Evaluation of Specimen Types and Saliva Stabilization Solutions for SARS-CoV-2 Testing
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Abstract
Identifying SARS-CoV-2 infections through aggressive diagnostic testing remains critical to tracking and curbing the spread of the COVID-19 pandemic. Collection of nasopharyngeal swabs (NPS), the preferred sample type for SARS-CoV-2 detection, has become difficult due to the dramatic increase in testing and consequent supply strain.
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SciScore for 10.1101/2020.06.16.20133041: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: Specimen collection sites and patients: This study was granted non-research determination under the emergency response criterion by the New York State Department of Health Institutional Review Board. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable Two-sample Wilcoxon rank-sum tests were used to compare mean ranks of Ct values between males and females for each specimen type. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources NIH/ATCC Manassas, VA) and amplified in Vero E6 cells, in accordance with Biosafety Level 3 procedures (BSL-3) Vero E6suggested: …SciScore for 10.1101/2020.06.16.20133041: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: Specimen collection sites and patients: This study was granted non-research determination under the emergency response criterion by the New York State Department of Health Institutional Review Board. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable Two-sample Wilcoxon rank-sum tests were used to compare mean ranks of Ct values between males and females for each specimen type. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources NIH/ATCC Manassas, VA) and amplified in Vero E6 cells, in accordance with Biosafety Level 3 procedures (BSL-3) Vero E6suggested: RRID:CVCL_XD71)Software and Algorithms Sentences Resources Testing: Saliva specimens with excessive mucus were digested prior to extraction with Snap n’ Digest (Scientific Device Laboratory, Snapsuggested: (SNAP, RRID:SCR_007936)Ct values were averaged and plotted using GraphPad Prism software version 8.3.0. GraphPad Prismsuggested: (GraphPad Prism, RRID:SCR_002798)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: We detected the following sentences addressing limitations in the study:Notably this sampling strategy has limitations: it may not be suitable for children, mentally challenged patients, or severely ill patients. The collection of saliva is clearly not suitable for intubated patients and the use of alternative sample types should be continued for those situations. Saliva contains many antibodies and enzymes that could ultimately affect the stability of virus particles or viral RNA, which could impede detection. In our sample comparison from the NR cohort, significantly lower Ct values were observed in saliva samples than those in NS or NPS. As a result, concerns were raised regarding viral stability in this sample type and a series of experiments were undertaken to assess this and the possibility of improving stability with solutions from commercial saliva collection kits. Overall, we found a surprising virus stability in saliva alone for up to 7 days, even at room temperature, whereas the addition of stabilization solutions had adverse effects. It must be noted that these solutions are intended for stabilizing DNA not RNA, and subsequent versions from the manufacturers that are currently being prepared specifically for RNA stabilization may have very different results. It must also be noted that virus stability was only measured with regard to molecular detection. For investigators interested in studies on culturable infectious particles, the stability of virus infectivity may be different. In symptomatic COVID-19 patients, SARS-CoV-2 viral RNA ...
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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