New initiative harnesses genomics in coronavirus fight

In the first of a two-part article, we look at how the NHS is teaming up with academia, researchers and public health agencies to combat Covid-19 with genomics

Last month, the government announced a new £20m initiative to bring together the UK’s leading clinicians and scientists to form the Covid-19 Genomics UK Consortium. But how will it all work, and in what ways could it help in the fight against the pandemic?

A new alliance

The Covid-19 Genomics UK Consortium is made up of the NHS, Wellcome Sanger Institute, public health agencies and academic institutions. It will deliver large-scale, rapid genome sequencing of the virus to improve understanding of how the SARS-CoV-2 virus is spreading, and if new strains are emerging.

The government’s chief scientific adviser Sir Patrick Vallance said: “The UK is one of the world’s leading destinations for genomics research and development, and I am confident that our best minds, working as part of this consortium, will make vital breakthroughs to help us tackle this disease.”

How will it work?

NHS staff will collect samples from patients with confirmed cases of Covid-19, which will be sent to sequencing centres around the UK, including Belfast, Birmingham, Cambridge, Cardiff, Edinburgh, Exeter, Glasgow, Liverpool, London, Norwich, Nottingham, Oxford and Sheffield.

Analysis of resulting data will be co-ordinated by the Wellcome Sanger Institute in Cambridge. Findings will be shared with hospitals, regional NHS centres and the government, who can use the information for public health planning, clinical care strategies as well as for researchers developing and testing vaccines and therapies.

“This virus is one of the biggest threats our nation has faced in recent times and crucial to helping us fight it is understanding how it is spreading,” said consortium lead Professor Sharon Peacock, director of the National Infection Service at Public Health England. “Harnessing innovative genome technologies will help us tease apart the complex picture of coronavirus spread in the UK, and rapidly evaluate ways to reduce the impact of this disease on our society.”

What are the benefits?

By looking at small genomic changes in the virus samples collected from different patients, a phylogenetic tree (like a family tree) can be drawn up, showing which patients’ viruses are more closely related to others – meaning that they share a more recent common host.

This can have two benefits: first, it can be used to track how the virus moves through the population over time. Understanding this allows the main routes of infection to be identified. These could be people (‘super-spreaders’), geographical hotspots, cultural norms or workplace practices, for example. Identifying these allows public health measures to target these modes of transmission.

Secondly, tracking these genomic changes as they occur in the virus will allow swift identification of new strains that may emerge, especially if they are more virulent or are resistant to one or more available treatments. The sooner such strains are detected, the more likely it is that they can be prevented from spreading.

Potential for drug development

The research will also be useful to researchers working on a vaccine or trying to identify drug treatments.

Although the viral genome has already been published, it will be helpful to see which aspects of the genome change as the virus evolves, and which stay the same. Any new changes may make the virus susceptible – or resistant – to drug treatments, so keeping track of the genome over time is vital.

Read the second part of our article, where we look in more detail at the science and technology behind the consortium’s approach