Tracking Covid at the Sanger Institute

The Wellcome Sanger's DNA Pipelines team are sequencing coronavirus

The Wellcome Sanger's DNA Pipelines team who are sequencing coronavirus - Credit: Dan Ross / Wellcome Sanger Institute

Scientists across the globe are identifying and tracking new, emerging genetic variants of coronavirus.

This has brought genomic surveillance - the systematic and regular collection and analysis of genetic sequence data - into the spotlight.

Rapid surveillance is also helping public health authorities, and informing the development of next generation Covid-19 vaccines.

The UK has one of the most comprehensive genomic surveillance systems in the world for SARS-CoV-2.

The COVID-19 Genomics UK (COG-UK) consortium, which was started in March 2020, has now sequenced over 300,000 SARS-CoV-2 genomes – just under half of the global total.

The Sanger Institute in Hinxton, with one of the largest genome sequencing facilities in the world, is the central sequencing hub for the consortium and has read 163,000 coronavirus genomes over the past 12 months. Data are rapidly and openly published.

The genome sequence data details the virus’s full genetic code, including any mutations that have occurred as it replicates in our bodies.

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Viruses mutate all the time, and while most mutations don’t affect their function, some do.

Those that affect the virus’s spike protein, which it uses to bind to and enter human cells, are of particular interest.

Scientists and public health agencies are using 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.

Sanger Institute scientists helped identify the B.1.1.7 variant in the UK in late 2020, showing it was more transmissible than previous variants.

The world was swiftly alerted to the threat. Different surveillance projects have picked up other worrying variants as the pandemic continues, and researchers expect 2021 to bring even more.

As people are vaccinated, there is the huge question of how the virus will respond.

There is a possibility that new mutations will enable variants to ‘escape’ vaccines. Sequencing any virus that infects a person who has had the vaccine is a priority for COG-UK.

Early detection of such variants will enable public health authorities, and vaccine manufacturers, to act swiftly.

The genetic changes can also be used as a ‘barcode’ to follow the virus as it moves from person to person.

The data helps to uncover previously hidden routes of transmission, and can be used to rule out or rule in a specific path, or identify a super spreading event.

LINKED: Science at Sanger, from Covid-19 to all of life on Earth