Temporal Detection and Phylogenetic Assessment of SARS-CoV-2 in Municipal Wastewater
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SciScore for 10.1101/2020.04.15.20066746: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: The study was reviewed by the Montana State University Institutional Review Board (IRB) For the Protection of Human Subjects (FWA 00000165) and was exempt from IRB oversight in accordance with Code of Federal regulations, Part 46, section 101.
Consent: All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived.Randomization not detected.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 20 ng of final library DNA was loaded onto the MinION flowcell for sequencing. MinIONsuggested: (MinION, RRID:SCR_017985)SciScore for 10.1101/2020.04.15.20066746: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: The study was reviewed by the Montana State University Institutional Review Board (IRB) For the Protection of Human Subjects (FWA 00000165) and was exempt from IRB oversight in accordance with Code of Federal regulations, Part 46, section 101.
Consent: All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived.Randomization not detected.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 20 ng of final library DNA was loaded onto the MinION flowcell for sequencing. MinIONsuggested: (MinION, RRID:SCR_017985)SARS-CoV-2 genome assembly: Nanopore raw reads (304.77 Mb) were basecalled with MinKNOW software in high-accuracy mode. MinKNOWsuggested: NonePhylogenetic and Position-specific Mutation Analysis: Phylogenetic analysis was performed by aligning the consensus sequence to 14,970 SARS-CoV-2 genomes retrieved from GISAID on 5/5/2020, 8:25:22 AM (https://www.gisaid.org/), using the FFT-NS-2 setting in MAFFT v7.429 (Katoh et al., 2019; Shu and McCauley, 2017). MAFFTsuggested: (MAFFT, RRID:SCR_011811)Columns composed of more than 70% gaps were removed with trimAl v1.2rev59 (Capella-Gutierrez et al., 2009). trimAlsuggested: (trimAl, RRID:SCR_017334)The APE v5.3 package in R was used to re-root the tree relative to RaTG13 bat coronavirus genome sequence (Paradis and Schliep, 2019), and the tree was plotted using ggtree v3.10 package in R (Yu et al., 2017). ggtreesuggested: (ggtree, RRID:SCR_018560)The subtree, visualized in Figure 2B, was rendered in FigTree v1.4.4 (Rambaut, 2017). FigTreesuggested: (FigTree, RRID:SCR_008515)Position specific mutation analysis was conducted in R using the BioStrings package (Pagès et al., 2019), and chromatograms of Sanger sequencing reads were rendered in SnapGene (GSL Biotech; available at snapgene.com). BioStringssuggested: (Biostrings, RRID:SCR_016949)SnapGenesuggested: (SnapGene, RRID:SCR_015052)Quantification and Statistical Analyses: All statistical analyses were performed in RStudio v1.2.1335. RStudiosuggested: (RStudio, RRID:SCR_000432)Data was plotted and analyzed using geom_smooth function from ggplot2 R package, with method = ‘lm’. ggplot2suggested: (ggplot2, RRID:SCR_014601)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: 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.
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