Scientists and clinicians from the University of Sheffield and Sheffield Teaching Hospitals NHS Foundation Trust have joined a UK consortium to map how COVID-19 (coronavirus) spreads and behaves.Backed by the UK government, a £20 million investment will allow the consortium to work together – and through whole genome sequencing – to create valuable intelligence that could provide breakthroughs in how to fight this, and future pandemics; saving lives around the world.
The COVID-19 Genomics UK Consortium includes the NHS, public health agencies, Wellcome Sanger Institute, and numerous academic institutions including the University of Sheffield.
Expert groups across the country will work together to rapidly analyse the genetic code of coronavirus samples circulating in the UK. In doing so, the consortium will provide unique cutting-edge intelligence about the cause of the disease to share with public health agencies, hospitals, regional NHS centres and the government to help combat the virus.
Work to rapidly sequence whole genomes of coronavirus has already been successful at the University, with a collaborative team contributing sequences from patients with confirmed cases of coronavirus. As part of their work for the consortium, the team has been expanding its capacity to be able to sequence around 120 samples per week; initially over a 12 week period.
Dr Thushan de Silva, Senior Clinical Lecturer and Honorary Consultant Physician in Infectious Diseases from the University of Sheffield’s Department of Infection, Immunity and Cardiovascular Disease, is leading a collaborative team including specialists from the University’s Florey Institute for Host Pathogen Interactions, Sheffield Institute for Translational Neuroscience (SITraN), Department of Animal and Plant Sciences and Department of Computer Science.
The team is working in partnership with Consultant Virologists Dr Cariad Evans and Dr Mohammad Raza at the Sheffield Teaching Hospitals NHS Foundation Trust’s regional NHS virology laboratory based at the Northern General Hospital, to respond to the rapidly evolving outbreak of the virus in the Yorkshire region.
Dr de Silva said: “By looking at the whole virus genome in people who have had confirmed cases of coronavirus, we can monitor changes in the virus at a national and global scale to understand how the virus is spreading and whether different strains are emerging. This will help coordinate agile responses to new infectious diseases as they spread and mutate in local populations, informing clinical care of patients and even saving lives.
“The facilities and expertise we have here in Sheffield are key to a successful project like this. Our work will contribute to the UK effort to generate timely, accessible data to help in the management of the current outbreak for the national consortium.”
The team is also publishing its samples to a global research consortium, where the genome sequences are accessible on a public database used by researchers and scientists working on solutions to the coronavirus outbreak worldwide.
Dr de Silva added: “Collecting and sharing standardised global clinical data and samples on patients infected with coronavirus is a critical process in how the health research community can contribute to our understanding of outbreaks of new infectious diseases.”
The bioinformatics analysis supporting this COVID-19 project will be led by Dr Matthew Parker and Dr Dennis Wang in the National Institute of Health Research (NIHR) Sheffield Biomedical Research Centre and the Department of Computer Science.
Dr Parker said: “Using expertise in the Sheffield Bioinformatics Core, we have built a robust pipeline which will take the genomic data from viral cases in our region and compare it to those from around the world to identify new mutations. By collaborating with our national and international partners, we will be able to track the spread of the virus.”
The consortium network of sequencing centres currently includes Belfast, Birmingham, Cambridge, Cardiff, Edinburgh, Exeter, Glasgow, Liverpool, London, Norwich, Nottingham, Oxford and Sheffield.
Professor Sharon Peacock, Director of the National Infection Service, Public Health England, said: “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.
“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.”
Government Chief Scientific Adviser, Sir Patrick Vallance, said: “Genomic sequencing will help us understand COVID-19 and its spread. It can also help guide treatments in the future and see the impact of interventions.
“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.”
- The GISAID database can be accessed here.
- The UK Consortium, supported by the Government, including the NHS, Public Health England, UK Research and Innovation (UKRI), and Wellcome, will enable clinicians and public health teams to rapidly investigate clusters of cases in hospitals, care homes and the community, to understand how the virus is spread and implement appropriate infection control measures.