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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.
  • Aynaud MM; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, M5G 1X5, ON, Canada.
  • Hernandez JJ; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, M5G 1X5, ON, Canada.
  • Barutcu S; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, M5S 3E1, ON, Canada.
  • Braunschweig U; Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, ON, Canada.
  • Chan K; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, M5G 1X5, ON, Canada.
  • Pearson JD; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, M5S 3E1, ON, Canada.
  • Trcka D; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, M5G 1X5, ON, Canada.
  • Prosser SL; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, M5G 1X5, ON, Canada.
  • Kim J; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, M5G 1X5, ON, Canada.
  • Barrios-Rodiles M; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, M5G 1X5, ON, Canada.
  • Jen M; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, M5G 1X5, ON, Canada.
  • Song S; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, M5G 1X5, ON, Canada.
  • Shen J; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, M5G 1X5, ON, Canada.
  • Bruce C; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, M5S 3E1, ON, Canada.
  • Hazlett B; Department of Biochemistry, University of Toronto, Toronto, M5S 1A8, ON, Canada.
  • Poutanen S; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, M5G 1X5, ON, Canada.
  • Attisano L; Department of Microbiology, Mount Sinai Hospital/University Health Network, Toronto, M5G 1X5, ON, Canada.
  • Bremner R; Department of Microbiology, Mount Sinai Hospital/University Health Network, Toronto, M5G 1X5, ON, Canada.
  • Blencowe BJ; Department of Microbiology, Mount Sinai Hospital/University Health Network, Toronto, M5G 1X5, ON, Canada.
  • Mazzulli T; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, M5S 3E1, ON, Canada.
  • Han H; Department of Biochemistry, University of Toronto, Toronto, M5S 1A8, ON, Canada.
  • Pelletier L; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, M5G 1X5, ON, Canada.
  • Wrana JL; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, M5S 3E1, ON, Canada.
Nat Commun ; 12(1): 1405, 2021 03 03.
Article in English | MEDLINE | ID: covidwho-1117349
Preprint
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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.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: High-Throughput Nucleotide Sequencing / SARS-CoV-2 Type of study: Cohort study / Diagnostic study / Observational study / Prognostic study / Randomized controlled trials / Systematic review/Meta Analysis Limits: Humans Language: English Journal: Nat Commun Journal subject: Biology / Science Year: 2021 Document Type: Article Affiliation country: S41467-021-21653-y

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Full text: Available Collection: International databases Database: MEDLINE Main subject: High-Throughput Nucleotide Sequencing / SARS-CoV-2 Type of study: Cohort study / Diagnostic study / Observational study / Prognostic study / Randomized controlled trials / Systematic review/Meta Analysis Limits: Humans Language: English Journal: Nat Commun Journal subject: Biology / Science Year: 2021 Document Type: Article Affiliation country: S41467-021-21653-y