Broad and strong memory CD4+ and CD8+ T cells induced by SARS-CoV-2 in UK convalescent individuals following COVID-19
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SciScore for 10.1101/2020.06.05.134551: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Consent: Written informed consent was obtained from all patients. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Antibodies Sentences Resources To determine EPTs to RBD and NP, immunoplates were coated with 0.125ug of Tetra-His antibody (34670; QIAGEN) followed by 2 ug/ml and 5 ug/ml of soluble RBD and NP, respectively. NPsuggested: NoneOn the second day, the PBMCs were stimulated with pooled or individual peptides at a final concentration of 10 μg/mL per individual peptide for 1 h in the presence of 2 μg/mL monoclonal antibodies against human CD28 (BD Pharmingen) and CD49d (BD … SciScore for 10.1101/2020.06.05.134551: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Consent: Written informed consent was obtained from all patients. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Antibodies Sentences Resources To determine EPTs to RBD and NP, immunoplates were coated with 0.125ug of Tetra-His antibody (34670; QIAGEN) followed by 2 ug/ml and 5 ug/ml of soluble RBD and NP, respectively. NPsuggested: NoneOn the second day, the PBMCs were stimulated with pooled or individual peptides at a final concentration of 10 μg/mL per individual peptide for 1 h in the presence of 2 μg/mL monoclonal antibodies against human CD28 (BD Pharmingen) and CD49d (BD Pharmingen) then for an additional 5h with GolgiPlug ( human CD28suggested: NoneCD49dsuggested: NoneDead cells were first labelled for FACS analysis using LIVE/DEAD™ Fixable Aqua Dead Cell Stain Kit (Invitrogen) and with CD3-BUV395, CD8-PerCP.Cy5.5 as well as a panel of antibodies for dumping, cell activation, differentiation and inhibitory markers : CD14-BV510 (Biolegend UK), CD16-BV510 (Biolegend UK), CD19-BV510 (Biolegend UK), CD28-BV711, CD27-APC-R700, HLA-DR-BB515, CD38-BUV737, CD45RA-APC-H7, PD-1-BV650, CD57-BV785 (Biolegend, UK) and NKG2A (R&D). CD14-BV510suggested: NoneCD16-BV510suggested: NoneCD19-BV510suggested: NoneCD57-BV785suggested: NoneNKG2Asuggested: NoneSoftware and Algorithms Sentences Resources Synthetic peptides: A total of 423 15- to 18-mer peptides overlapping by 10 amino acid residues and spanning the full proteome of the SARS-CoV-2 except ORF-1 (253 spike, 29 M, 9 E, 35 ORF3a, 7ORF6, 15 ORF7a, 16 ORF8, 59 NP) were designed using the Los Alamos National Library web-based software PeptGen (http://www.hiv.lanl.gov/content/sequence/PEPTGEN/peptgen.html) and synthesized (purity >75%; Proimmune). PeptGensuggested: NoneFinally, surface markers including BUV395-anti-CD3 (BD Biosciences), BUV737-anti-CD4 (BD Biosciences), PerCP-Cy5.5-anti-CD8 (BD Biosciences), BV510-anti-CD14 (Biolegend), BV510-anti-CD16 (Biolegend) and BV510-anti-CD19 (Biolegend) were stained. BD Biosciencessuggested: (BD Biosciences, RRID:SCR_013311)All samples were acquired on BD LSR Fortessa (BD Biosciences) flow cytometer and analyzed using FlowJo™ v.10 software for Mac (Becton, Dickinson and Company; 2019). FlowJo™suggested: (FlowJo, RRID:SCR_008520)Cell events were acquired on Fortessa X20 (BD Bioscience) and data files were analyzed using FlowJo software. FlowJosuggested: (FlowJo, RRID:SCR_008520)Statistical analysis: Statistical analysis was performed with IBM SPSS Statistics 25 and figures were made with GraphPad Prism 8. SPSSsuggested: (SPSS, RRID:SCR_002865)GraphPad Prismsuggested: (GraphPad Prism, RRID:SCR_002798)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).
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.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: Please consider improving the rainbow (“jet”) colormap(s) used on pages 32, 25 and 28. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.
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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