Comparison of 12 molecular detection assays for SARS-CoV-2
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Abstract
Molecular testing for SARS-CoV-2 is the mainstay for accurate diagnosis of the infection, but the diagnostic performances of available assays have not been defined. We compared 12 molecular diagnostic assays, including 8 commercial kits using 155 respiratory samples (65 nasopharyngeal swabs, 45 oropharyngeal swabs, and 45 sputum) collected at 2 Japanese hospitals. Sixty-eight samples were positive for more than one assay and one genetic locus and were defined as true positive samples. All the assays showed a specificity of 100% (95% confidence interval, 95.8 to 100). The N2 assay kit of the US Centers for Disease Control and Prevention (CDC) and the N2 assay of the Japanese National Institute of Infectious Disease (NIID) were the most sensitive assays with 100% sensitivity (95% confidence interval, 94.7 to 100), followed by the CDC N1 kit, E assay by Corman, and NIID N2 assay multiplex with internal control reactions. These assays are reliable as first-line molecular assays in laboratories when combined with appropriate internal control reactions.
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SciScore for 10.1101/2020.06.24.170332: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: Ethical statement: The Ethics Committee of Kyoto University Graduate School and the Faculty of Medicine approved this study (R2379). Randomization In this study, we included all 68 SARS-CoV-2-positive samples and 87 randomly selected negative samples from 107 patients. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources All statistical analyses were performed using SAS® Studio 3.8 (SAS Institute Inc. SAS Institutesuggested: (Statistical Analysis System, RRID:SCR_008567)Results from OddPub: Thank you for sharing your data.
Results from LimitationRecognizer: We detected …SciScore for 10.1101/2020.06.24.170332: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: Ethical statement: The Ethics Committee of Kyoto University Graduate School and the Faculty of Medicine approved this study (R2379). Randomization In this study, we included all 68 SARS-CoV-2-positive samples and 87 randomly selected negative samples from 107 patients. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources All statistical analyses were performed using SAS® Studio 3.8 (SAS Institute Inc. SAS Institutesuggested: (Statistical Analysis System, RRID:SCR_008567)Results from OddPub: Thank you for sharing your data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:The study limitations included a relatively small sample size of each specimen type and lack of clinical information, measurements by multiple investigators, and genomic variation analysis. In conclusion, we validated the NIID N2 assay with EAV control reaction and found that the CDC EUA kit (N1/N2/RNaseP), NIID N2 with/without EAV, and Corman E assays were the most sensitive assays. They are feasible as references and clinical diagnostic tests until commercial kits with internal control reactions or fully automated systems that have high diagnostic performances are available in clinical laboratories. Continuous efforts to improve COVID-19 diagnostics are important to control this pandemic.
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.
- No funding statement was detected.
- No protocol registration statement was detected.
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