Identifying SARS-CoV-2 Variants of Concern through Saliva-Based RT-qPCR by Targeting Recurrent Mutation Sites
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Abstract
SARS-CoV-2 variants of concern and their many sublineages can be characterized by mutations present within their genetic sequences. These mutations can provide selective advantages such as increased transmissibility and antibody evasion, which influences public health recommendations such as mask mandates, quarantine requirements, and treatment regimens.
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SciScore for 10.1101/2022.03.02.22271785: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
No key resources detected.
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:To address these limitations, our lab implemented a simple VOC screening method following our established saliva-based SARS-CoV-2 testing procedure28. We perform weekly surveillance testing of the entire population at Clemson University32, which allows for …
SciScore for 10.1101/2022.03.02.22271785: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
No key resources detected.
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:To address these limitations, our lab implemented a simple VOC screening method following our established saliva-based SARS-CoV-2 testing procedure28. We perform weekly surveillance testing of the entire population at Clemson University32, which allows for real-time monitoring of current and future VOCs. Deletion and SNP Assay Analyses: We designed two standard RT-qPCR assays for the SARS-CoV-2 deletion sites SΔ69-70 and ORF1aΔ3675-3677. The accuracy of the SΔ69-70 assay in saliva was 93.6% (Table 2). Two B.1.1.7 samples produced false negative results for both deletion assays, possibly due to non-specific binding of both reference probes. The accuracy of the ORF1aΔ3675-3677 assay was 68.0%; 85.9% of reference sequences could be successfully identified with the reference probe, but only 51.1% of deletion sequences could be successfully identified with the deletion probe. We believe this is due to the relative fluorescence intensity from the competitive probe pair rather than binding affinity or reaction efficiency, as both probes produced replicable amplification from synthetic RNA. The reference probe was tagged with the SUN fluor33, which produces high fluorescent output that can prevent the thermocycler from identifying amplification from the weaker Cy5-tagged deletion probe. We attempted to account for this by adjusting probe mixing ratios, but this did not improve the fluorescent output of the Cy5 probe. Altering the probe pairing would likely improve the efficacy of thi...
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.
- Thank you for including a protocol registration statement.
Results from scite Reference Check: We found no unreliable references.
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