Genome-Wide B Cell, CD4+, and CD8+ T Cell Epitopes That Are Highly Conserved between Human and Animal Coronaviruses, Identified from SARS-CoV-2 as Targets for Preemptive Pan-Coronavirus Vaccines

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1. Version published to 10.4049/jimmunol.2001438

   Jun 1, 2021
2. 

   ScreenIT

   Sep 30, 2020

   SciScore for 10.1101/2020.09.27.316018: (What is this?)

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

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   The cells were subsequently washed with FACS buffer (1% BSA and 0.1% sodium azide in phosphate-buffered saline) and stained with anti-HLA-A2 specific monoclonal antibody (clone BB7.2) (BD-Pharmingen, San Diego, CA) at 4°C for 30 minutes.	anti-HLA-A2 suggested: None
   The following antibodies were used: CD8, CD4, CD62L, CD107a/b, CD44, CD69, TNF-α and IFN-γ).	CD8 suggested: (RayBiotech Cat# CS-11-0250, RRID:AB_1228199) CD4 suggested: (RayBiotech Cat# CS-11-0133, RRID:AB_1228052) CD62L suggested: None CD44 suggested: None CD69 suggested: None TNF-α suggested: None
   Wells of 96-well Multiscreen HTS Plates (Millipore, …

   SciScore for 10.1101/2020.09.27.316018: (What is this?)

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

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   The cells were subsequently washed with FACS buffer (1% BSA and 0.1% sodium azide in phosphate-buffered saline) and stained with anti-HLA-A2 specific monoclonal antibody (clone BB7.2) (BD-Pharmingen, San Diego, CA) at 4°C for 30 minutes.	anti-HLA-A2 suggested: None
   The following antibodies were used: CD8, CD4, CD62L, CD107a/b, CD44, CD69, TNF-α and IFN-γ).	CD8 suggested: (RayBiotech Cat# CS-11-0250, RRID:AB_1228199) CD4 suggested: (RayBiotech Cat# CS-11-0133, RRID:AB_1228052) CD62L suggested: None CD44 suggested: None CD69 suggested: None TNF-α suggested: None
   Wells of 96-well Multiscreen HTS Plates (Millipore, Billerica, MA) were pre-wet with 70% methanol and then coated with 100 µl primary anti-IFN-γ antibody solution (10 µg/ml of 1-D1K coating antibody from Mabtech in PBS, pH 7.4, V-E4) OVN at 4°C.	anti-IFN-γ suggested: None
   Plates were incubated at 4°C overnight with the sera, then washed with PBS-Tween 0.01% before to add anti-mouse IgG antibody (Mabtech – 1/500 dilution).	anti-mouse IgG suggested: None
   Experimental Models: Organisms/Strains
   Sentences	Resources
   Immunization of mice: Groups of age-matched HLA transgenic mice/B6 mice (n = 3) were immunized subcutaneously, on days 0 and 14, with a mixture of four SARS-CoV-2-derived human CD4+ T/ CD8+T /B cell peptide epitopes delivered in alum and CpG1826 adjuvants.	mice/B6 suggested: None
   Sera of C57BL/6 mice immunized either with pool B cell peptides alum/CpG or adjuvant alone (control) were added into the wells at various dilutions (1/5, 1/25, 1/125 and 1/625 or PBS only, in triplicate).	C57BL/6 suggested: None
   Software and Algorithms
   Sentences	Resources
   The sequences were aligned using ClustalW algorithm in MEGA X.	ClustalW suggested: (ClustalW, RRID:SCR_017277)
   The acquired data were analyzed with FlowJo software (BD Biosciences, San Jose, CA) and expression was measured by mean fluorescence intensity (MFI).	FlowJo suggested: (FlowJo, RRID:SCR_008520)
   Constructing the Phylogenetic Tree: Phylogenetic analyses were conducted in MEGA X.	MEGA suggested: (Mega BLAST, RRID:SCR_011920)
   Genome sequences of previous strains of SARS-CoV for human, bat, civet, and camel were retrieved from the NCBI GeneBank.	NCBI GeneBank suggested: None
   Statistical differences observed in the measured CD8-, CD4-T cells and antibody responses between heatlhy donors and COVID-19 patients or across the different group of disease severity were calculated using ANOVA and multiple t-test comparison procedures in GraphPad Prism.	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)

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   Results from OddPub: Thank you for sharing your data.

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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 10.1101/2020.09.27.316018v1 on bioRxiv

   Sep 28, 2020