Longitudinal analysis of humoral immunity against SARS-CoV-2 Spike in convalescent individuals up to 8 months post-symptom onset

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1. Version published to 10.1016/j.xcrm.2021.100290

   Jun 1, 2021
2. 

   ScreenIT

   Jan 26, 2021

   SciScore for 10.1101/2021.01.25.428097: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	Consent: Ethics Statement: All work was conducted in accordance with the Declaration of Helsinki in terms of informed consent and approval by an appropriate institutional board.
   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
   Horseradish peroxidase (HRP)-conjugated antibodies able to detect all Ig isotypes (anti-human IgM+IgG+IgA; Jackson ImmunoResearch Laboratories, Inc.) or specific for the Fc region of human IgG (Invitrogen), the Fc region of human IgM (Jackson ImmunoResearch Laboratories, inc.) or the Fc region …

   SciScore for 10.1101/2021.01.25.428097: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	Consent: Ethics Statement: All work was conducted in accordance with the Declaration of Helsinki in terms of informed consent and approval by an appropriate institutional board.
   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
   Horseradish peroxidase (HRP)-conjugated antibodies able to detect all Ig isotypes (anti-human IgM+IgG+IgA; Jackson ImmunoResearch Laboratories, Inc.) or specific for the Fc region of human IgG (Invitrogen), the Fc region of human IgM (Jackson ImmunoResearch Laboratories, inc.) or the Fc region of human IgA (Jackson ImmunoResearch Laboratories, inc) were used as secondary antibodies to detect antibody binding in ELISA and cell-based ELISA experiments.	anti-human IgM+IgG+IgA suggested: None human IgG suggested: None
   Alexa Fluor-647-conjugated goat anti-human Abs able to detect all Ig isotypes (anti-human IgM+IgG+IgA; Jackson ImmunoResearch Laboratories, Inc.) were used as secondary antibodies to detect plasma binding in flow cytometry experiments.	anti-human Abs suggested: None
   ADCC assay: For evaluation of anti-SARS-CoV-2 antibody-dependent cellular cytotoxicity (ADCC), parental CEM.	anti-SARS-CoV-2 suggested: None
   The detection of SARS-CoV-2-antigen specific B cells was done by adding the RBD probes to the following antibody cocktail: IgM BUV737 (Clone UCH-B1, #748928), CD24 BUV805	CD24 suggested: (BD Biosciences Cat# 742010, RRID:AB_2871308)
   Experimental Models: Cell Lines
   Sentences	Resources
   Cell surface staining and flow cytometry analysis: 293T and 293T-Spike cells were mixed at a 1:1 ratio and stained with the anti-RBD CR3022 monoclonal Ab (5 μg/ml) or plasma (1:250 dilution).	293T-Spike suggested: None
   Briefly, 293T cells were transfected by the calcium phosphate method with the lentiviral vector pNL4.3 R-E-Luc (NIH AIDS Reagent Program) and a plasmid encoding for SARSCoV-2 Spike at a ratio of 5:4.	293T suggested: NCBI_Iran Cat# C498, RRID:CVCL_0063)
   Software and Algorithms
   Sentences	Resources
   All samples were acquired on an LSRII cytometer (BD Biosciences) and data analysis performed using FlowJo v10.7.1 (Tree Star).	FlowJo suggested: (FlowJo, RRID:SCR_008520)
   CD27 APC R700 (Clone M-T271, #565116) all from BD Biosciences; CD19 BV650 (Clone SJ25C1, #363026) from Biolegend and IgA PE (Clone IS11-8E10, #130-113-476) from Miltenyi.	BD Biosciences suggested: (BD Biosciences, RRID:SCR_013311)
   Statistical analyses: Statistics were analyzed using GraphPad Prism version 9.0.0 (GraphPad, San Diego, CA).	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798) GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)
   Correlograms were generated using the corrplot and RColorBrewer packages in program R and RStudio using hierarchical clustering according to the first principal component (FPC).	RColorBrewer suggested: (RColorBrewer, RRID:SCR_016697)
   Edge bundling graphs were generated in undirected mode in R and RStudio using ggraph, igraph, tidyverse, and RColorBrewer packages.	RStudio suggested: (RStudio, RRID:SCR_000432)

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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 pages 32, 38 and 30. 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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3. 

   Version published to 10.1101/2021.01.25.428097v1 on bioRxiv

   Jan 25, 2021