Saliva TwoStep for rapid detection of asymptomatic SARS-CoV-2 carriers
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Abstract
Here, we develop a simple molecular test for SARS-CoV-2 in saliva based on reverse transcription loop-mediated isothermal amplification. The test has two steps: (1) heat saliva with a stabilization solution and (2) detect virus by incubating with a primer/enzyme mix. After incubation, saliva samples containing the SARS-CoV-2 genome turn bright yellow. Because this test is pH dependent, it can react falsely to some naturally acidic saliva samples. We report unique saliva stabilization protocols that rendered 295 healthy saliva samples compatible with the test, producing zero false positives. We also evaluated the test on 278 saliva samples from individuals who were infected with SARS-CoV-2 but had no symptoms at the time of saliva collection, and from 54 matched pairs of saliva and anterior nasal samples from infected individuals. The Saliva TwoStep test described herein identified infections with 94% sensitivity and >99% specificity in individuals with sub-clinical (asymptomatic or pre-symptomatic) infections.
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SciScore for 10.1101/2020.07.16.20150250: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IACUC: Protocols were approved by the Institutional Biosafety Committee. 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 The results were visualized and analyzed using ThermoFisher’s Design and Analysis software. ThermoFisher’ssuggested: 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 …SciScore for 10.1101/2020.07.16.20150250: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IACUC: Protocols were approved by the Institutional Biosafety Committee. 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 The results were visualized and analyzed using ThermoFisher’s Design and Analysis software. ThermoFisher’ssuggested: 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 10.1101/2020.07.16.20150250: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization Sample identification was recorded, sample tubes were shuffled randomly, and then passed blindly to a second member of our personnel to carry out our colorimetric RT-LAMP test. Blinding Sample identification was recorded, sample tubes were shuffled randomly, and then passed blindly to a second member of our personnel to carry out our colorimetric RT-LAMP test. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Stabilizing saliva: Liberating RNA genomes from virions, protecting RNA from degradation, and dealing with pH variability in human saliva … SciScore for 10.1101/2020.07.16.20150250: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization Sample identification was recorded, sample tubes were shuffled randomly, and then passed blindly to a second member of our personnel to carry out our colorimetric RT-LAMP test. Blinding Sample identification was recorded, sample tubes were shuffled randomly, and then passed blindly to a second member of our personnel to carry out our colorimetric RT-LAMP test. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Stabilizing saliva: Liberating RNA genomes from virions, protecting RNA from degradation, and dealing with pH variability in human saliva Multiple studies have developed methods for using saliva samples in combination with RT-LAMP specifically with a colorimetric readout (Lalli et al., 2020; L’Helgouach et al., 2020; Rabe and Cepko, 2020). RT-LAMPsuggested: NoneThe results were visualized and analyzed using ThermoFisher’s Design and Analysis software. ThermoFisher’ssuggested: NoneData from additional tools added to each annotation on a weekly basis.
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