Optimization of SARS-CoV-2 detection by RT-QPCR without RNA extraction
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Abstract
Rapid and reliable screening of SARS-CoV-2 is fundamental to assess viral spread and limit the pandemic we are facing. In this study we evaluated the reliability and the efficiency of a direct RT-QPCR method (without RNA extraction) using SeeGene Allplex™ 2019-nCoV RT-QPCR and the influence of swab storage media composition on further viral detection.
We show that SeeGene’s assay provides similar efficiency as the RealStar ® SARS-CoV-2 RT-PCR kit (Altona Diagnostics), and that RNA extraction is not necessary nor advantageous if samples are stored in UTM or molecular water but is recommended if samples are stored in saline solution and in Hanks medium.
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SciScore for 10.1101/2020.04.06.028902: (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. Table 2: Resources
Software and Algorithms Sentences Resources RNA was extracted from 700 μl of 2 ml of patient’s swab medium using Abbott mSample Preparation Systems DNA kit on m2000sp instrument; the eluate was 90 μl. Abbott mSample Preparation Systemssuggested: NoneRT-QPCR plates were automated: prepared on the Abbott m2000sp and routinely detected on m2000rt using the Altona RealStar® SARS-CoV-2 RT-PCR Kit RUO according to the manufacturer’s instruction. Abbottsuggested: (Abbott, RRID:SCR_010477)Results from OddPub: We did not detect open …
SciScore for 10.1101/2020.04.06.028902: (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. Table 2: Resources
Software and Algorithms Sentences Resources RNA was extracted from 700 μl of 2 ml of patient’s swab medium using Abbott mSample Preparation Systems DNA kit on m2000sp instrument; the eluate was 90 μl. Abbott mSample Preparation Systemssuggested: NoneRT-QPCR plates were automated: prepared on the Abbott m2000sp and routinely detected on m2000rt using the Altona RealStar® SARS-CoV-2 RT-PCR Kit RUO according to the manufacturer’s instruction. Abbottsuggested: (Abbott, RRID:SCR_010477)Results 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:- No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
- No funding statement was detected.
- No protocol registration statement was detected.
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