A direct RT-qPCR approach to test large numbers of individuals for SARS-CoV-2
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Abstract
SARS-CoV-2 causes substantial morbidity and mortality in elderly and immunocompromised individuals, particularly in retirement homes, where transmission from asymptomatic staff and visitors may introduce the infection. Here we present a cheap and fast screening method based on direct RT-qPCR to detect SARS-CoV-2 in single or pooled gargle lavages (“mouthwashes”). This method detects individuals with large viral loads (Ct≤29) and we use it to test all staff at a nursing home daily over a period of three weeks in order to reduce the risk that the infection penetrates the facility. This or similar approaches can be implemented to protect hospitals, nursing homes and other institutions in this and future viral epidemics.
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SciScore for 10.1101/2020.06.24.20139501: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Consent: Each individual gave written informed consent before entry into the study.
IRB: The study was approved by the Ethics Committee of the Saxonian medical chamber (EK-allg-37/10-1).Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources RT-qPCR reaction was run on BioRad CFX96 Real-Time system and results analyzed with Bio-Rad CFX Manager software where the Ct determination mode was set to “regression”. Bio-Rad CFX Managersuggested: NoneCFXsuggested: NoneResults from OddPub: We did not detect open data. We also did not detect open code. …
SciScore for 10.1101/2020.06.24.20139501: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Consent: Each individual gave written informed consent before entry into the study.
IRB: The study was approved by the Ethics Committee of the Saxonian medical chamber (EK-allg-37/10-1).Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources RT-qPCR reaction was run on BioRad CFX96 Real-Time system and results analyzed with Bio-Rad CFX Manager software where the Ct determination mode was set to “regression”. Bio-Rad CFX Managersuggested: NoneCFXsuggested: NoneResults from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
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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SciScore for 10.1101/2020.06.24.20139501: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement After appropriate informed consent , all staff working at the facility delivered a daily gargle lavage sample at the beginning or end of their working shifts . Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources RT-qPCR reaction was run on BioRad CFX96 Real-Time system and results analyzed with Bio-Rad CFX Manager software where the Ct determination mode was set to “regression” . Bio-Rad CFX Managersuggested: None<div style="margin-bottom:8px"> <div><b>CFX</b></div>SciScore for 10.1101/2020.06.24.20139501: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement After appropriate informed consent , all staff working at the facility delivered a daily gargle lavage sample at the beginning or end of their working shifts . Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources RT-qPCR reaction was run on BioRad CFX96 Real-Time system and results analyzed with Bio-Rad CFX Manager software where the Ct determination mode was set to “regression” . Bio-Rad CFX Managersuggested: None<div style="margin-bottom:8px"> <div><b>CFX</b></div> <div>suggested: None</div> </div> </td></tr></table>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 Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).
Results from OddPub: We did not find a statement about open data. We also did not find a statement about open code. Researchers are encouraged to share open data when possible (see Nature blog).
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