SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay

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1. 

   ScreenIT

   Mar 1, 2021

   SciScore for 10.1101/2020.10.08.20208546: (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
   Sequencing reads were demultiplexed with Illumina bcl2fastq v2.20 requiring a perfect match to indexing barcode sequences, and aligned to the reference SARS-CoV-2 genome (NC_045512.2, wuhCor1).	bcl2fastq suggested: (bcl2fastq , RRID:SCR_015058)
   Statistics: D’Agostino & Pearson normality tests were performed to assess whether data values followed Gaussian distribution and whether parametric or nonparametric statistical tests were indicated (GraphPad Prism v.8).	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)
   Correlation coefficients (r), P-values, adjusted P-values, and q values …

   SciScore for 10.1101/2020.10.08.20208546: (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
   Sequencing reads were demultiplexed with Illumina bcl2fastq v2.20 requiring a perfect match to indexing barcode sequences, and aligned to the reference SARS-CoV-2 genome (NC_045512.2, wuhCor1).	bcl2fastq suggested: (bcl2fastq , RRID:SCR_015058)
   Statistics: D’Agostino & Pearson normality tests were performed to assess whether data values followed Gaussian distribution and whether parametric or nonparametric statistical tests were indicated (GraphPad Prism v.8).	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)
   Correlation coefficients (r), P-values, adjusted P-values, and q values were calculated in Prism.	Prism suggested: (PRISM, RRID:SCR_005375)
   Correlation analyses with a sample size of 44 had 80.7% power (α = 0.05) to distinguish correlation coefficients that differ by 0.4 standard deviation units (G*Power 3.1.9.4).	G*Power suggested: (G*Power, RRID:SCR_013726)
   SARS-CoV-2 reference sequences were downloaded from GISAID EpiCoV and combined with our Uruguayan study sequences in MEGA v.	MEGA suggested: (Mega BLAST, RRID:SCR_011920)
   Sequence alignments were performed using MAFFT v7.471, FFT-NS-2 method [18].	MAFFT suggested: (MAFFT, RRID:SCR_011811)
   The manually-edited alignment was then used to construct a maximum likelihood tree with ultra-fast bootstraps of 1000 replicates in IQ-TREE version 2.0.3 [20], using the GTR+F+I nucleotide substitution model selected by Bayesian information criterion using model test implemented in IQ-TREE.	IQ-TREE suggested: (IQ-TREE, RRID:SCR_017254)
   TempEst [21] was used to check for outlier sequences in the tree resulting in the removal of a further ten sequences, to make up a final data set of 1810 sequences.	TempEst suggested: (TempEst, RRID:SCR_017304)
   The time-scaled maximum clade credibility tree (MCC) tree from the discrete model phylogeography analysis conducted in BEAST was then identified using TreeAnnotator, available as part of the BEAST package and visualized in FigTree v.	BEAST suggested: (BEAST, RRID:SCR_010228) FigTree suggested: (FigTree, RRID:SCR_008515)
   The BEAST log files were inspected for convergence using Tracer version 1.7.1 [25].	Tracer suggested: (Tracer, RRID:SCR_019121)

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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: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

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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.
   • Thank you for including a protocol registration statement.

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2. Version published to 10.1080/22221751.2020.1863747

   Jan 1, 2021
3. 

   Version published to 10.1101/2020.10.08.20208546 on medRxiv

   Oct 11, 2020