis. By using the postcodes of the people who supplied the samples researchers mapped the spread of different variants across 315 local authorities in England.

Researchers also analysed infection data for a similar period using publicly available data published by the Lighthouse Laboratories and Office of National Statistics, and published the results in a paper in Nature.

They found the Alpha variant spread grew in the third lockdown from January and hypothesised this was due to it being 52 percent more transmissible than the B.1.1 variant, due to a spike mutation that facilitated ACE2 receptor binding. The authors also theorised its spread was driven by social interaction during the Christmas period of 2020.

While authors did not model the effect of immunity on the epidemic they hypothesise that the Delta variant infection cases rose due to increased transmissibility and it being able to evade immunity. They also suggest that the presence of the Delta variant means almost 100 percent vaccination rates are required for herd immunity in England.  

The World Health Organisation has identified four variants of concern, Alpha, Beta, Gamma and Delta and asks that member states submit genome sequences to the international GISAID database. The UK Government recently announced the UK had submitted over one million SARS-CoV-2 whole genome sequences to the database with help from the Wellcome Sanger Institute and COVID-19 Genomics UK, representing nearly a quarter of the total database.

Genomic reconstruction of the SARS-CoV-2 epidemic in England
Nature |  14 October 2021
The inside story of England COVID pandemic described in new study
Wellcome Sanger Institute |  14 October 2021
UK completes over one million SARS-CoV-2 whole genome sequences |  11 October 2021
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