COVIDFast™: A high-throughput and RNA extraction-free method for SARS-CoV-2 detection in swab (SwabFAST™) or saliva (SalivaFAST™)
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Abstract
There is an urgent need of having a rapid, high throughput, yet accurate SARS-COV-2 PCR testing to control the COVID19 pandemic. However, the RNA extraction step in conventional PCR creates a major bottle neck in the diagnostic process. In this paper we modified the CDC COVID-19 assay and developed an RNA-extraction free RT-qPCR assay for SARS-CoV-2, i.e. COVIDFast ™ . Depending on sample types, the assay is further divided into SwabFAST ™ , which uses anterior nares nasal swab, and SalivaFAST ™ , which uses saliva. By utilizing the proprietary buffer for either swab or saliva samples, the performance of SwabFAST or SalivaFAST is equivalent to RNA-extraction SARS-CoV-2 RT-qPCR in both contrived and clinical samples. The limit of detection of either assay is 4 copies/μL. We further developed a semi-automatic system, which is easy to adapt by clinical lab for implementation of a high-throughput SARS-CoV-2 test. Working together with the COVIDCheck Colorado, we have tested over 400,000 samples using COVIDFast (83.62% SwabFAST and 16.38% SalivaFAST) in less than a year, resulting in significant clinical contribution in the battle against COVID-19 during the pandemic.
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SciScore for 10.1101/2021.12.29.21268527: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Field Sample Permit: Anterior nares swab sample collection for SwabFAST: The anterior nares nasal swab was collected under the supervision of a trained healthcare worker. Sex as a biological variable not detected. Randomization not detected. Blinding Remnants of 40 clinical saliva samples that were tested positive or negative for SARS-CoV-2 were assigned a blind random number (1-40) and sent to the Summit Biolabs for testing with SalivaFAST using the protocol detailed below. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Contrived samples: All the contrived samples described in this paper were assembled by spiking … SciScore for 10.1101/2021.12.29.21268527: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Field Sample Permit: Anterior nares swab sample collection for SwabFAST: The anterior nares nasal swab was collected under the supervision of a trained healthcare worker. Sex as a biological variable not detected. Randomization not detected. Blinding Remnants of 40 clinical saliva samples that were tested positive or negative for SARS-CoV-2 were assigned a blind random number (1-40) and sent to the Summit Biolabs for testing with SalivaFAST using the protocol detailed below. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Contrived samples: All the contrived samples described in this paper were assembled by spiking the heat-inactivated SARS-Cov-2 virus (VR-1986HK, ATCC) into known negative anterior nares nasal swab or saliva samples. VR-1986HKsuggested: 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 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 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.
Results from scite Reference Check: We found no unreliable references.
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