Sensitive extraction-free SARS-CoV-2 RNA virus detection using a chelating resin
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SciScore for 10.1101/2021.01.29.21250790: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Consent: Human samples: Samples were collected from healthy volunteers and subjects who provided informed consent to National Institutes of Health (NIH) Institutional Review Board (IRB)-approved protocols (20-D-0094, NCT04348240; 20-CC-0128, NCT04424446) at the NIH Clinical Center.
IRB: Human samples: Samples were collected from healthy volunteers and subjects who provided informed consent to National Institutes of Health (NIH) Institutional Review Board (IRB)-approved protocols (20-D-0094, NCT04348240; 20-CC-0128, NCT04424446) at the NIH Clinical Center.Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not … SciScore for 10.1101/2021.01.29.21250790: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Consent: Human samples: Samples were collected from healthy volunteers and subjects who provided informed consent to National Institutes of Health (NIH) Institutional Review Board (IRB)-approved protocols (20-D-0094, NCT04348240; 20-CC-0128, NCT04424446) at the NIH Clinical Center.
IRB: Human samples: Samples were collected from healthy volunteers and subjects who provided informed consent to National Institutes of Health (NIH) Institutional Review Board (IRB)-approved protocols (20-D-0094, NCT04348240; 20-CC-0128, NCT04424446) at the NIH Clinical Center.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 , heat-inactivated FBS, 293FT cells were procured from Thermo Fisher Scientific 293FTsuggested: ATCC Cat# PTA-5077, RRID:CVCL_6911)Software and Algorithms Sentences Resources Clinical laboratory CDC SARS-CoV-2 Assay: The conventional RNA-extraction RT-qPCR method following CDC guideline has been reported, and herein referred as easyMAG-CL (clinical laboratory) assay.21 Briefly, nucleic acid from individual specimens was extracted from 200 μL of Saliva/NPspecimens using the NucliSENS® easyMAG® platform (bioMérieux, Marcy l’Etoile, France) with an elution volume of 50 μL. NucliSENS®suggested: NoneMolecular biology grade water (cat# 351-029-101), TE pH 8.0 (cat# 351-011-131), 1M Tris-HCl pH7.5 (cat# 351-006-101), HBSS with Ca2+/Mg2+ (cat# 114-061-101) were from Quality Biological (Gaithersburg, MD). Quality Biologicalsuggested: NoneThe Luna Universal Probe One-Step RT-qPCR Kit (#E3006X, NEB) was used for RT-qPCR with the following cycling conditions using a QuantStudio 3 real-time PCR system (ThermoFisher Scientific): NEB-Luna-Program I: 55°C for 10 min, 95°C for 1 min, and 45 cycles of 95 °C for 10 sec and 60 °C for 40 sec or NEB-Luna-Program II: 55°C for 10 min, 95°C for 1 min, and 45 cycles of 95 °C for 5 sec and 60 °C for 20 sec. ThermoFisher Scientific)suggested: 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: We detected the following sentences addressing limitations in the study:One limitation of the current study was the low-level contamination observed in the RT-ddPCR assay, where one or two positive droplets were observed in the no-template control reactions. The contamination could result from either viral RNA or PCR amplicon present in the research laboratory. Due to the background contamination, we used 1.8 copies/µl as the low limit of detection for the SARS-CoV-2 N1/N2 RT-ddPCR assay. According to the FDA Emergency Use Authorization (EUA) by the manufacturer Bio-Rad, the low limit of detection in the 1-well RT-ddPCR assay system is 2 positive droplets and no positive droplets observed in no-template controls. Thus the low limit of detection in a RT-ddPCR assay could reach 0.1 copy/µl if performing in a clean room. In summary, we robustly demonstrate improvements in COVID-19 viral testing workflow using synthetic and real-world samples employing the Chelex-based extraction-free workflow. This methodology has the clear benefit of dramatic improvements in sensitivity, cost, and time savings for clinical laboratory testing. Additionally, this method exhibits improved safety characteristics including obviating the need for the use of a biological safety cabinet and harsh disinfection chemicals prior to testing. Finally, this method is easily adapted to both clinical and research laboratories and could be standard of care for nucleic acid testing and transport in the near future.
Results from TrialIdentifier: We found the following clinical trial numbers in your paper:
Identifier Status Title NCT04348240 Recruiting Transmissibility and Viral Load of SARS-CoV-2 in Oral Secret… NCT04424446 Recruiting Saliva as Source of Detection for SARS-CoV-2 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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