Monocytes and macrophages, targets of SARS-CoV-2: the clue for Covid-19 immunoparalysis

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1. 

   ScreenIT

   Sep 21, 2020

   SciScore for 10.1101/2020.09.17.300996: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Immunofluorescence: After a 24 or 48-hour infection, cells were incubated in blocking buffer (Phosphate buffer saline (PBS) supplemented with 5% FBS and 0.5% Triton X-100) for 30 minutes and washed before incubation with an anti-SARS-CoV-2 spike protein antibody (Life Technologies).	anti-SARS-CoV-2 spike protein suggested: None
   Flow cytometry: PBMCs from healthy donors or Covid-19 patients were resuspended in PBS (Life Technologies) containing 5% FBS and 2mM …

   SciScore for 10.1101/2020.09.17.300996: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Immunofluorescence: After a 24 or 48-hour infection, cells were incubated in blocking buffer (Phosphate buffer saline (PBS) supplemented with 5% FBS and 0.5% Triton X-100) for 30 minutes and washed before incubation with an anti-SARS-CoV-2 spike protein antibody (Life Technologies).	anti-SARS-CoV-2 spike protein suggested: None
   Flow cytometry: PBMCs from healthy donors or Covid-19 patients were resuspended in PBS (Life Technologies) containing 5% FBS and 2mM EDTA (Sigma-Aldrich) for 20 minutes before staining using the following fluorochrome-conjugated antibodies (mouse IgG1): CD3 (UCHT1), CD20 (B9E9), CD14 (RMO52), CD16 (3G8) purchased from Beckman Coulter, Paris, France; HLA-DR (G46-6) and CD163 (GHI/61) from BD Biosciences, Le Pont de Claix, France, and appropriate isotype controls.	mouse IgG1) suggested: None CD20 suggested: (BioLegend Cat# 348805, RRID:AB_2889063) CD14 suggested: (BioLegend Cat# 348805, RRID:AB_2889063) RMO52 suggested: None CD16 suggested: None 3G8 suggested: None G46-6 suggested: None CD163 suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Virus production and cell infection: SARS-CoV-2 strain IHU-MI3 was obtained after Vero E6 cells (American type culture collection ATCC® CRL-1586(tm)) infection in Minimum Essential Media (MEM) (Life Technologies) supplemented with 4% FBS as previously described (20).	Vero E6 suggested: None
   Experimental Models: Organisms/Strains
   Sentences	Resources
   Virus production and cell infection: SARS-CoV-2 strain IHU-MI3 was obtained after Vero E6 cells (American type culture collection ATCC® CRL-1586(tm)) infection in Minimum Essential Media (MEM) (Life Technologies) supplemented with 4% FBS as previously described (20).	SARS-CoV-2 suggested: None
   Software and Algorithms
   Sentences	Resources
   A minimum of 50,000 events were acquired for each sample using a BD Canto II instrument (BD Biosciences) and data were analyzed with FlowJo software (Tree Star, Ashland, OR).	FlowJo suggested: (FlowJo, RRID:SCR_008520)
   Statistical analysis: Statistical analysis was performed with GraphPad Prism (7.0, La Jolla, CA), using the two-way ANOVA test for viral quantification (Ct values) and transcriptional analysis, nonparametric Kruskall-Wallis test for group comparison, nonparametric Mann-Whitney U test for cytokine levels, and nonparametric t-test for flow cytometry results with monocyte populations and surface marker expression.	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)
   qRT-PCR data for monocytes and macrophages, including principal component analysis (PCA) and hierarchical clustering of gene expression, were analyzed using the ClustVis webtool (23).	ClustVis suggested: (ClustVis, RRID:SCR_017133)

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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: Please consider improving the rainbow (“jet”) colormap(s) used on page 24. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

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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 10.1101/2020.09.17.300996 on bioRxiv

   Sep 17, 2020