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

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  • AbstractPopulation 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.


  • 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

publication date

  • March 3, 2021