UCL Institute of Health Informatics


Infection response through virus genomics (ICONIC)

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.


Precision medicine

Public health

Other work

Real-time detection of influenza outbreaks in hospitals: demonstrating infection response through virus genomics (ICONIC)


Prof Andrew Hayward

Dr Laura Shallcross

Dr Zisis Kozlakidis

Dr Ruth Blackburn

Dr Ellen Fragaszy

Mr Anil Gunesh

Ms Dewi Aisyah

Ms Fatima Wurie


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



MRC HIV Drug Resistance Database

HCV Research UK Biobank


Woolhouse MJ, Rambaut A & Kellam P. Lessons from Ebola: improving infectious disease surveillance to inform outbreak management. Science Translational Medicine 2015;7(307):307rv5