Expecting the unexpected: can viral metagenomics enhance optimised standard diagnostic pathways for detection of imported pathogens?


Current testing practices for imported fever syndromes in Ireland are heterogenous and suboptimal, prolonging clinical care and limiting data capture for early warning surveillance systems. Identifying and diagnosing aetiological pathogens for imported fever syndromes with a standardised approach would benefit individual patients, healthcare organisations and public health surveillance of infectious diseases with outbreak potential. Imported, new and emerging viral pathogens are of particular interest due to concern around transmissibility and pandemic potential. Clinical metagenomics is emerging as a diagnostic tool to supplement traditional methods and the extent to which it may improve the diagnostic yield for imported fever syndromes is not known. 

Aims and hypotheses 

This project aims to optimise national testing pathways for imported fever in Ireland. It is hypothesised that a national integrated clinical and laboratory pathway can increase diagnostic yield for clinical and surveillance purposes, and that the addition of viral metagenomics can increase pathogen detection in those not identified after optimisation of traditional methods.  


  1. Develop a standardised clinical pathway for imported fever using currently available clinical platforms. 
  2. Establish a national clinical cohort of patients presenting with imported fever. 
  3. Assess the additional diagnostic utility of viral metagenomics when added to an optimised standard pathway.   
  4. Investigate factors that can elucidate the pathogenicity of organisms identified by clinical metagenomics alone. 


This project will achieve the following outputs: 

  1. A national optimised integrated clinical diagnostic pathway for imported fever 
  2. A national imported fever cohort with biobanked samples and associated metadata
  3. A recommendation for the use of clinical metagenomics in supplementing standard imported fever diagnostic pathways 
  4. Provision of granular data for reporting to ECDC early warning and threat detection systems 
Award Date
22 September 2023
Award Value
Principal Investigator
Dr Christine Kelly
Host Institution
University College Dublin
HRB Postdoctoral Fellowships: CSF 2023