Suboptimal SARS-CoV-2−specific CD8 + T cell response associated with the prominent HLA-A*02:01 phenotype
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Abstract
As the recall of CD8 + T cell memory promotes rapid recovery in, for example, influenza, we investigated circulating SARS-CoV-2−specific CD8 + T cells from COVID-19 patients. For two HLA-A*02:01 SARS-CoV-2−specific CD8 + T cell epitopes, we found that, while ex vivo frequencies of responding T cells were approximately fivefold higher than for pre−COVID-19 samples, they were ∼10-fold lower than for influenza or EBV-specific memory CD8 + T cells. Additionally, SARS-CoV-2−specific CD8 + T cells recovered from convalescent COVID-19 patients had an atypically high prevalence of stem cell memory, central memory, and naïve phenotypes. Might this unexpectedly low prevalence of classical effector memory T cells be a negative consequence of the infectious process that could be avoided by prior priming with an appropriately constituted vaccine?
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SciScore for 10.1101/2020.08.17.20176370: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Consent: Written informed consents were obtained from all blood donors prior to the study.
IRB: ) Human Research Ethics Committees.Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Overlapping synthetic peptides spanning the entire Nucleocapsid (N) and Membrane (M) proteins, and selected regions of SARS-CoV2 Spike (S) were purchased from Miltenyi Biotec (PepTivator SARS-CoV-2 Prot_N (130–126–699), Prot_M (130–126–703) and Prot_S (130–126–701)) and reconstituted in 80% DMSO. Prot_Msuggested: NoneFlow cytometry data were analyzed using FlowJo … SciScore for 10.1101/2020.08.17.20176370: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Consent: Written informed consents were obtained from all blood donors prior to the study.
IRB: ) Human Research Ethics Committees.Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Overlapping synthetic peptides spanning the entire Nucleocapsid (N) and Membrane (M) proteins, and selected regions of SARS-CoV2 Spike (S) were purchased from Miltenyi Biotec (PepTivator SARS-CoV-2 Prot_N (130–126–699), Prot_M (130–126–703) and Prot_S (130–126–701)) and reconstituted in 80% DMSO. Prot_Msuggested: NoneFlow cytometry data were analyzed using FlowJo v10 software. FlowJosuggested: (FlowJo, RRID:SCR_008520)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 16, 17 and 15. 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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