Marie-Ming Aynaud1, J Javier Hernandez1,2,3, Seda Barutcu1, Ulrich Braunschweig2, Kin Chan1, Joel D Pearson1, Daniel Trcka1, Suzanna L Prosser1, Jaeyoun Kim1, Miriam Barrios-Rodiles1, Mark Jen1, Siyuan Song2,4, Jess Shen1, Christine Bruce5, Bryn Hazlett5, Susan Poutanen5, Liliana Attisano2,4, Rod Bremner1, Benjamin J Blencowe2,3, Tony Mazzulli5, Hong Han2, Laurence Pelletier6,7, Jeffrey L Wrana8,9. 1. Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, M5G 1X5, ON, Canada. 2. Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, M5S 3E1, ON, Canada. 3. Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, ON, Canada. 4. Department of Biochemistry, University of Toronto, Toronto, M5S 1A8, ON, Canada. 5. Department of Microbiology, Mount Sinai Hospital/University Health Network, Toronto, M5G 1X5, ON, Canada. 6. Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, M5G 1X5, ON, Canada. pelletier@lunenfeld.ca. 7. Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, ON, Canada. pelletier@lunenfeld.ca. 8. Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, M5G 1X5, ON, Canada. wrana@lunenfeld.ca. 9. Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, ON, Canada. wrana@lunenfeld.ca.
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.
Population scale sweeps of viral pathogens, such as SARS-CoV-2, require high iene">nteene">nsity testiene">ng for effective managemeene">nt. Here, we describe "Systematic Parallel Analysis of Rn class="Gene">NA 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.
Authors: Robert Warneford-Thomson; Parisha P Shah; Patrick Lundgren; Jonathan Lerner; Jason Morgan; Antonio Davila; Benjamin S Abella; Kenneth Zaret; Jonathan Schug; Rajan Jain; Christoph A Thaiss; Roberto Bonasio Journal: Elife Date: 2022-05-09 Impact factor: 8.713
Authors: Alexander Yermanos; Kai-Lin Hong; Andreas Agrafiotis; Jiami Han; Sarah Nadeau; Cecilia Valenzuela; Asli Azizoglu; Roy Ehling; Beichen Gao; Michael Spahr; Daniel Neumeier; Ching-Hsiang Chang; Andreas Dounas; Ezequiel Petrillo; Ina Nissen; Elodie Burcklen; Mirjam Feldkamp; Christian Beisel; Annette Oxenius; Miodrag Savic; Tanja Stadler; Fabian Rudolf; Sai T Reddy Journal: BMC Genomics Date: 2022-04-11 Impact factor: 3.969
Authors: Faizah A AlMalki; Salim Albukhaty; Amal A Alyamani; Moayad N Khalaf; Sabu Thomas Journal: Environ Sci Pollut Res Int Date: 2022-02-17 Impact factor: 5.190
Authors: Victor H Ferreira; Javier T Solera; Queenie Hu; Victoria G Hall; Berta G Arbol; W Rod Hardy; Reuben Samson; Tina Marinelli; Matthew Ierullo; Avneet Kaur Virk; Alexandra Kurtesi; Faranak Mavandadnejad; Beata Majchrzak-Kita; Vathany Kulasingam; Anne-Claude Gingras; Deepali Kumar; Atul Humar Journal: Nat Commun Date: 2022-08-04 Impact factor: 17.694