Correlation of Population SARS-CoV-2 Cycle Threshold Values to Local Disease Dynamics: Exploratory Observational Study

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1. Version published to 10.2196/28265

   Jun 3, 2021
2. 

   ScreenIT

   Mar 1, 2021

   SciScore for 10.1101/2021.02.16.21251844: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Institutional Review Board Statement

   IRB: The Pearl Independent Institutional Review Board (IRB) approved this study (IRB Protocol 21-DASC-127).

   Randomization

   As the purpose of the present analysis was to investigate how the trough of daily median CT correlated with the peak of the other signals, to aid visualization the following modifications were made: (1) for each signal, the z-score was used instead of the absolute value; (2) the negative value of the z-score of daily median CT value was used to ensure a positive peak in the cross correlation plots; (3) 20% of positive samples were randomly sampled five times each day to estimate the variation in the cross-correlation between daily median CT …

   SciScore for 10.1101/2021.02.16.21251844: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Institutional Review Board Statement	IRB: The Pearl Independent Institutional Review Board (IRB) approved this study (IRB Protocol 21-DASC-127).
   Randomization	As the purpose of the present analysis was to investigate how the trough of daily median CT correlated with the peak of the other signals, to aid visualization the following modifications were made: (1) for each signal, the z-score was used instead of the absolute value; (2) the negative value of the z-score of daily median CT value was used to ensure a positive peak in the cross correlation plots; (3) 20% of positive samples were randomly sampled five times each day to estimate the variation in the cross-correlation between daily median CT value and epidemiological signals.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   The algorithm is a Python script based on a Bayesian Estimation Model developed by Bettencourt & Ribeiro (28), with slight modification to introduce gaussian noise to the prediction.	Python suggested: (IPython, RRID:SCR_001658)
   Statistical Analysis: All analyses were conducted in Python (31) using the following packages: pandas, matplotlib, plotly, scipy and statsmodels.	matplotlib suggested: (MatPlotLib, RRID:SCR_008624) scipy suggested: (SciPy, RRID:SCR_008058)

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   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).

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   Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

   Limitations: While the study sample was large, other variables and forms of bias (e.g., sampling bias), may have influenced the results. Indeed, differences in the comprehensiveness of the El Paso dataset versus the supplementary site datasets-or in, other words, the relative proportion of tests conducted by the Dascena laboratory versus other testing providers-may have contributed to skew in the supplementary samples. Future directions for research on population CT values may therefore include analyzing whether significant differences in results can be detected in different sub-samples of tested populations, and evaluating methods to collate CT data across testing providers in a given geographic area. No data on symptomatology was associated with samples at the time of collection, such that these data do not enable a distinction between samples collected as part of clinical evaluation of symptoms consistent with COVID-19, or for other reasons (e.g., clearance for work or travel). Prior research assessing population distribution of CT values in relation to community outbreaks has explicitly used surveillance samples (23,24). The variability in the observed correlations between median CT and outbreak measures in El Paso versus other testing locations may reflect, in part, variability in the proportion of symptomatically indicated versus non-symptomatically indicated tests in a given location. However, other differences between the testing site populations may also have contrib...

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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   Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

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   Results from JetFighter: We did not find any issues relating to colormaps.

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   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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3. Version published to 10.2196/preprints.28265

   Mar 1, 2021
4. 

   Version published to 10.1101/2021.02.16.21251844v1 on medRxiv

   Feb 19, 2021