RT-PCR/MALDI-TOF Diagnostic Target Performance Reflects Circulating SARS-CoV-2 Variant Diversity in New York City
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SciScore for 10.1101/2021.12.04.21267265: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Ethics statement: This study was reviewed and approved by the Institutional Review Board of the ISMMS (HS#13-00981).
Field Sample Permit: Details of processing and SARS-CoV-2 testing of upper respiratory and saliva specimens have been described previously 28,31.Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication Authentication: SARS-CoV-2 sequencing, assembly and phylogenetic analyses: SARS-CoV-2 viral RNA underwent reverse-transcription, PCR amplification and next-generation sequencing followed by genome assembly and lineage assignment using a phylogenetic-based nomenclature as described by Rambaut … SciScore for 10.1101/2021.12.04.21267265: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Ethics statement: This study was reviewed and approved by the Institutional Review Board of the ISMMS (HS#13-00981).
Field Sample Permit: Details of processing and SARS-CoV-2 testing of upper respiratory and saliva specimens have been described previously 28,31.Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication Authentication: SARS-CoV-2 sequencing, assembly and phylogenetic analyses: SARS-CoV-2 viral RNA underwent reverse-transcription, PCR amplification and next-generation sequencing followed by genome assembly and lineage assignment using a phylogenetic-based nomenclature as described by Rambaut et al. 32 using the Pangolin v3.1.14 tool and PANGO-v1.2.81 nomenclature scheme 33 as previously described 29,30. Table 2: Resources
Software and Algorithms Sentences Resources Alignment of specimen sequences with each primer/probe sequence was performed using the Multiple Alignment using Fast Fourier Transform (MAFFT) platform 35,36 as previously described 28. MAFFTsuggested: (MAFFT, RRID:SCR_011811)All distributions were non-parametric, and thus, a Mann-Whitney test (two-tailed) was performed (GraphPad). GraphPadsuggested: (GraphPad Prism, RRID:SCR_002798)Display Items: All figures are original and were generated using the GraphPad Prism software 9.2.0, Microsoft Excel v16.54, and finished in Adobe Illustrator 2021 (v.25.4.1). GraphPad Prismsuggested: (GraphPad Prism, RRID:SCR_002798)Microsoft Excelsuggested: (Microsoft Excel, RRID:SCR_016137)Alignment plots were developed using the package ggmsa (v.1.1.0) on R 39 and finished in Adobe Illustrator. Adobe Illustratorsuggested: (Adobe Illustrator, RRID:SCR_010279)Results from OddPub: Thank you for sharing your code and data.
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.
Results from scite Reference Check: We found no unreliable references.
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