Classification of Omicron BA.1, BA.1.1, and BA.2 sublineages by TaqMan assay consistent with whole genome analysis data
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SciScore for 10.1101/2022.04.03.22273268: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Ethics approval: The Institutional Review Board of the Clinical Research and Genome Research Committee at Yamanashi Central Hospital approved this study and the use of an opt-out consent method (Approval No. C2019-30).
Consent: Ethics approval: The Institutional Review Board of the Clinical Research and Genome Research Committee at Yamanashi Central Hospital approved this study and the use of an opt-out consent method (Approval No. C2019-30).Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources WGS analysis was performed as previously described [21-23]. WGSsuggested: …SciScore for 10.1101/2022.04.03.22273268: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Ethics approval: The Institutional Review Board of the Clinical Research and Genome Research Committee at Yamanashi Central Hospital approved this study and the use of an opt-out consent method (Approval No. C2019-30).
Consent: Ethics approval: The Institutional Review Board of the Clinical Research and Genome Research Committee at Yamanashi Central Hospital approved this study and the use of an opt-out consent method (Approval No. C2019-30).Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources WGS analysis was performed as previously described [21-23]. WGSsuggested: 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:There are, however, several limitations. TaqMan assays do not always accurately determine the sublineages in some situations. WGS analysis may be necessary when the characteristic mutations of newly-emerging strains or sublineages remain under investigation. It should also be noted that if mutations occur at the TaqMan probe or primer locations, the PCR amplification efficiency will be reduced and the signal will be attenuated, which may make interpretation difficult (Figure 3B). Our study showed that the TaqMan assay can be used to specifically detect Omicron viruses and classify subvariants. By applying this method to SARS-CoV-2-positive specimens, it is possible to analyze multiple specimens rapidly. Although accumulated data are still needed [8, 11, 14, 34], BA.1 and BA.2 show different susceptibilities to antibody and antiviral therapy. Rapid classification of Omicron sublineages may be clinically critical in providing appropriate treatment to patients with COVID-19.
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.
Results from scite Reference Check: We found no unreliable references.
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