A model of persistent post SARS-CoV-2 induced lung disease for target identification and testing of therapeutic strategies

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   ScreenIT

   Feb 18, 2022

   SciScore for 10.1101/2022.02.15.480515: (What is this?)

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

   Table 1: Rigor

   Ethics	IRB: Ethics and biosafety: The generation of SARS-CoV-2 MA10 was approved for use under BSL3 conditions by the University of North Carolina at Chapel Hill Institutional Review Board (UNC-CH IBC) and by a Potential Pandemic Pathogen Care and Oversight committee at the National Institute of Allergy and Infectious Diseases (NIAID). IACUC: All animal work was approved by Institutional Animal Care and Use Committee at University of North Carolina at Chapel Hill according to guidelines outlined by the Association for the Assessment and Accreditation of Laboratory Animal Care and the U.S. Department of Agriculture.
   Sex as a biological variable	not detected.
   Randomization	At indicated harvest time …

   SciScore for 10.1101/2022.02.15.480515: (What is this?)

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

   Table 1: Rigor

   Ethics	IRB: Ethics and biosafety: The generation of SARS-CoV-2 MA10 was approved for use under BSL3 conditions by the University of North Carolina at Chapel Hill Institutional Review Board (UNC-CH IBC) and by a Potential Pandemic Pathogen Care and Oversight committee at the National Institute of Allergy and Infectious Diseases (NIAID). IACUC: All animal work was approved by Institutional Animal Care and Use Committee at University of North Carolina at Chapel Hill according to guidelines outlined by the Association for the Assessment and Accreditation of Laboratory Animal Care and the U.S. Department of Agriculture.
   Sex as a biological variable	not detected.
   Randomization	At indicated harvest time points, randomly assigned animals were euthanized by an overdose of isoflurane and samples for analyses of titer (caudal right lung lobe) and histopathology (left lung lobe) were collected.
   Blinding	Disease incidence scoring: Profibrotic disease incidence was scored by a blinded veterinary pathologist using serial H&E and Picrosirius Red stained slides.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   After pretreatment, slides were incubated with primary antibodies (see Key Resources Table) for 1h followed with Novolink Polymer (RE7260-K) secondary.	RE7260-K suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   A large working stock of SARS-CoV-2 MA10 was generated by passaging the plaque purified clonal isolate sequentially on Vero E6 cells at 37°C (passage 3, SARS-CoV-2 P3).	Vero E6 suggested: None
   Experimental Models: Organisms/Strains
   Sentences	Resources
   In vivo infection: All BALB/c mice used in this study were purchased from Envigo (BALB/cAnNHsd; strain 047) and housed at the University of North Carolina at Chapel Hill until the start of the experiment.	BALB/c suggested: None
   Software and Algorithms
   Sentences	Resources
   Images were viewed with ImageJ.	ImageJ suggested: (ImageJ, RRID:SCR_003070)
   Pre-ranked gene set enrichment analysis (GSEA) was performed using the Bioconductor R package, fgsea (84), with gene set collections obtained from Gene Ontology Biological Process (85), and Reactome pathways (86).	Bioconductor suggested: (Bioconductor, RRID:SCR_006442) Reactome suggested: (Reactome, RRID:SCR_003485)
   Plots and hierarchical clustering heatmaps were generated using the R package, ggplot2 (87), and ComplexHeatmap (88).	ComplexHeatmap suggested: (ComplexHeatmap, RRID:SCR_017270)
   Preliminary analysis of the log2 transformed and scaled Q3 normalized data identified a putative batch effect between two runs as identified using the PCA in the R package FactoMineR.	FactoMineR suggested: (FactoMineR, RRID:SCR_014602)
   Sets of differentially expressed genes were tested for overrepresentation of the genes in the databases (GO: Biological Process, GO: Molecular Function, GO: Cellular Components, KEGG, and Reactome) using R package enrichR (93).	GO: Biological suggested: None KEGG suggested: (KEGG, RRID:SCR_012773) enrichR suggested: (Enrichr, RRID:SCR_001575)
   Various plots and heatmaps were generated using the R packages ggplot2 and heatmap3 (94).	ggplot2 suggested: (ggplot2, RRID:SCR_014601)
   Stained areas of Sirius Red and SMA detected by IHC in the alveolar regions were quantitated using Fiji software.	Fiji suggested: (Fiji, RRID:SCR_002285)
   Statistical significance was evaluated with the R lmerTest package(92), using the Satterthwarte’s degrees of freedom method.	lmerTest suggested: (R package: lmerTest, RRID:SCR_015656)
   Supplemental Table 1: Cytokine and chemokine protein levels in SARS-CoV-2 MA10 infected young and old mice Supplemental Table 2: Gene lists in heat maps Supplemental Table 3: Mouse whole transcriptome GeoMx data Supplemental Table 4: Mouse GeoMx differential gene expression analysis Supplemental Table 5: Mouse GeoMx pathway enrichment analysis Supplemental Table 6: Human donor demographics Supplemental Table 7: Human whole transcriptome GeoMx data Supplemental Table 8: Reagent and Resource descriptions References and Notes:	Notes suggested: None

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

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   Version published to 10.1101/2022.02.15.480515v1 on bioRxiv

   Feb 15, 2022