A multiplexed, next generation sequencing platform for high-throughput detection of SARS-CoV-2

Abstract Population scale sweeps of viral pathogens, such as SARS-CoV-2, require high intensity testing for effective management. Here, we describe “Systematic Parallel Analysis RNA coupled to Sequencing Covid-19 screening” (C19-SPAR-Seq), a multiplexed, scalable, readily automated platform SARS-CoV-2 detection that is capable analyzing tens thousands patient samples in single run. To address strict requirements control assay parameters and output demanded by clinical diagnostics, employ control-based Precision-Recall Receiver Operator Characteristics (coPR) analysis assign run-specific quality metrics. C19-SPAR-Seq coPR on trial cohort several hundred patients performs with specificity 100% sensitivity 91% low loads, >95% loads associated disease onset peak transmissibility. This study establishes the feasibility employing large-scale monitoring other pathogens.