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

Aynaud, Marie-Ming; Hernandez, J. Javier; Barutcu, Seda; Braunschweig, Ulrich; Chan, Kin; Pearson, Joel D.; Trcka, Daniel; Prosser, Suzanna L.; Kim, Jaeyoun; Barrios-Rodiles, Miriam; Jen, Mark; Song, Siyuan; Shen, Jess; Bruce, Christine; Hazlett, Bryn; Poutanen, Susan; Attisano, Liliana; Bremner, Rod; Blencowe, Benjamin J.; Mazzulli, Tony; Han, Hong; Pelletier, Laurence; Wrana, Jeffrey L.

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.