1. SciScore for 10.1101/2021.07.20.21260845: (What is this?)

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

    Table 1: Rigor

    EthicsConsent: All participants provided informed written consent.
    IRB: Approval for the study design and sample collection was obtained within the framework of study “Establishment and validation of epitope-specific SARS-CoV-2 blood-based testing methods” (EPI-SARS) by the ethics committee of the Technical University of Munich (reference number 182/20) and the Institutional Ethics Committee of the University Medicine Mannheim (reference number 2020-556N).
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    After incubation, cells were stained with EMA solution (1:1000) for live/dead discrimination and subsequently with surface antibodies: CD19-ECD (1:100), CD8-PE (1:200), CD3-BV421 (1:100) and murine TCR β-chain-APC/Fire750 (1:100).
    CD19-ECD
    suggested: None
    CD8-PE
    suggested: None
    CD3-BV421
    suggested: None
    HLA type for asymptomatic seropositive and seronegative donors was determined via surface antibody staining using commercially available antibodies targeting HLA-A*02-FITC (1:200,), HLA-A*03-APC (1:200), HLA-B*07-PE (1:100), HLA-B*08-APCVio770 (1:200).
    HLA-A*03-APC
    suggested: None
    HLA-B*07-PE
    suggested: None
    HLA-B*08-APCVio770
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    A549-ACE2 RFP+ cells were then retrovirally transduced with plasmids encoding HLA-A*01:01 or HLA-A*03:01.
    A549-ACE2 RFP+
    suggested: None
    For the production of retroviral particles, RD114 cells were transfected with pMP71 expression vector (containing the HLA heavy chain construct, gag/pol and amphotropic envelope) by calcium phosphate precipitation.
    RD114
    suggested: ATCC Cat# PTA-4440, RRID:CVCL_1J88)
    1*105 A549 ACE2 RFP+ cells were then transduced via spinoculation on virus-coated plates.
    A549
    suggested: NCI-DTP Cat# A549, RRID:CVCL_0023)
    For the Incucyte killing assay, 5*103 A549-ACE2+ RFP+ HLA-A*01 or A549-ACE2+ RFP+ HLA-A*03 cells were seeded 24 h prior infection with SARS-CoV-2 GFP virus (MOI 5).
    HLA-A*03
    suggested: None
    Recombinant DNA
    SentencesResources
    For the production of retroviral particles, RD114 cells were transfected with pMP71 expression vector (containing the HLA heavy chain construct, gag/pol and amphotropic envelope) by calcium phosphate precipitation.
    pMP71
    suggested: RRID:Addgene_141355)
    Software and Algorithms
    SentencesResources
    After import of sequence raw data in the uType software, the sequences were analyzed for HLA type creation by aligning to recent IMGT HLA allele
    uType
    suggested: None

    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: We detected the following sentences addressing limitations in the study:
    A limitation of our study is the use of an in vitro expansion step prior T cell analyses, which may bias the relative abundance of clonotypes and may favor outgrowing of some clones at the expense of others. However, this approach of peptide stimulation offered the possibility of exploiting signatures of recent activation to discriminate epitope-specific and functional TCRs66. Indeed, we identified signatures of T cell function and recent activation correlating with TCR functionality, which allowed a broad in silico investigation of the functional landscape of entire TCR repertoires, otherwise unfeasible by conventional experimental validation. Remarkably, we predicted highly functional TCRs for each of the eleven immunodominant SARS-CoV-2 epitopes analyzed, despite a certain degree of functional heterogeneity. Together with the observed polyclonality, our data indicate that functional and diverse CD8+ T cell immunity should normally establish in non-severe SARS-CoV-2 infections. Polyclonality and high functionality are hallmarks of a protective TCR repertoire67, thus strongly supporting a similar role also in the context of SARS-CoV-2 infections. Nevertheless, the extension of TCR repertoire analyses to settings of severe infections remains a fundamental next step to assign CD8+ T cell responses a role as correlates of protection. Overall, our data provide first evidence that SARS-CoV-2-specific CD8+ T cells persists up to 12 months after infection and are composed of a poly...

    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: We did not find any issues relating to colormaps.


    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.

    Results from scite Reference Check: We found no unreliable references.


    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

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