CD8+ T cell responses in convalescent COVID-19 individuals target epitopes from the entire SARS-CoV-2 proteome and show kinetics of early differentiation

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1. 

   ScreenIT

   Oct 9, 2020

   SciScore for 10.1101/2020.10.08.330688: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	Consent: Eligible individuals were enrolled in the study under full, written informed consent, after which whole blood (25 mL) samples were collected.
   Randomization	Fifteen individuals were randomly selected from each tertile for HLA typing using the donor PMBC samples.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Sample selection, antibody titers, HLA typing and cytokine testing: The study samples were collected from individuals who were at least 18 years old, who had recovered from COVID-19, and expressed a willingness to donate COVID-19 convalescent plasma (CCP).	CCP suggested…

   SciScore for 10.1101/2020.10.08.330688: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	Consent: Eligible individuals were enrolled in the study under full, written informed consent, after which whole blood (25 mL) samples were collected.
   Randomization	Fifteen individuals were randomly selected from each tertile for HLA typing using the donor PMBC samples.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Sample selection, antibody titers, HLA typing and cytokine testing: The study samples were collected from individuals who were at least 18 years old, who had recovered from COVID-19, and expressed a willingness to donate COVID-19 convalescent plasma (CCP).	CCP suggested: None
   SARS-CoV-2 neutralizing antibody (nAbs) titers against 100 50% tissue culture infectious doses (TCID50) per 100 uL were determined using a microneutralization (NT) assay, as previously described 3.	SARS-CoV-2 neutralizing antibody suggested: (ABclonal Cat# A19215, RRID:AB_2862633)
   After 30 mins a unique metal (Cd-111 and Cd-113) labelled anti-CD45 antibody was added into each of the wells to further barcode the cells that were stained with the different tetramer configurations.	anti-CD45 suggested: None
   For intracellular staining, cells were incubated in 1× permeabilization buffer (Biolegend) for 5 min on ice and incubated with metal conjugated anti-GranzymeB antibodies for 30 min on ice.	anti-GranzymeB suggested: None
   Software and Algorithms
   Sentences	Resources
   High-dimensional phenotypic profiles and sample distributions were shown using uniform manifold approximation and projection 34 and Phenograph for automated cell clustering 35.	Phenograph suggested: (Phenograph, RRID:SCR_016919)
   Data analysis was performed using CYTOGRAPHER®, immunosCAPE’s cloud based analytical software, custom R-scripts, GraphPad Prism and Flowjo software.	GraphPad suggested: (GraphPad Prism, RRID:SCR_002798) Flowjo suggested: (FlowJo, RRID:SCR_008520)
   A correlation matrix was calculated comparing phenotypic and serological marker variables in a pairwise fashion, using the corr.test function from the psych CRAN package; the corrplot package was subsequently used to graphically display the correlation matrix.	CRAN suggested: (CRAN, RRID:SCR_003005)

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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:

   This study has limitations. Foremost is the relatively small sample size. The need to generate a well characterized sample set, limited the number of subjects that could be included. Second, the study is confined to a sampling of COVID-19 convalescent individuals from the greater Baltimore/Washington DC area. As such, this is a geographically restricted population and may not be broadly representative. Third, a low proportion of those who were evaluated had been hospitalized. While this limited our ability to investigate T cell responses in those who were severely ill, it has afforded insight into those with milder disease, which is a more commonly encountered form of COVID-19 and could alternatively be considered a strength of our study. Fourth, while the HLA types which were included account for ~73% of the continental US population, the technology was restricted to only six HLA types. Lastly, the study was cross-sectional and restricted to a relatively narrow time period. Specifically, individuals were evaluated 27-62 days post-symptom resolution. At a minimum, they needed to be at least 28 days post-resolution to donate samples. This limits the conclusions with respect to earlier and/or later in the convalescent period. Of note, even within the period that was evaluated, changes in the T cell and cytokine responses were observed over time. For example, those later in the convalescent period exhibited T cell maturation with effector cells remaining, possibly to clear resid...

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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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   Version published to 10.1101/2020.10.08.330688v1 on bioRxiv

   Oct 8, 2020