Rapid, inexpensive multiplex pathogen detection using resequencing microarrays

Humanity faces an ongoing battle at the microscopic level to identify, contain, and treat outbreaks of numerous pathogens each year. Global genomic surveillance is the first step in monitoring outbreaks, but high-throughput methods are expensive and time-consuming. To solve this problem, we designed and manufactured a resequencing microarray capable of identifying 35 viral pathogens, 21 pathogenic bacteria, 16 antibiotic resistance genes, and 6 controls. We then developed an assay using these microarrays for the rapid detection of SARS-CoV-2, influenza A, and influenza B. Here, we present the clinical validation data for this test. The assay requires less than two hours to complete and has high-sensitivity, with limits of detection of 125 copies per mL for SARS-CoV-2, 0.01-0.05 TCID₅₀/mL for influenza A, and 0.005-0.01 TCID₅₀/mL for influenza B. The microarrays used for these assays are easily mass-produced using wafer-scale synthesis, making this an affordable option for pathogen screening with broad implications in public health.