Distinct systemic and mucosal immune responses during acute SARS-CoV-2 infection

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1. Version published to 10.1038/s41590-021-01028-7

   Sep 1, 2021
2. 

   ScreenIT

   Mar 15, 2021

   SciScore for 10.1101/2021.03.01.21251633: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	Consent: Biological collection and informed consent were approved by the Direction de la Recherche Clinique et Innovation (DRCI) and the French Ministry of Research (N°2019-3677). IRB: The study conforms to the principles outlined in the Declaration of Helsinki, and received approval by the appropriate Institutional Review Board (Cochin-Port Royal Hospital, Paris
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	The median age of the patients was 55 years (interquartile range, 50 to 63) and 78% were male, while median age of healthy controls was 51 years (interquartile range, 38 to 60) and 72% were male.
   Cell …

   SciScore for 10.1101/2021.03.01.21251633: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	Consent: Biological collection and informed consent were approved by the Direction de la Recherche Clinique et Innovation (DRCI) and the French Ministry of Research (N°2019-3677). IRB: The study conforms to the principles outlined in the Declaration of Helsinki, and received approval by the appropriate Institutional Review Board (Cochin-Port Royal Hospital, Paris
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	The median age of the patients was 55 years (interquartile range, 50 to 63) and 78% were male, while median age of healthy controls was 51 years (interquartile range, 38 to 60) and 72% were male.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   For the IFNγ assay, the MD-1 antibody clone (BioLegend) was used as a capture antibody after coating on paramagnetic beads (0.3 mg/mL), the 25718 antibody clone (R&D Systems) was biotinylated (biotin/antibody ratio = 40/1) and used as the detector antibody at a concentration of 0.3ug/mL.	MD-1 suggested: None
   For the IL-17A assay, the BL23 antibody clone (BioLegend) was used as a capture antibody after coating on paramagnetic beads (0.3 mg/mL), the MT504 antibody clone (MabTech), already biotinylated, was used as the detector antibody at a concentration of 0.3ug/mL.	BL23 suggested: (BioLegend Cat# 512705, RRID:AB_2783336) MT504 suggested: None
   For the IFNβ assay, the 710322-9 IgG1, kappa, mouse monoclonal antibody (PBL Assay Science) was used as a capture antibody after coating paramagnetic beads (0.3 mg/mL), the 710323-9 IgG1, kappa, mouse monoclonal antibody (PBL Assay Science) was biotinylated (biotin/antibody ratio = 40/1) and used as the detector antibody, and recombinant protein (PBL Assay Science) were used to quantify IFNβ concentrations.	IgG1 suggested: None
   For the IFNλ3 assay, the MMHL-3 IgG1 kappa mouse monoclonal antibody (PBL Assay Science) was used as a capture antibody after coating paramagnetic beads (0.3 mg/mL), the 567107R IgG2a mouse monoclonal antibody (R&D systems) was biotinylated (biotin/antibody ratio = 60/1) and used as the detector antibody, and recombinant protein (PBL Assay Science) were used to quantify IFNλ3 concentrations.	MMHL-3 IgG1 suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Briefly, a standard ELISA assay using as target antigens the extracellular domain of the S protein in the form of a trimer (ELISA tri-S) and the S-Flow assay, which is based on the recognition of SARS-CoV-2 S protein expressed on the surface of 293T cells (293T-S), were used to quantify SARS-CoV-2 specific IgG and IgA subtypes in plasma and nasal swab supernatants.	293T suggested: RRID:CVCL_LC70)
   Software and Algorithms
   Sentences	Resources
   Briefly, amplicons were clustered into operational taxonomic units (OTU) with VSEARCH (v1.4) and aligned against the SILVA database.	VSEARCH suggested: None SILVA suggested: (SILVA, RRID:SCR_006423)
   Statistical analysis: GraphPad Prism was used for statistical analysis.	GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)
   Plots were made using the ggplot2 package (v3.3.2).	ggplot2 suggested: (ggplot2, RRID:SCR_014601)

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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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3. 

   Version published to 10.1101/2021.03.01.21251633 on medRxiv

   Mar 2, 2021