The UCL Pathogen Genomics Unit (PGU) has pioneered new methods to sequence bacteria and viruses (pathogens) directly from clinical material which are now used worldwide to monitor hospital and community-acquired infections and drug resistance. During the COVID pandemic the PGU has been the London hub for COG-UK, the COVID-19 Genomics UK consortium, providing rapid sequencing of SARS-CoV-2 genomes.
The PGU was established in 2016 by UCL Professor Judith Breuer funded by the UCLH-BRC and the MRC. The PGU was the first not-for-profit pathogen sequencing service in the UK and currently supports over 300 national and international collaborators. The PGU pioneered methodology for enriching samples of hard-to-grow pathogens to allow them to be rapidly sequenced directly from clinical material. These methods are now used globally by public health authorities to monitor how pathogens spread, develop drug resistance and acquire mutations to increase infectivity. The team’s unique compound used in these processes was licensed to Aglient PLC (2017).
The PGU collaborated with Public Health England (PHE) to optimise Hepatitis C virus sequencing(1), identified vaccine escape mutants in Ns.meningitidis (causes meningitis/ septicaemia) and investigated drug resistance in recurrent Chlamydia? It also established a national encephalitis (brain inflammation) diagnosis service(2) and identified previously undetected pathogens in almost half of the encephalitis cases it has assessed.??
The PGU played a vital role in the fight against COVID-19 by hosting the London hub of COG-UK to provide rapid sequencing of SARS-CoV-2 genomes. Supporting nine hospitals across London the PGU generated more than 15,000 sequences, providing important data on virus spread to inform local and national public health policy.
The PGU also led the Hospital Onset Covid Infection (HOCI) study(3), with a large proportion of samples from UCLH. HOCI demonstrated the impact of the COVID-19 alpha-variant on hospital deaths and outbreaks. Data from the study influenced decision making by government committees SAGE and NERVTAG.
In collaboration with hVivo-plc and Wellcome, the PGU is leading genome sequencing and quality assurance of SARS-CoV-2 being tested in the world’s only human challenge clinical trial, commissioned by the UK Vaccine Task Force. The PGU is one of only two sites providing ongoing SARS-CoV-2 sequencing for the Department of Health and PHE.
- Thomson et al. J Clin Microbiology, 2016; 2. Morfopoulou et al. N Engl J Med, 2016; 3. Stirrip O et al. eLife, 2021
