Metrics to relate COVID-19 wastewater data to clinical testing dynamics
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SciScore for 10.1101/2021.06.10.21258580: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Cts were called from raw fluorescence data using the Cy0 algorithm from the qpcR package (v1.4-1) in R (Guescini et al., 2008), and manually inspected for agreement with the raw traces in the native BioRad Maestro software. BioRad Maestrosuggested: NoneWe used the L-BFGS method in the scipy.optimize.minimize function to find parameters α, β, c of the beta distribution that minimized the SSE. scipysuggested: (SciPy, RRID:SCR_008058)MCMC simulation was done with python 3.6.5, numpy 1.14.3, pandas 0.23.0, and scipy 1.1.0. pythonsuggested: (IPython, RRID:SCR_001658)Results from OddPub: We did …
SciScore for 10.1101/2021.06.10.21258580: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Cts were called from raw fluorescence data using the Cy0 algorithm from the qpcR package (v1.4-1) in R (Guescini et al., 2008), and manually inspected for agreement with the raw traces in the native BioRad Maestro software. BioRad Maestrosuggested: NoneWe used the L-BFGS method in the scipy.optimize.minimize function to find parameters α, β, c of the beta distribution that minimized the SSE. scipysuggested: (SciPy, RRID:SCR_008058)MCMC simulation was done with python 3.6.5, numpy 1.14.3, pandas 0.23.0, and scipy 1.1.0. pythonsuggested: (IPython, RRID:SCR_001658)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:Wastewater surveillance is not subject to these social and logistical limitations and can therefore serve as a more instantaneous and unbiased readout of new cases during the pandemic. We and others have shown that wastewater likely detects a short period of high viral shedding early in infection (Hoffmann and Alsing, 2021; Wu et al., 2020a), whereas patients can test positive during PCR testing of respiratory samples for longer periods of time (Wölfel et al., 2020; Zheng et al., 2020), suggesting that wastewater could be more specific to newly infected patients. However, wastewater surveillance does not necessarily provide a readout of hospitalizations or deaths because these numbers also depend on who is infected and their access to healthcare, which cannot be distinguished via wastewater monitoring (Olesen et al., 2021). Therefore, wastewater should be used in conjunction with additional clinical data streams when making public health decisions related to hospitalizations and mortality. This study has several limitations. First, the interpretation of the WC ratio relies on the assumption that the viral shedding rate did not drastically change over the course of the pandemic. While some variants of SARS-CoV-2 have been reported to have higher shedding rates or longer shedding duration (Frampton et al., 2021; Kissler et al., 2021), the B.1.1.7 variant did not make up a large proportion of wastewater viral titers in the Boston Area until March 2021, well past the periods in t...
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.
- No funding statement was detected.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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