Transmission Dynamics of Severe Acute Respiratory Syndrome Coronavirus 2 in High-Density Settings, Minnesota, USA, March–June 2020
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SciScore for 10.1101/2020.12.30.20248277: (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 federal human subjects protection regulations at 45 CFR §46.101c and §46.102d and with the Guidelines for Defining Public Health Research and Public Health Non-Research, the project was reviewed by a human subjects protection coordinator at the CDC and in Minnesota DOH and determined to be a non-research, public health response exempt from institutional review board evaluation. 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 WGS was performed by the MDH Public Health Laboratory (PHL) on available SARS-CoV-2 RT-PCR … SciScore for 10.1101/2020.12.30.20248277: (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 federal human subjects protection regulations at 45 CFR §46.101c and §46.102d and with the Guidelines for Defining Public Health Research and Public Health Non-Research, the project was reviewed by a human subjects protection coordinator at the CDC and in Minnesota DOH and determined to be a non-research, public health response exempt from institutional review board evaluation. 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 WGS was performed by the MDH Public Health Laboratory (PHL) on available SARS-CoV-2 RT-PCR positive specimens, collected from March 6 through June 30, 2020. WGSsuggested: NoneSequencing Libraries for Illumina next-generation sequencing were prepared according to the Nextera DNA Flex protocol created by the State Public Health Bioinformatics Group (StaPH-B) (27) and sequenced using 2×250 bp Illumina V2 chemistry on MiSeq instruments. MiSeqsuggested: (A5-miseq, RRID:SCR_012148)Genomes were aligned with MAFFT version 7.310 with options “--keeplength -- reorder --anysymbol --nomemesave --adjustdirection” (31). MAFFTsuggested: (MAFFT, RRID:SCR_011811)IQ-TREE version 1.6.1 was used for phylogenetic tree creation with parameters “-ninit 2 -n 2 -me 0.05” (32). IQ-TREEsuggested: (IQ-TREE, RRID:SCR_017254)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:There are several important limitations to this study. First, only a subset of specimens were available for sequencing due to different laboratory specimen retention policies. For example, at LTCF B, samples from only 5 staff were available for sequencing. Similarly, in Processing Plant B, only 5 samples were available due to a clinical testing laboratory protocol that resulted in the discarding of samples after approximately 7 days. In addition, not all available patient samples were able to be successfully sequenced, owing primarily to degraded or low concentrations of viral RNA in the specimen. Another limitation is that not all staff and employees at the LTCFs, correctional facilities and processing plants agreed to be tested. Because of the incomplete genomic picture at each setting, definitive conclusions about single introductions in LTCF A and LTCF D are speculative, and these individual introductions may have actually resulted in some viral transmission that was not identified in the study. Finally, we were not able to present sociodemographic data such as race or ethnicity pertaining to cases, or the facility population, associated with these eight outbreaks in Minnesota, due to limitations in the case investigation process and incomplete case data. This limitation is of particular importance, due to the disproportionate impact of COVID-19 on Black, Indigenous, and People of Color (BIPOC). Since BIPOC disproportionately experience incarceration, and a high proportio...
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).
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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