Pediatric COVID-19 in Southern California: clinical features and viral genetic diversity

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1. 

   ScreenIT

   Jun 9, 2020

   SciScore for 10.1101/2020.05.28.20104539: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IRB: Ethics approval: Study design conducted at Children’s Hospital Los Angeles was approved by the Institutional Review Board under IRB CHLA-16-00429.
   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
   Viral genome library construction and sequencing: WGS from extracted RNA was performed as previously described using Paragon Genomics CleanPlex SARS-CoV-2 Research and Surveillance NGS Panel18.	WGS suggested: None
   Sample performance was selected based on the following metrics: average depth ≥ 1000x, percent bases covered at 10x ≥ 80% Consensus …

   SciScore for 10.1101/2020.05.28.20104539: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IRB: Ethics approval: Study design conducted at Children’s Hospital Los Angeles was approved by the Institutional Review Board under IRB CHLA-16-00429.
   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
   Viral genome library construction and sequencing: WGS from extracted RNA was performed as previously described using Paragon Genomics CleanPlex SARS-CoV-2 Research and Surveillance NGS Panel18.	WGS suggested: None
   Sample performance was selected based on the following metrics: average depth ≥ 1000x, percent bases covered at 10x ≥ 80% Consensus genome assembly: Nucleotide sequences were aligned with NovoAlign.	NovoAlign suggested: (NovoAlign, RRID:SCR_014818)
   Variants were called, and the profile was compared against the global collection of about 30,000 available virus sequences in CARD.	CARD suggested: (CARD, RRID:SCR_016602)
   Missing bases “N” were trimmed off from the 5’ and 3’ end, and the genomes were aligned to generate a multiple sequence alignment (MSA) with MAFFT (version 7.460) using speed-oriented option - FFT-NS-i (iterative refinement method, two cycles) optimized for large datasets19.	MAFFT suggested: (MAFFT, RRID:SCR_011811)
   The phylogenetic tree was visualized in FigTree v1.4.421.	FigTree suggested: (FigTree, RRID:SCR_008515)
   A Maximum likelihood tree using Bayesian information criteria was generated with IQ-TREE (version 1.15.0)22 using GTR substitution model.	IQ-TREE suggested: (IQ-TREE, RRID:SCR_017254)
   P-value for selection was calculated using Fisher’s exact test for selection in MEGA.	MEGA suggested: (Mega BLAST, RRID:SCR_011920)

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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.
   • No protocol registration statement was detected.

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2. 

   Version published to 10.1101/2020.05.28.20104539 on medRxiv

   Jun 1, 2020