A multiplexed, next generation sequencing platform for high-throughput detection of SARS-CoV-2
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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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SciScore for 10.1101/2020.10.15.20212712: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources HEK293T RNA was extracted using the Total RNA extraction kit (Qiagen) HEK293Tsuggested: NCBI_Iran Cat# C498, RRID:CVCL_0063)Software and Algorithms Sentences Resources All libraries were sequenced with MiSeq or NextSeq 500 (Illumina) using 75 bp paired-end sequencing. MiSeqsuggested: (A5-miseq, RRID:SCR_012148)(scripts are available at https://github.com/seda-barutcu/FASTQstitch and … SciScore for 10.1101/2020.10.15.20212712: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources HEK293T RNA was extracted using the Total RNA extraction kit (Qiagen) HEK293Tsuggested: NCBI_Iran Cat# C498, RRID:CVCL_0063)Software and Algorithms Sentences Resources All libraries were sequenced with MiSeq or NextSeq 500 (Illumina) using 75 bp paired-end sequencing. MiSeqsuggested: (A5-miseq, RRID:SCR_012148)(scripts are available at https://github.com/seda-barutcu/FASTQstitch and https://github.com/seda-barutcu/MultiplexedPCR-DeepSequence-Analysis) The top enriched sequence variant from each sample is used for multiple alignment analysis using CLUSTALW. CLUSTALWsuggested: (ClustalW, RRID:SCR_017277)Results from OddPub: Thank you for sharing your code.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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