Division of Infection and Immunity


Spread of COVID-19 mapped in hospitals to ‘break the chain’ of transmission

7 October 2020

A first-of-its kind clinical trial, led by scientists at UCL, will evaluate the use of ‘real time’ viral genomic data to reduce the spread of COVID-19 within hospitals.

Scientist holding up glass slide used for a run on a sequencing machine

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 Professor Judith Breuer, Director of UCL/UCLH/GOSH Biomedical Research Centres funded Pathogen Genomics Unit (PGU/UCLG), together with the UCL Comprehensive Clinical Trials Unit (CCTU), 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.

Explaining the trial’s importance, Professor Breuer, an expert in the use of genomics for tracking hospital infections, 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 National Institute for Health Research (NIHR). This study is one of a number of COVID-19 studies that have been given urgent public health research status by the Department of Health and Social Care.

The COG-UK Hospital Onset COVID-19 Infection (HOCI) trial has been developed with the NIHR UCL/UCLH BRC supported Pathogen Genomics Unit at UCL in collaboration with Imperial College Healthcare Trust, Sheffield Teaching Hospitals NHS Foundation Trust with The University of Sheffield, and the Glasgow Royal Infirmary 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.

Professor 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.”

COVID-19 viruses that are closely related (transmitted from one patient to another or to a healthcare worker) will have the same sequence, while COVID-19 viruses from two people that have different sequences will rule out the possibility of COVID-19  transmission between patients or healthcare workers.   

Professor Alison Holmes, Director of the NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, based at Imperial College London, said: “The understanding and prevention of hospital onset COVID-19 infections will be an important aspect of any recovery strategy for hospitals.

“Established infection prevention methods and surveillance approaches used to track and trace infections and antimicrobial resistance will be applied, but now supported with the additional information provided by genetic fingerprinting.”

The COG-UK project is made up of NHS, Public Health Agencies and academic institutions – including UCL and UCLH – and will deliver large scale sequencing of COVID-19, and intelligence sharing with hospitals, regional NHS centres and the government. In COG-UK samples from patients with confirmed cases of COVID-19 are being sent to a network of sequencing centres all over the UK.

Professor Breuer added: “Using viral genomics we can now track how COVID-19 spreads in hospitals as well as in national and international settings. Our trial will hopefully provide valuable information for the hospitals involved revealing the chains of transmission that must be stopped in order to control COVID-19.”

The following NHS Trusts have confirmed they are participating in the HOCI trial:

  • Imperial College Healthcare NHS Trust
  • Sheffield Teaching Hospitals NHS Foundation Trust
  • NHS Glasgow and Greater Clyde
  • NHS Lothian
  • Guy's and St Thomas' NHS Foundation Trust
  • Manchester University NHS Foundation Trust
  • University College London Hospitals NHS Foundation Trust
  • Royal Free London NHS Foundation Trust
  • University Hospital Southampton NHS Foundation Trust
  • Newcastle Hospitals NHS Foundation Trust
  • Royal Devon & Exeter NHS Foundation Trust
  • Norfolk and Norwich University Hospitals NHS Foundation Trust
  • Liverpool University Hospitals NHS Foundation Trust
  • Leeds Teaching Hospitals NHS Trust

UCL is in discussion with a further six NHS trusts about participating in the trial.



Further information