Real-Time Genomic Surveillance Systems

Abstract

Real-time genomic surveillance systems sequence pathogen genomes during active outbreaks to track transmission, detect variants, and inform public health responses, and the COVID-19 pandemic demonstrated the transformative potential of genomic surveillance at global scale, yet adoption of different surveillance architectures varies across pathogen contexts and health system capacities. We evaluated 214 real-time genomic surveillance programmes across centres in Germany and Sweden between 2018 and 2022, spanning five system categories: centralised national pathogen sequencing pipelines, decentralised portable sequencing networks, cloud-based phylodynamic analysis platforms, AI-enhanced variant detection systems, and integrated One Health surveillance frameworks. A Genomic Surveillance Index (GSI) was constructed from five sub-scores -- turnaround time from sample to sequence, variant detection sensitivity, public health action integration, geographic coverage completeness, and cross-sector data sharing-- with weights from regression against sustained adoption. GSI correlated with adoption at r = +0.84 and discriminated adopted from non-adopted systems with an AUC of 0.884. Centralised national pipelines scored highest (mean GSI 0.826), while integrated One Health trailed at 0.600. Only 35.6 percent exceeded the 0.75 threshold. Turnaround time carried the largest weight (beta = +0.278), followed by variant detection sensitivity (beta = +0.230).