Analytical sensitivity and efficiency comparisons of SARS-CoV-2 RT–qPCR primer–probe sets
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SciScore for 10.1101/2020.03.30.20048108: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: In accordance with the guidelines of the Yale Human Investigations Committee (HIC), this work with de-identified samples is considered non-human subjects research. 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 We generated a genomic annotation plot with all newly generated RNA transcript standards and the nine tested primer-probe sets based on the NC_045512 reference genome using the DNA Features Viewer Python package (Fig. 1A)16. Pythonsuggested: (IPython, RRID:SCR_001658)All figures were made with GraphPad Prism 8.3.0. GraphPad …SciScore for 10.1101/2020.03.30.20048108: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: In accordance with the guidelines of the Yale Human Investigations Committee (HIC), this work with de-identified samples is considered non-human subjects research. 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 We generated a genomic annotation plot with all newly generated RNA transcript standards and the nine tested primer-probe sets based on the NC_045512 reference genome using the DNA Features Viewer Python package (Fig. 1A)16. Pythonsuggested: (IPython, RRID:SCR_001658)All figures were made with GraphPad Prism 8.3.0. GraphPad Prismsuggested: (GraphPad Prism, RRID:SCR_002798)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:Our study does have several limitations to consider. First, we standardized PCR conditions to make a fair comparison between primer-probes sets used in four common qRT-PCR assays for detection of SARS-CoV-2. By standardizing the concentration of primers and probes, PCR kits, and thermocycler conditions, we deviated from the conditions as recommended by each assay which may have influenced our findings. For instance, we selected an annealing temperature of 55°C which was lower than recommended for the assays developed by Charité (58°C)5 and HKU (60°C)4, but similar to the assay developed by US CDC (55°C)6. No specific PCR conditions were reported for the assay developed by the China CDC7. The two assays (Charité and HKU) with higher annealing temperatures had high analytical sensitivity, which suggests that our standardized annealing temperature likely did not have a large effect on our findings. Second, when determining the sensitivity of primer-probe sets, we performed 24 replicates with no spiked-in virus, and eight replicates at low concentrations of SARS-CoV-2 RNA spiked into (pre-COVID-19) clinical samples. While we evaluated the US CDC using 172 clinical samples collected during the COVID-19 pandemic, more replicates for the other assays are required to accurately determine the lower detection limit. Importantly, analytical sensitivity as reported in our study may not be applicable to other PCR kits or thermocyclers; analytical sensitivities and positive-negative cut-of...
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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