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

Author

Listed:
  • Marie-Ming Aynaud

    (Mount Sinai Hospital)

  • J. Javier Hernandez

    (Mount Sinai Hospital
    University of Toronto
    University of Toronto)

  • Seda Barutcu

    (Mount Sinai Hospital)

  • Ulrich Braunschweig

    (University of Toronto)

  • Kin Chan

    (Mount Sinai Hospital)

  • Joel D. Pearson

    (Mount Sinai Hospital)

  • Daniel Trcka

    (Mount Sinai Hospital)

  • Suzanna L. Prosser

    (Mount Sinai Hospital)

  • Jaeyoun Kim

    (Mount Sinai Hospital)

  • Miriam Barrios-Rodiles

    (Mount Sinai Hospital)

  • Mark Jen

    (Mount Sinai Hospital)

  • Siyuan Song

    (University of Toronto
    University of Toronto)

  • Jess Shen

    (Mount Sinai Hospital)

  • Christine Bruce

    (Mount Sinai Hospital/University Health Network)

  • Bryn Hazlett

    (Mount Sinai Hospital/University Health Network)

  • Susan Poutanen

    (Mount Sinai Hospital/University Health Network)

  • Liliana Attisano

    (University of Toronto
    University of Toronto)

  • Rod Bremner

    (Mount Sinai Hospital)

  • Benjamin J. Blencowe

    (University of Toronto
    University of Toronto)

  • Tony Mazzulli

    (Mount Sinai Hospital/University Health Network)

  • Hong Han

    (University of Toronto)

  • Laurence Pelletier

    (Mount Sinai Hospital
    University of Toronto)

  • Jeffrey L. Wrana

    (Mount Sinai Hospital
    University of Toronto)

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 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.

Suggested Citation

  • Marie-Ming Aynaud & J. Javier Hernandez & Seda Barutcu & Ulrich Braunschweig & Kin Chan & Joel D. Pearson & Daniel Trcka & Suzanna L. Prosser & Jaeyoun Kim & Miriam Barrios-Rodiles & Mark Jen & Siyuan, 2021. "A multiplexed, next generation sequencing platform for high-throughput detection of SARS-CoV-2," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-21653-y
    DOI: 10.1038/s41467-021-21653-y
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