COG-UK Project Hospital Onset COVID-19 Infections study

The Hospital Onset COVID-19 Infections (HOCI) study, led by Prof Judith Breuer from University College London (UCL), aims to use our understanding of the genome of SARS-CoV-2 to have a direct impact on infection control in hospitals. As the virus spreads, it mutates slowly meaning that direct infections will share more similarities in their genomes than non-linked independent infections. In this way, we can distinguish transmission chains within hospitals from introduction from the community. Working within the COVID-19 Genomics UK (COG-UK) framework, we aim to use whole genome sequencing to generate rapid reports of shared infections within clinical settings for use by infection prevention and control (IPC) teams at hospitals across the UK. This project is a collaboration between multiple COG-UK sequencing hubs and 15 NHS Trusts across the UK. The University of Portsmouth sequencing hub have worked closely with clinicians and IPC teams from University Hospital Southampton NHS Foundation Trust as part of this work.

Hospitals and other healthcare settings have been shown to play a major role in transmission of COVID-19. While rapid testing of patients and staff can be used to identify positive cases, this does not make it clear how infection spreads in hospital outbreaks. This project uses whole genome sequencing of the virus to provide rapid reporting (under 48 hours) of potential direct links between cases. This provides clinicians with evidence of where best to focus infection prevention and control measures to minimise onward spread.