Algorithm for the Quantitation of Variants of Concern for Rationally Designed Vaccines Based on the Isolation of SARS-CoV-2 Hawaiʻi Lineage B.1.243

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   ScreenIT

   Aug 21, 2021

   SciScore for 10.1101/2021.08.18.455536: (What is this?)

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

   Table 1: Rigor

   Ethics	not detected.
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	After observing significant CPE at 48 hours, supernatant was blind passaged three times in the Vero E6 cells.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Experimental Models: Cell Lines
   Sentences	Resources
   After observing significant CPE at 48 hours, supernatant was blind passaged three times in the Vero E6 cells.	Vero E6 suggested: RRID:CVCL_XD71)
   Briefly, on the day of the assay, DMEM in 10% FBS was removed from wells with Vero cells, wells were washed twice with serum-free DMEM, and inoculated with multiplicity of infection (MOI) 0.1 and 1 virus isolates diluted in 500 µL …

   SciScore for 10.1101/2021.08.18.455536: (What is this?)

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

   Table 1: Rigor

   Ethics	not detected.
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	After observing significant CPE at 48 hours, supernatant was blind passaged three times in the Vero E6 cells.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Experimental Models: Cell Lines
   Sentences	Resources
   After observing significant CPE at 48 hours, supernatant was blind passaged three times in the Vero E6 cells.	Vero E6 suggested: RRID:CVCL_XD71)
   Briefly, on the day of the assay, DMEM in 10% FBS was removed from wells with Vero cells, wells were washed twice with serum-free DMEM, and inoculated with multiplicity of infection (MOI) 0.1 and 1 virus isolates diluted in 500 µL DMEM in 2% FBS and incubated at 37°C and 5% CO2 for two hours.	Vero suggested: None
   Software and Algorithms
   Sentences	Resources
   All qRT-PCR and Genomic Equivalence data were analyzed and visualized using GraphPad Prism 9 Version 9.2.0.	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)
   WGS was conducted by the ASGPB Core, UHM.	WGS suggested: None
   Trimmed result quality was confirmed with FASTQC.	FASTQC suggested: (FastQC, RRID:SCR_014583)
   The trimmed-paired-end reads were then mapped to the NC_045512 reference genome using Bowtie223 and variants called with samtools mpileup24 and transformed from VCF to FASTQ using bcftools and vcfutils25 and finally converted to FASTA using seqtk.	samtools suggested: (SAMTOOLS, RRID:SCR_002105)
   The SNPs were inputted into the SnapGene sequence feature and Nextclade45 to determine amino acid substitutions (AAS).	SnapGene suggested: (SnapGene, RRID:SCR_015052)
   14 Pearson’s was calculated using RStudio version 1.3.1093 (R version 4.0.3) and plotted with the ggplot2 package.	RStudio suggested: (RStudio, RRID:SCR_000432) ggplot2 suggested: (ggplot2, RRID:SCR_014601)
   Separately, the following search parameter was used in PubMed to locate in silico studies predicting vaccine epitopes to SARS-CoV-2: “((B-cell) OR (B cell)) AND (	PubMed suggested: (PubMed, RRID:SCR_004846)
   All predicted epitopes able to be searched and defined with SnapGene’s “Find Protein Sequence” feature were included.	SnapGene’s suggested: None

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   Results from OddPub: Thank you for sharing your code and data.

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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: We found the following clinical trial numbers in your paper:
   

   Identifier	Status	Title
   NCT04360551	Recruiting	Pilot Clinical Trial of the Safety and Efficacy of Telmisart…

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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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   Results from scite Reference Check: We found no unreliable references.

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   Read the original source
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   Version published to 10.1101/2021.08.18.455536v1 on bioRxiv

   Aug 19, 2021