Exeter part of UK-wide genomics consortium in £12.2million funding boost

As part of the COVID-19 Genomics UK (COG-UK) Consortium (COG-UK), the work has been backed by the Department for Health and Social Care Testing Innovation Fund to expand whole genome sequencing of SARS-CoV-2

The £12.2 million in funding will facilitate the genome sequencing capacity needed to meet the increasing numbers of COVID-19 cases expected in the UK this winter.

Dr Ben Temperton is part of the University of Exeter team involved in the work. He said: “We’re delighted at this funding extension, which will increase our capacity for delivering to this important national collaboration, which has placed the UK as global leaders in genomic epidemiology of COVID-19. To date, Exeter has sequenced over 1000 samples to assist in understanding the spread of this disease at both the national level and in our local hospitals. That insight is crucial to helping us stop the spread of the disease, from understanding and stemming outbreaks to ensuring vaccines can remain effective.”

COG-UK is made up of an innovative partnership of NHS organisations, the four Public Health Agencies of the UK, and researchers from academic partners across the UK, including the University of Birmingham, University of Cambridge, Cardiff University, University of Edinburgh, University of Glasgow, Imperial College London, University of Liverpool, University of Nottingham, Northumbria University, University of Oxford, University of Portsmouth, the Quadram Institute – Norwich, Queens University – Belfast, University of Sheffield, University College London, and the Wellcome Sanger Institute. In addition, a large number of other institutes and partners are essential to the COG-UK effort (a full list is here).

COG-UK researchers have built a central database and developed cutting-edge analytical methodology and data pipelines for SARS-CoV-2 genomics. COG-UK has led the development of analytical software to define viral lineages and shares methods globally. Collectively, these data and tools have provided important scientific insights into the spread and evolution of the virus, at local, regional, national and international scales.

Since its launch in March 2020, COG-UK has generated and made publicly available more than 100,000 SARS-CoV-2 genomes, making up over 45 per cent of the global total. This unprecedented effort has not been achieved previously for any pathogen, anywhere in the world.

However, the steadily rising numbers of cases in the UK requires a prompt increase in the national SARS-CoV-2 genome sequencing capacity, to ensure that the benefits of using genome sequence data can be realised in a rapid and robust manner.

The additional investment will enable COG-UK to grow and strengthen current genomic surveillance efforts, with the aim of increasing sequencing capacity across the national network and reducing turnaround time from patient sample to genome sequence.

The viral genome sequencing data will be integrated within the four UK Public Health Agencies & NHS Test and Trace to help understand outbreaks and strengthen infection control measures. It will also be used to detect and track mutations that could be harmful to human health, such as those that could reduce vaccine efficacy.

Dr Cressida Auckland, Consultant in Microbiology and Infection at the Royal Devon and Exeter NHS Foundation trust, said, “This funding announcement is great news for the consortium and for Exeter and the South West. The work of the COG to sequence the genome of the coronavirus  is a vital component in the Trust’s fight against COVID-19, and we are proud to be part of the cutting edge science behind it.”

Looking ahead, researchers from all of partner organisations will continue to make immense contributions to sequencing, analysis, working on research priorities and R&D, supporting the CLIMB-COVID database and developing cutting-edge analytical tools.

Professor Sharon Peacock, Director of the COVID-19 Genomics UK (COG-UK) Consortium, Professor of Public Health and Microbiology at the University of Cambridge and a Director of Science (Pathogen Genomics) at Public Health England, said:“I am delighted by this award, which will support our further expansion of whole genome sequencing of SARS-CoV-2. Our purpose is to provide data that influences public health interventions and policy decisions, and through this make a contribution towards reducing the toll of COVID-19 on our population.

“I want to acknowledge the unstinting dedication, innovation, generosity and hard work of COG-UK Consortium Members, which has made this award possible. The network of laboratories and people in them underpins our productivity, outputs and success, and they will be vital in our ongoing success.”