Peptide vaccine candidate mimics the heterogeneity of natural SARS-CoV-2 immunity in convalescent humans and induces broad T cell responses in mice models

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   ScreenIT

   Oct 19, 2020

   SciScore for 10.1101/2020.10.16.339937: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	Consent: All donors provided written informed consent. IRB: All procedures described in this study have been reviewed and approved by the local ethic committee (CELEAG) and validated by the French Ministry of Research.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	Large, US cohort (n=16,000) The database comprising anonymized HLA-genotype data from 16,000 individuals was created by obtaining 1,000 donors from each of 16 ethnic groups (500 male and 500 female) from the National Marrow Donor Program (NMDP).
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Thereafter, cells were …

   SciScore for 10.1101/2020.10.16.339937: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	Consent: All donors provided written informed consent. IRB: All procedures described in this study have been reviewed and approved by the local ethic committee (CELEAG) and validated by the French Ministry of Research.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	Large, US cohort (n=16,000) The database comprising anonymized HLA-genotype data from 16,000 individuals was created by obtaining 1,000 donors from each of 16 ethnic groups (500 male and 500 female) from the National Marrow Donor Program (NMDP).
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Thereafter, cells were incubated in FcR blocking reagent at 4°C for 5 min, and then staining mixture (containing anti-CD3, Biolegend, anti-CD4, and anti-CD8 antibodies; BD Biosciences) was added to each well.	anti-CD3 suggested: None anti-CD4 suggested: None anti-CD8 suggested: None
   After fixation, cytokine staining mixture (containing anti-IFN-γ, anti-IL-2, anti-IL-4, anti-IL-10 and anti-TNF-α antibodies, Biolegend) was added to each well.	anti-IFN-γ suggested: (Bio-Rad Cat# M6000007NY, RRID:AB_2784537) anti-IL-2 suggested: None anti-IL-4 , suggested: None anti-IL-10 suggested: None anti-TNF-α suggested: None
   The Anti-SARS-CoV-2 ELISA plates ere coated with recombinant S-1 structural protein from SARS-CoV-2 to which antibodies against SARS-CoV-2 bind.	Anti-SARS-CoV-2 suggested: None
   ELISAs were performed by Mikromikomed Kft (Budapest, Hungary) using a DiaPro COVID-19 IgM Enzyme Immunoassay for the determination of IgM antibodies to COVID-19 in human serum and plasma, DiaPro COVID-19	IgM suggested: None
   IgG Enzyme Immunoassay for the determination of IgG antibodies to COVID-19 in human serum and plasma, and DiaPro COVID-19 IgA Enzyme Immunoassay for the determination of IgA antibodies to COVID-19 in human serum and plasma according to the manufacturer’s instructions (Dia.Pro Diagnostic Bioprobes S.r.l., Italy).	IgA suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Vero E6 cells expressing the ACE-2 receptor (Vero C1008 [ATCC No. CRL-1586, US]), were seeded at 20 000 cells/well to reach a cell confluence of 80%.	Vero E6 suggested: None Vero suggested: ATCC Cat# CRL-1586, RRID:CVCL_0574) C1008 suggested: ATCC Cat# CRL-1586, RRID:CVCL_0574)
   Experimental Models: Organisms/Strains
   Sentences	Resources
   ) Peptides and PolyPEPI-SCoV-2 vaccine preparation: The 9-mer (s2, s5, s9, n1, n2, n3, n4, e1, m1) and 30-mer (S2, S5, S7, N1, N2, N3, N4, E1, M1) peptides were manufactured by Intavis Peptide Services GmbH&Co. KG (Tübingen, Germany) and PEPScan (Lelystad, The Netherlands) using solid-phase peptide synthesis.	e1 suggested: None
   The following stains were used for BALB/c mice cohorts: 11B11 562915 (BD)	BALB/c suggested: None
   Software and Algorithms
   Sentences	Resources
   Then, the translated coding sequences of the four structural protein sequences were aligned and compared using a multiple sequence alignment (Clustal Omega, EMBL-EBI, United Kingdom).	Clustal Omega suggested: (Clustal Omega, RRID:SCR_001591)
   (47–49) Characterization of the Model Population was reported previously.(34) A second cohort of 356 individuals with characterized HLA class II genotypes (2 × HLA-DRB, 2 × HLA-DP, and 2 × HLA-DQ) at four-digit allele resolution was obtained from the dbMHC database(50), an online available repository operated by the National Center for Biotechnology Information (NCBI).	dbMHC suggested: (dbMHC, RRID:SCR_002302)
   Large, US cohort (n=16,000) The database comprising anonymized HLA-genotype data from 16,000 individuals was created by obtaining 1,000 donors from each of 16 ethnic groups (500 male and 500 female) from the National Marrow Donor Program (NMDP).	National Marrow Donor Program suggested: None
   Flow-cytometry was performed using a BD Cytofix/Cytoperm Plus Kit with BD GolgiStop™	BD GolgiStop™ suggested: None
   Spot counts ≥25 were background corrected by subtracting unstimulated (DMSO) control.	Spot suggested: (Spot, RRID:SCR_018915)
   All flow cytometry data were acquired with LSRFortessa™ X-20 and analyzed using FlowJo V10 software.	FlowJo suggested: (FlowJo, RRID:SCR_008520)
   Absorbance were read on an Epoch Microplate Reader (Biotech) and analyzed using Gen5 software.	Gen5 suggested: (Gen5, RRID:SCR_017317)
   Luminescence results for each dilution were used to generate a titration curve using a 4-parameter logistic regression (4PL) using Microsoft Excel (for Microsoft Office 365).	Microsoft Excel suggested: (Microsoft Excel, RRID:SCR_016137)

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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 found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

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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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   Version published to 10.1101/2020.10.16.339937 on bioRxiv

   Oct 16, 2020