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Rapid and accurate detection of viral pathogens is essential for public health surveillance and outbreak response. With the Biomark™ X9 System for High-Throughput Genomics, labs can efficiently detect and subtype multiple viral pathogens in a single run without the challenges of multiplexing. This technical note demonstrates how we used a custom assay panel with the 48.48 Dynamic Array™ IFC-X (integrated fluidic circuit) to detect and differentiate influenza, RSV, SARS-CoV-2, coronaviruses, enteroviruses and more with high specificity, no cross-reactivity and minimal reagent use.