4 Oct 2022

Viral sequencing could be key in managing hospital-acquired infection rates as we learn to live with COVID-19

At the height of the pandemic, hospitals were shown to play a considerable role in the spread of SARS-CoV-2. Professor Judith Breuer and her team at University College London set about investigating whether ‘real-time’ viral genomic sequencing might have a role in helping to limit the spread of SARS-CoV-2 in hospitals.

Protecting the most vulnerable populations during the COVID-19 pandemic has been at the forefront of infection control strategies across the globe. Unfortunately, populations who are at higher risk for severe COVID-19 and therefore have a higher rate of mortality, are also most likely to be exposed to hospital settings during the peaks of infections. Hospital-acquired infections accounted for more than 5% of lab-confirmed cases from March-August 2020 in the UK, representing more than 11% of SARS-CoV-2 cases within hospitals during this period.

It is within this context that scientific investigations such as the COG-UK Hospital-Onset COVID-19 Infections (HOCI) study demonstrate themselves to be valuable. The study’s aims were to understand whether rapid, real-time genomic sequencing can support infection control teams in preventing the spread of SARS-CoV-2 in hospitals. This study involved several hospitals across the country, namely: University College London Hospitals NHS Foundation Trust, Imperial College Healthcare NHS Trust, Royal Free NHS Foundation Trust, Guys and St Thomas NHS Foundation Trust, St George’s University Hospitals NHS Foundation Trust, Barts Health NHS Trust, University Hospital Southampton NHS Foundation Trust, Sandwell and West Birmingham NHS Trust, NHS Greater Glasgow and Clyde, Liverpool University Hospitals NHS Foundation Trust, Manchester University NHS Foundation Trust, Nottingham University Hospitals NHS Trust, Newcastle Hospitals NHS Foundation Trust, and Sheffield Teaching Hospitals NHS Foundation Trust.

Professor Judith Breuer, Chief Investigator for the study, explains that the key research question was “whether rapid sequencing of SARS-CoV-2 could help to identify who had infected whom in the hospital more accurately than infection prevention control alone.”  This question built on previous research by many groups that has shown that pathogen sequencing can better identify the sources of infection and transmission chains than infection prevention and control (IPC) alone. “By matching the letters of code that make up the nucleic acid in one virus with the letters of code that make up another virus – we can link infections more accurately.”

While sequencing is a potentially powerful tool, there is currently limited information about its feasibility for use in routine IPC, whether can change on IPC actions, and whether it will reduce transmission of infection in hospitals. The HOCI study harnessed the power of COG-UK sequencing to provide information as to whether routine SARS-CoV-2 sequencing could help interrupt the spread of the infection in the hospital.

A total of 2,170 hospital-acquired infections were recorded from 15 October 2020 to 26 April 2021 across 14 UK hospitals, with a median age of 76.7 years, and 80% of subjects having at least one clinically significant co-morbidity (e.g., pre-existing cardiovascular disease). SARS-CoV-2 genome sequence reports were generated for 49.2% of the cases reported in hospitals that carried out real-time genomic sequencing during study. The results showed that sequencing SARS-CoV-2 changed IPC actions in 20% of cases returned within 5 days. Importantly, over 80% of IPC teams found the information helpful.

Perhaps the most important outcome of the HOCI study has been to measure and document, through detailed interviewing of staff involved, what would need to change for pathogen sequencing to be incorporated into routine IPC practice. According to Judith, there are three critical steps: “rapid transport and sequencing of samples, automated issuing of simple reports directly to IPC teams to identify where linked infections are occurring, and training of hospital teams to use the information effectively”.  With new rapid sequencing methods and growing familiarity with sequence generation and interpretation, two of the three barriers are already being addressed.  We now need the computer tools that will rapidly and automatically link data on patient movements and risk factors to the sequence data providing seamless rapid delivery of results.

To read the full publication, please click HERE.

COVID-19 Genomics UK (COG-UK)

The COVID-19 Genomics UK (COG-UK) consortium works in partnership to harness the power of SARS-CoV-2 genomics in the fight against COVID-19.

Led by Professor Sharon Peacock of the University of Cambridge, COG-UK is made up of an innovative collaboration of NHS organisations, the four public health agencies of the UK, the Wellcome Sanger Institute and sixteen academic partners. A full list of collaborators can be found here.

The COVID-19 pandemic, caused by SARS-CoV-2, represents a major threat to health. The COG-UK consortium was formed in March 2020 to deliver SARS-CoV-2 genome sequencing and analysis to inform public health policy and to support the establishment of a national pathogen sequencing service, with sequence data now predominantly generated by the Wellcome Sanger Institute and the Public Health Agencies.

SARS-CoV-2 genome sequencing and analysis plays a key role in the COVID-19 public health response by enabling the identification, tracking and analysis of variants of concern, and by informing the design of vaccines and therapeutics. COG-UK works collaboratively to deliver world-class research on pathogen sequencing and analysis, maximise the value of genomic data by ensuring fair access and data linkage, and provide a training programme to enable equity in global sequencing.