1. SciScore for 10.1101/2022.01.13.22269205: (What is this?)

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

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    BlindingObservers received instructions and a set of stained slides and were then asked to categorize each slide in a blinded fashion, using a published four-tiered semiquantitative approach (none (0), slight (+), moderate (++), and severe (+++) 25 (Figure 3).
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    Large-scale electron microscopy and transmission electron microscopy: Four large sections prepared from different resin blocks of two autopsy lung samples (case 1) and two sections prepared from different resin blocks from SARS-CoV-2-infected Vero cells were completely digitized at 3-4 nm pixel size as recently described 27 to screen for SARS-CoV-2 particles (Supplementary Material).
    suggested: None
    Software and Algorithms
    Correlation of RT-qPCR (Pearson r) values and scoring was analyzed using Graphpad Prism (GraphPad Software Version 8, La Jolla, USA) with 34 pairs.
    Graphpad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    suggested: (GraphPad Prism, RRID:SCR_002798)
    The screening datasets were processed via Fiji software/TrakEM2 plugin 28 and nip2 software to generate high-resolution tif files 27 for in-depth analysis using QuPath software 0.2.0. 29.
    suggested: (QuPath, RRID:SCR_018257)
    The maximal diameter of intracellular particles (without spikes), based on TEM images, was measured using Fiji 30 and the “straight line” tool.
    suggested: (Fiji, RRID:SCR_002285)

    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:
    During the COVID-19 pandemic, autopsy-driven research, using multimodal approaches, attempted at defining organ tropism of the virus and at unraveling organ-specific pathomechanisms 8,9,25,41-43, yet a critical and systematic study investigating the limitations of in situ detection of SARS-CoV-2 in autopsy tissues has not been performed. Looking into the discrepancy of results from studies using autopsy material to determine organ tropism and especially identification of organ-specific target cell types of SARS-CoV-2 for most organ systems led to conflicting results hampering research progress 3,8-10,44,45. For instance, published data include studies revealing direct infection of neurons by SARS-CoV-2 with substantial neuroinvasion 46, single infected cells in a subset of patients 25, but also the absence of virus and COVID-19-specific alterations 47. Validations are complicated by the use of various, often not well-evaluated antibodies in different studies and the lack of sufficient positive and negative controls. Here we determined the limitations of SARS-CoV-2 detection by IHC and thin section EM using a defined set of control tissues including FFPE highly susceptible human cell lines and autopsy tissues with expectable high SARS-CoV-2 viral load. Finally, we performed a multicenter study assessing how well IHC performs in detecting SARS-CoV-2 proteins in autopsy tissues. Assessment of a wide range of commercially available antibodies directed at SARS-CoV-2 proteins showe...

    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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