Real time viral genomic data to reduce spread of COVID-19 within hospitals

The genomic data is likely to enable clinical teams in each hospital to see if newly infected patients have picked up the virus from a known positive COVID-19 patient within the hospital, or from outside the hospital

A pioneering clinical trial will evaluate the use of ‘real time’ viral genomic data to reduce the spread of COVID-19 within hospitals. The study’s findings could help the NHS reduce further transmission of the virus by determining if an individual caught the virus from someone else within the same hospital.

The trial, led by University College London (UCL), in partnership with scientists from the University of Sheffield, forms part of the government’s £20 million COVID-19 Genomics UK Consortium (COG-UK) – which has established a network of rapid genome sequencing centres across the UK, allowing scientists to map the virus’ spread across the country.


Dr Thushan de Silva, from the University of Sheffield’s Department of Infection, Immunity and Cardiovascular Disease who is leading the study in Sheffield, said, “We hope that our ability to analyse viral sequencing data in real-time and map the virus’ spread in this unique way will not only help reduce the risk of SARS-CoV-2 within hospitals, but also consolidate the routine use of pathogen genome sequencing within NHS service delivery.

“This pioneering study will provide vital evidence on the role of rapid viral genome sequencing in helping to reduce the spread of SARS-CoV-2 within hospitals. Our work is all the more crucial as infection rates continue to rise again across the country.”

The research is led by Professor Judith Breuer, Director of the University College London Hospital / Great Ormond Street Hospital Biomedical Research Centres funded Pathogen Genomics Unit, together with the UCL Comprehensive Clinical Trials Unit (CCTU).

Explaining the trial’s importance, Professor Breuer said, “Spread of COVID-19 infections in hospitals is now recognised to be a major problem for both healthcare workers and patients, and ‘breaking the chain’ of these transmissions is critical.

“Tried and tested procedures to minimise infection spread in hospitals are already in use,  including separating COVID-19 infected patients from uninfected patients, extensive cleaning, the use of PPE, and continual hand washing. Despite these measures, COVID-19 transmission to patients and staff is still occurring and has sadly proven fatal. So it is essential that we try out new tools such as viral sequencing to find out why this is happening and to help reduce hospital spread.”

The importance of this research area has been recognised by the UK Government and National Institute of Health Research (NIHR), with the trial being designated of ‘Urgent Public Health’ importance.

The COG-UK Hospital Onset COVID-19 Infection (HOCI) trial has been developed in collaboration with Sheffield Teaching Hospitals NHS Foundation Trust, Imperial College Healthcare Trust and the Queen Elizabeth University Hospital Glasgow with the MRC-University of Glasgow Centre for Virus Research.

COG-UK HOCI will involve over 15 hospitals linked to COG-UK sequencing hubs across the UK.

Each site will analyse the COVID-19 sequences in nasal and throat samples from all known COVID-19 patients in the hospital, along with newly infected hospital patients and frontline NHS staff. The trial will evaluate whether results from whole virus genome sequencing of all COVID-19 samples (now available within 24-48 hours) reduces the number of hospital outbreaks compared with standard methodologies.

Specifically, the genomic data is likely to enable clinical teams in each hospital to see if newly infected patients have picked up the virus from a known positive COVID-19 patient within the hospital, or from outside the hospital.

There is already evidence emerging from COG-UK that COVID-19 sequences can help teams to control hospital infections better. The COG-UK HOCI trial will quantify by how much sequencing helps, how important it is to return results rapidly, what is the best way to implement COVID-19 sequencing across the NHS, and how much it costs. This information will help to make more precise plans as to how to use COVID-19 sequencing in the future.

Breuer added, “We already know that comparing the sequence of letters that make up one COVID-19 virus genome with the sequence of letters from COVID-19 in another sample, can tell us whether the two viruses are the same or different. Therefore by sequencing COVID-19 viruses rapidly, we hope to establish how hospital staff and patients became infected. This will allow hospitals to put effective measures in place faster, to try to interrupt onward transmission of the virus and reduce the number and size of outbreaks. Such measures might include more regular deep cleans, checking and double-checking the effectiveness of PPE equipment, and moving other vulnerable patients out of the hospital entirely to another setting.”

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