Favourable antibody responses to human coronaviruses in children and adolescents with autoimmune rheumatic diseases

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1. 

   ScreenIT

   Mar 1, 2021

   SciScore for 10.1101/2021.02.15.431291: (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	Contamination: Cell lines and plasmids: HEK293T cells and Vero E6 were obtained from the Cell Services facility at The Francis Crick Institute and verified as mycoplasma-free.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Patients were treated as being ‘autoantibody positive’ if any of rheumatoid factor (RF), anti-nuclear antibodies (ANA) or myositis-specific/myositis-associated autoantibodies were recorded as positive.	anti-nuclear suggested: None
   Flow cytometric detection of antibodies to spike and envelope …

   SciScore for 10.1101/2021.02.15.431291: (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	Contamination: Cell lines and plasmids: HEK293T cells and Vero E6 were obtained from the Cell Services facility at The Francis Crick Institute and verified as mycoplasma-free.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Patients were treated as being ‘autoantibody positive’ if any of rheumatoid factor (RF), anti-nuclear antibodies (ANA) or myositis-specific/myositis-associated autoantibodies were recorded as positive.	anti-nuclear suggested: None
   Flow cytometric detection of antibodies to spike and envelope glycoproteins: HEK293T cells expressing HCoV-OC43 spike were mixed with cells expressing ERV3-1 envelope glycoprotein and GFP and HEK293T cells expressing SARS-CoV-2 spike were mixed with cells expressing HERV-K113 envelope glycoprotein and GFP at equal rations.	ERV3-1 envelope glycoprotein suggested: None GFP suggested: None HERV-K113 envelope glycoprotein suggested: None
   , APC anti-IgM (clone MHM-88, Biolegend) and PE anti-IgA (clone IS11-8E10, Miltenyi Biotech) for 30 min (all antibodies diluted 1:200 in FACS buffer).	anti-IgM suggested: None anti-IgA suggested: None
   Flow cytometric detection of antibodies to nucleoproteins: Aliquots of recombinant HCoV-OC43 and SARS-CoV-2 nucleoproteins were conjugated with aldehyde functionalized polymethylmethacrylate-based microspheres (PolyAn GmbH, Berlin, Germany), according to manufacturer’s instructions, and kept at 4°C until use.	PolyAn GmbH , Berlin , Germany suggested: None
   Outcome variables modelled were the total, IgG and IgA antibody levels for SARS-CoV-2 and OC43 spike proteins and nucleoproteins.	total, IgG suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Cell lines and plasmids: HEK293T cells and Vero E6 were obtained from the Cell Services facility at The Francis Crick Institute and verified as mycoplasma-free.	Vero E6 suggested: RRID:CVCL_XD71)
   Beads were then stained with serum and plasma samples, as described above for HEK293T cells used in flow cytometric detection of antibodies to spike and envelope glycoproteins.	HEK293T suggested: NCBI_Iran Cat# C498, RRID:CVCL_0063)
   Software and Algorithms
   Sentences	Resources
   Samples were run on a Ze5 analyzer (Bio-Rad) running Bio-Rad Everest software v2.4 or an LSR Fortessa with a high-throughput sampler (BD Biosciences) running BD FACSDiva software v8.0, and analyzed using FlowJo v10	Bio-Rad Everest suggested: None BD FACSDiva suggested: (BD FACSDiva Software, RRID:SCR_001456) FlowJo suggested: (FlowJo, RRID:SCR_008520)
   Virus plaques were quantified and IC50 values were calculated using LabView software as described previously (35) or SigmaPlot v14.0 (Systat Software).	LabView suggested: (LabView , RRID:SCR_014325)
   Statistical analyses: Data were analysed and plotted in GraphPad Prism v8 (GraphPad Software) or SigmaPlot v14.0 (Systat Software).	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798) GraphPad suggested: (GraphPad Prism, RRID:SCR_002798) SigmaPlot suggested: (SigmaPlot, RRID:SCR_003210)

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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 10.1101/2021.02.15.431291v1 on bioRxiv

   Feb 16, 2021