Hundreds of Yorkshire coronavirus patients help pioneering Sheffield study

Samples from hospital patients, NHS staff who have contracted Covid-19 and people in the community with confirmed cases from South and East Yorkshire have been used by scientists in Sheffield tasked with sequencing the genome of the virus.

The teams have now reached the milestone of uploading more than 1,000 genome sequences to the Covid-19 Genomics UK (COG-UK) Consortium, helping researchers around the world.

Work is being carried out by scientists at the University of Sheffield and clinicians from Sheffield Teaching Hospitals NHS Foundation Trust as part of a national effort to map the spread of coronavirus. Laboratory staff have been sequencing more than 100 genomes per week after being provided with samples taken from nasal or throat swabs from patients.

The samples mainly come from people in South Yorkshire, although some are from East Yorkshire and other areas in the region as well.

The research is being backed by the Government as part of a £20m investment in the COG-UK Consortium and it hoped the genetic code could equip public health agencies and doctors with information on how Covid-19 spreads, behaves and mutates so the virus can be fought more effectively.

The work will be published in full on a public database used by researchers and scientists working on solutions to the coronavirus outbreak worldwide.

Experts across the UK are working together to rapidly analyse the genetic code of coronavirus samples circulating in the UK in what it is hoped will prove to be life-saving research.

The Covid-19 Genomics UK Consortium includes the NHS, public health agencies, Wellcome Sanger Institute, and numerous academic institutions including the University of Sheffield.

Dr Thushan de Silva, Senior Clinical Lecturer and Honorary Consultant Physician in Infectious Diseases from the University of Sheffield, is leading the collaborative Sheffield Covid-19 Genomics Group.

“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 it is spreading," he said.

“The work is helping to coordinate agile responses to new infectious diseases as they spread and mutate in local populations. This is critical for the health research community to be able to contribute to our understanding of outbreaks of new infectious diseases, informing clinical care of patients and even saving lives.”

Members include specialists from the University’s Florey Institute for Host Pathogen Interactions, Sheffield Institute for Translational Neuroscience (SITraN), Department of Animal and Plant Sciences, Department of Molecular Biology and Biotechnology, and Department of Computer Science.

Dr Matthew Parker and Dr Dennis Wang have been leading the bioinformatics analysis for the project 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 takes the genomic data from viral cases in our region and compares 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 and the facilities and expertise we have here in Sheffield are key to a successful project like this

“Our collaborative team has rapidly expanded its capacity and formulated new processes to be able to sequence genomes on a scale we have not done before. The laboratory staff are now sequencing genomes from samples taken from patients with confirmed cases of Covid-19 at a rate of over 100 a week.”

“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 it is spreading.

“The work is helping to coordinate agile responses to new infectious diseases as they spread and mutate in local populations. This is critical for the health research community to be able to contribute to our understanding of outbreaks of new infectious diseases, informing clinical care of patients and even saving lives.”

The team is working in partnership with Consultant Virologists Dr Cariad Evans, Dr Mohammad Raza, Dr Alison Cope and Consultant Microbiologist Dr Dave Partridge, from 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 Cariad Evans said: “We have national and international experts in Virology working in our laboratories and we are very proud to be involved in this important work to determine how this new virus behaves and how that knowledge could then inform future care or treatment.”

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