Establishing sequencing-based viral diagnostics for pandemic and outbreak diagnostics in the clinical laboratory

Effective pandemic and outbreak management, coupled with the study of infectious disease transmission and antimicrobial resistance, constitute critical focal points in virus diagnostics. We anticipate that the implementation of whole-genome sequencing (WGS)-based diagnostic methods for both known and unknown viral infections within the clinical laboratory progressively will gain significance in terms of patient care and societal impact. This proposal specifically aims to establish a flexible pathogen detection approach, based on shotgun metagenomic sequencing and real-time bioinformatic detection, allowing for detection of unknown pathogens from clinical samples, and use in the clinical laboratory. Simultaneously, the approach will enhance pandemic and outbreak preparedness in the clinical laboratory.