BCG vaccination of Diversity Outbred mice induces cross-reactive antibodies to SARS-CoV-2 spike protein

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1. 

   ScreenIT

   Apr 22, 2022

   SciScore for 10.1101/2022.04.18.488640: (What is this?)

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

   Table 1: Rigor

   Ethics	IACUC: BCG-vaccinated mice: Studies were performed under protocols approved by the Animal Care and Use Committee (ACUC) of CBER/FDA protocol #2011-14.
   Sex as a biological variable	Briefly, female C57BL/6J and female Diversity Outbred (DO) mice, purchased from Jackson Laboratories (Bar Harbor, ME), were used at 6-10 weeks of age.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   In-house ELISA to SARS-CoV-2 Antigens: We optimized an in-house ELISA to detect cross-reactive IgG antibodies in mouse sera.	SARS-CoV-2 suggested: None Antigens suggested: None IgG suggested: None
   On day 3, the same detection antibody, goat anti-mouse …

   SciScore for 10.1101/2022.04.18.488640: (What is this?)

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

   Table 1: Rigor

   Ethics	IACUC: BCG-vaccinated mice: Studies were performed under protocols approved by the Animal Care and Use Committee (ACUC) of CBER/FDA protocol #2011-14.
   Sex as a biological variable	Briefly, female C57BL/6J and female Diversity Outbred (DO) mice, purchased from Jackson Laboratories (Bar Harbor, ME), were used at 6-10 weeks of age.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   In-house ELISA to SARS-CoV-2 Antigens: We optimized an in-house ELISA to detect cross-reactive IgG antibodies in mouse sera.	SARS-CoV-2 suggested: None Antigens suggested: None IgG suggested: None
   On day 3, the same detection antibody, goat anti-mouse IgG-HRP, was added followed by the addition of TMB and then HCl, as described above.	anti-mouse IgG-HRP suggested: None
   Experimental Models: Organisms/Strains
   Sentences	Resources
   Briefly, female C57BL/6J and female Diversity Outbred (DO) mice, purchased from Jackson Laboratories (Bar Harbor, ME), were used at 6-10 weeks of age.	C57BL/6J suggested: None
   Software and Algorithms
   Sentences	Resources
   Basic Local Alignment Search Tool (BLAST) from NCBI was used to align the selected epitopes with the Swiss-Prot reviewed proteome of BCG strain Pasteur (Mycobacterium bovis (strain BCG / Pasteur 1173P2).	BLAST suggested: None NCBI suggested: (NCBI, RRID:SCR_006472)
   The BCG protein and cellular component, as described on the UniprotKB database, was obtained for each peptide fitting the above criteria.	UniprotKB suggested: (UniProtKB, RRID:SCR_004426)
   Figures 4a and 4b were created using the R software package ggplot2.	ggplot2 suggested: None
   Concentration of bound-IgG was computed based on a 4-parameter logistic (4PL) regression model of the standard curve using the program Gen5.	Gen5 suggested: (Gen5, RRID:SCR_017317)
   Statistical Analysis: Graphs were made using Prism GraphPad version 9.1.0.	Prism suggested: (PRISM, RRID:SCR_005375) GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)

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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: We detected the following sentences addressing limitations in the study:

   Future research could explore this study’s limitations by characterizing the binding site of the cross-reactive IgG antibodies and assessing the antibodies for neutralizing efficacy, or by investigating the genetic basis for the cross-reactive humoral response in DO mice. To the first point, affinity purification mass spectrometry (AP-MS) could confirm antibody concentration and purify the cross-reactive antibodies for affinity testing against peptides identified by our in silico analysis. To the second point, genotype-phenotype association studies, such as quantitative trait locus mapping, could be performed on larger sample sizes to identify gene candidates and polymorphisms.

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   Results from TrialIdentifier: We found the following clinical trial numbers in your paper:
   

   Identifier	Status	Title
   NCT03296423	Completed	Bacillus Calmette-guérin Vaccination to Prevent Infections o…
   NCT04327206	Active, not recruiting	BCG Vaccination to Protect Healthcare Workers Against COVID-…
   NCT04369794	Active, not recruiting	COVID-19: BCG As Therapeutic Vaccine, Transmission Limitatio…

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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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   Read the original source
2. 

   Version published to 10.1101/2022.04.18.488640v1 on bioRxiv

   Apr 19, 2022