DNA Pipelines team, Sanger Institute. Credit: Dan Ross / Wellcome Sanger Institute

Categories: COVID-1931 May 20224.2 min read

COVID-19: update on SARS-CoV-2 genome sequencing at the Sanger Institute

The Sanger Institute began sequencing SARS-CoV-2 genomes in March 2020, as part of the COVID-19 Genomics UK consortium (COG-UK). The work was quickly scaled up and sped up to aid the public health response. Sanger Institute staff have sequenced over 2.5 million SARS-CoV-2 genomes to date. This currently represents about 20 per cent of the global total of sequences publicly available¹.

Sequencing SARS-CoV-2 genomes is done to identify and track new variants of the virus, enable research, and assist the public health response. The viral genome data are also immediately made available to scientists around the world for analysis. The work builds on the Sanger Institute’s history and capacity for genomic surveillance in other diseases including malaria, cholera and the monitoring of antibiotic resistance in a range of bacteria.

In early 2021, the Institute began working in partnership with the UK Health Security Agency (UKHSA) to undertake viral genome sequencing. The Institute now delivers hourly reports to UKHSA of the sequencing results, showing which variants are present, to aid rapid public health decision making. These data are a vital piece of information for tracking and analysing SARS-CoV-2 in the UK in real-time.

Processing SARS-CoV-2 for genome sequencing

Current genome sequencing

The majority of SARS-CoV-2 samples sequenced at the Institute came from the nine UK Lighthouse Laboratories which processed PCR tests from the community - including postal tests, drive-through or walk-in testing sites.

The Institute is currently sequencing SARS-CoV-2 genomes from the Rosalind Franklin laboratory and ONS COVID-19 infection survey samples processed in Glasgow.

The viral genome data are analysed by scientists at the Sanger Institute, UKHSA, across UK academia and beyond.

Genomic surveillance - new mutations and variants

Sequencing of the SARS-CoV-2 virus allows researchers to identify mutations in the genome. Mutations occur naturally as the virus replicates in our bodies, though most do not affect its functions. Mutations that affect the virus’s spike protein, which it uses to bind to and enter human cells, are of particular interest. The spike protein is also the target of immunity (e.g. antibodies) generated by natural infection or COVID-19 vaccines.

Sequencing virus genomes from across the UK means there are comprehensive data that can be used to rapidly assess how the virus is evolving. Scientists use the genomic data alongside other information to assess which mutations may affect the virus’s ability to transmit, cause disease or evade the immune response, which may have been generated by a previous infection with the virus, or a vaccine.

The Sanger Institute COVID-19 Genomic Surveillance Dashboard

COVID-19 Genomic Surveillance Dashboard

You can view the variants detected in the samples on the Sanger Institute COVID-19 Genomic Surveillance Dashboard: https://covid19.sanger.ac.uk/lineages/raw.

Please also visit UKHSA for the latest information on variants. https://www.gov.uk/government/news/covid-19-variants-identified-in-the-uk.

1. For global sequence data, please visit ENA or GISAID.

Find out more

Photo essay: Sequencing COVID-19

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  • 29 June 2021

    The second COVID connections talk brought together experts from COG-UK to discuss SARS-CoV-2 variants.

  • 27 May 2021

    Experts from the COVID-19 Genomics UK Consortium discuss sequencing SARS-CoV-2, variants, and viral fitness landscapes.