Article activity feed

  1. SciScore for 10.1101/2022.06.01.494373: (What is this?)

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

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    High-density peptide array (HDPA): To analyze the antibody responses to SARS-CoV-2 at the epitope level we used a recently developed high-density peptide array (HDPA), the PEPperCHIP® Microarray (PEPperPRINT GmbH, Germany), covering the proteome of the SARS-CoV-2 isolate Wuhan-Hu-1 as well as the four seasonal hCoVs OC43, HKU1, NL63 and 229E (see Table S12 for accession numbers used).
    suggested: None
    Microarrays were then washed (three times with PBS-T for 1 minute) and peptide binding was detected with isotype-specific secondary goat anti-human IgG (Fc) DyLight680 (ThermoFisher Scientific) and goat anti-human IgA (alpha chain) DyLight800 (Rockland Immunochemicals) antibodies at a final concentration of 0.1 μg/ml and 1 μg/ml, respectively (in 10% RL/PBS-T for 45 minutes at room temperature).
    anti-human IgG
    suggested: (Rockland Cat# 609-145-130, RRID:AB_2614820)
    anti-human IgA
    suggested: (Rockland Cat# 609-145-130, RRID:AB_2614820)
    To identify the top IgG and IgA antibody responses of the human serum samples, the averaged intensity values were sorted by decreasing spot intensities.
    suggested: None
    Software and Algorithms
    Using ImageJ software the resulting 32-bit gray-scale TIFF files were converted into 16-bit gray-scale TIFF files and then further analyzed using the PepSlide® Analyzer (SICASYS
    suggested: (ImageJ, RRID:SCR_003070)
    Pymol was used for visualization.
    suggested: (PyMOL, RRID:SCR_000305)

    Results from OddPub: Thank you for sharing your code.

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    Sensitivity limitations of PhIP-seq to broadly detected polio epitopes have been previously reported (20, 22) and might contribute to the observed differences, similarly affecting detectability of CoV antigens. Such limitations are not observed in our HDPA approach (44) which typically yielded strong polio responsiveness in over 90% of sampled individuals (45). Importantly, the cross-reactivity in identified B cell epitope sites positively relates to previous infections with seasonal common cold hCoVs. This suggests that immune memory conferred by previous seasonal hCoV infections positively influences SARS-CoV-2-specific antibody responses and may explain the large portion of SARS-CoV-2-infected individuals with mild and asymptomatic disease symptoms (4). Notably, there was little to no correlation between cross-reactivity and immune response in COVID-19 negative patients, suggesting that resistance to infection is not easily explained by cross reactivity. However, this molecular cross-reactivity can pose important complications in serological tests, particularly when studying asymptomatic patients. Cross-reactivity in immunodominant epitopes can be molecular determinants of strong immunity in individuals and therefore may serve as the basis for future pan-coronavirus vaccine design strategies. In turn, mutations in these cross-reactive epitopes can potentially breach pre-existing immune protection conferred by previous viral exposures, contributing to viral evolution, immun...

    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.
    • No funding statement was detected.
    • 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.

    Read the original source
    Was this evaluation helpful?