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The world’s first whole genome sequencing of viral pathogens integrated into routine healthcare to support patient stratification and viral outbreak surveillance.
The Problem
Viral infections represent a significant burden to the NHS. Annual treatment and care costs for Human Immunodeficiency Virus (HIV) and Hepatitis C Virus (HCV) approximate to £1billion per virus. Norovirus infections have an estimated cost of >£100M per year, and influenza pandemics bring national costs in excess of £2billion. Current clinical treatments of viral infections are largely conservative and without taking into account the genetic information of the infecting pathogen. On the other hand new molecular methods generate a wealth of data that requires specialist staff and a long time to process and utilise.
Our Research
ICONIC, a major project funded by the UK Department of Health and the Wellcome Trust, has developed sustainable next generation technology for the viral full-length genome sequencing using residual diagnostic samples within the diagnostic value chain. ICONIC processes and assembles de novo the virus genomes using high performance computation available in ‘cloud resources’ bypassing the need for embedding complex computer technology in the NHS and specialist staff. It links virus genetics and diagnostic information to hospital based clinical information and generates the appropriate clinical reporting tools.
The significant genomic variation of viruses underpins pathogenicity, drug resistance and transmission and allows genetics based patient stratification, infection control and molecular epidemiology. ICONIC uses specific examples to address the potential embedding of this new technology within the UK diagnostic environment.
- Direct Patient Management
ICONIC aims to enhance the current HIV drug resistance reports with details on full virus genomes providing a clinical reporting system, with predicted drug susceptibilities. This is expected to lead to continued improvements in response to therapy and alter HIV management guidelines This will be extended to HCV where there is a need for virus genetic monitoring of treatment responses.
- Hospital Infection Control
Norovirus and influenza outbreaks in hospitals are due to the introduction of a single case but often it is unclear if the outbreak persistence is due to ongoing person-to-person transmission or from community introductions. ICONIC aims to deliver rapid, real-time results on these questions determining optimal infectious control management.
- Epidemiology and Surveillance
Understanding the community spread of influenza and measles infections is essential for implementing appropriate control measures, ranging from local immunisation, to national surveillance. The resolution offered by whole genome sequencing will be used to enhance/inform local outbreak investigation and national/international surveillance.
Themes
Other work
People
Prof Andrew Hayward
Dr Laura Shallcross
Dr Zisis Kozlakidis
Dr Ruth Blackburn
Dr Ellen Fragaszy
Mr Anil Gunesh
Ms Dewi Aisyah
Ms Fatima Wurie
Collaborators
Public Health England
Wellcome Trust Sanger Institute
University College London Hospitals NHS Foundation Trust
Barts Health NHS Trust
Royal Free London NHS Foundation Trust
Guy’s and St. Thomas’ NHS Foundation Trust
Nottingham University Hospitals NHS Trust
States of Guernsey – Health and Social Services
The University of Nottingham
The University of Edinburgh
IntelTM
IlluminaTM
MRC HIV Drug Resistance Database
HCV Research UK Biobank
Publications
Woolhouse MJ, Rambaut A & Kellam P. Lessons from Ebola: improving infectious disease surveillance to inform outbreak management. Science Translational Medicine 2015;7(307):307rv5