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

Categories: COVID-191 March 20227.5 min read

Sequencing COVID variants: latest stats

The Sanger Institute is contracted by the UK Health Security Agency (UKHSA) to sequence coronavirus genomes. This is done to identify and track new variants of the virus, and assist public health officials. The viral genome data are also immediately made publicly available to researchers 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.

The majority of SARS-CoV-2 samples we sequence come from the UK Lighthouse Laboratories which process PCR tests from the community - including postal tests, drive through or walk-in testing sites. We also sequence samples from other sites and for other projects.

Below is a snapshot of some of the key numbers from the Sanger Institute, including how many genomes we have sequenced since March 2020, and how quickly. Please note this post is no longer being regularly updated.

COVID-19 Genomes Sequenced - 23/05/2022

SARS-CoV-2 genomes sequenced by Sanger
Sanger Institute staff involved
SARS-CoV-2 genome sequences available globally

As of 23/05/2022, the Sanger Institute has sequenced 2,176,743* coronavirus genomes. All are freely available for analysis via ENA and GISAID**. Across the globe, there are a total of 10,975,766** sequences available.

At the Sanger Institute, we have received and handled more than 27 million samples since March 2020. These samples are the residues of PCR tests, which test for the presence of the virus.

We receive up to 200,000 samples a week and currently sequence about 60,000 per week. These 60,000 are chosen using an algorithm, agreed with UKHSA, which ensures geographic coverage and priority samples are sequenced.

Capacity is being increased to be able to sequence 64,000 per week.

The genome data are analysed by scientists at the Sanger Institute, UKHSA and beyond. The genome sequence determines which variant of the virus is present.

We do not hold or have any access to anyone’s personal information.

[*Please note these numbers are subject to change. **https://www.gisaid.org/]

Genomic surveillance - new mutations and variants

The Sanger Institute COVID-19 Genomic Surveillance Dashboard

COVID-19 Genomic Surveillance Dashboard

Sequencing of the SARS-CoV-2 virus allows researchers to track its genomic mutations. 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 current vaccines.

Sequencing genomes at this volume, across the UK, means there are comprehensive data that can be used to rapidly asses how the virus is evolving. Scientists use the genomic data alongside other information to asses 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.

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.


Discover the teams and tools behind Sanger's surveillance work

“The UK has become the world’s microscope for COVID-19. With large scale genomic sequencing, we can see how the virus is evolving day by day. We can monitor for new variants and observe them as they move. As vaccines are being rolled out, we are also the world’s binoculars, we can see what is coming over the horizon; how the virus will respond and evolve in response to those vaccines.”

Professor Sir Mike Stratton,
Director of the Sanger Institute

The process

See our photo essay, or watch our video, for details of how we process and sequence coronavirus samples.

  • 9 August 2021

    An expert panel discuss some of the latest research into human genetics, immunology and COVID-19.

  • 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.