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

Marie-Ming AynaudJ Javier HernandezSeda Avcioglu BarutcuUlrich BraunschweigKin ChanJoel D PearsonDaniel TrckaSuzanna L ProsserJaeyoun KimMiriam Barrios-RodilesMark JenSiyuan SongJess ShenChristine BruceBryn HazlettSusan PoutanenLiliana AttisanoRod BremnerBenjamin J BlencoweTony MazzulliHong HanLaurence PelletierJeffrey L Wrana
Published in: Nature communications (2021)
Population scale sweeps of viral pathogens, such as SARS-CoV-2, require high intensity testing for effective management. Here, we describe "Systematic Parallel Analysis of RNA coupled to Sequencing for Covid-19 screening" (C19-SPAR-Seq), a multiplexed, scalable, readily automated platform for SARS-CoV-2 detection that is capable of analyzing tens of thousands of patient samples in a single run. To address strict requirements for control of assay parameters and output demanded by clinical diagnostics, we employ a control-based Precision-Recall and Receiver Operator Characteristics (coPR) analysis to assign run-specific quality control metrics. C19-SPAR-Seq coupled to coPR on a trial cohort of several hundred patients performs with a specificity of 100% and sensitivity of 91% on samples with low viral loads, and a sensitivity of >95% on high viral loads associated with disease onset and peak transmissibility. This study establishes the feasibility of employing C19-SPAR-Seq for the large-scale monitoring of SARS-CoV-2 and other pathogens.
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