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Genomic tracking of the COVID-19 pandemic in England

The COVID-19 crisis that gripped England between September 2020 and June 2021 can be thought of as a series of overlapping epidemics, rather than a single event, say researchers at the Wellcome Sanger Institute, EMBL's European Bioinformatics Institute (EMBL-EBI) and the German Cancer Research Center. During this period, the country wrestled with multiple variants of the SARS-CoV-2 virus that possessed different growth rates and required a different public health response.

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The 'story' of the pandemic

The study, published today in Nature, is the most detailed analysis of SARS-CoV-2 genomic surveillance information to date. It describes the scientific 'story' of the pandemic as it unfolded and underlines the importance of high-speed, large-scale genomic surveillance to understand and respond to infectious outbreaks.

In March 2020, just as England was preparing to enter the first of several lockdowns, the COVID-19 Genomics UK consortium was set up to monitor the spread and evolution of SARS-CoV-2 by sequencing the virus's genome.

Since then, the consortium has identified and monitored numerous viral lineages, including Alpha, first identified in Kent in September 2020 and Delta, first identified in India in April 2021. Both of these lineages subsequently changed the course of the pandemic, not only in England but globally.

For this study, researchers analysed SARS-CoV-2 genomic surveillance 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 lineages spread.

The rise and fall of new variants

At the end of 2020, the Alpha lineage (B.1.1.7) spread despite a series of restrictions, including a national lockdown in November and regional restrictions in December. Though these measures slowed the spread of other lineages, Alpha was found to possess a 50 to 60 per cent growth advantage over previous lineages and continued to spread rapidly.

In the system of tiered restrictions operating in December 2020, infection rates were higher in areas with fewer restrictions. Alpha was only brought under control in a third national lockdown between January and March 2021, which was introduced after a peak of 72,088 daily cases on 29 December. This measure simultaneously eliminated most lineages that had been dominant in September and October 2020. When restrictions began to be lifted on 8 March 2021, the daily case rate had fallen to 5,500.

While Alpha was being brought under control, lineages associated with a greater ability to circumvent immunity from vaccination or prior infection continued to appear in the UK at low levels in early 2021. These lineages were characterised by the spike mutation E484K, the most significant of which were the Beta lineage (B.1.351, first identified in South Africa) and Gamma lineage (P.1, first identified in Brazil). But despite repeated introductions of these lineages, they were confined to short-lived local outbreaks.

In March 2021, the first samples of B.1.617, which originated in India, began appearing in sequence data. This was in fact two lineages, Kappa (B.1.617.1) and Delta (B.1.617.2). The mutations in Delta made the virus much more transmissible than previous lineages. While Kappa spread slowly and has since faded away, Delta had spread to all local authorities and accounted for 98 per cent of viral genomes sequenced by 26 June 2021.