Assessing and improving the validity of COVID-19 autopsy studies - A multicentre approach to establish essential standards for immunohistochemical and ultrastructural analyses

Article activity feed

1. Version published to 10.1016/j.ebiom.2022.104193

   Sep 1, 2022
2. 

   ScreenIT

   Jan 16, 2022

   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

   Ethics	not detected.
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	Observers 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 Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Experimental Models: Cell Lines
   Sentences	Resources
   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 …

   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

   Ethics	not detected.
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	Observers 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 Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Experimental Models: Cell Lines
   Sentences	Resources
   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).	Vero suggested: None
   Software and Algorithms
   Sentences	Resources
   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) GraphPad 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.	QuPath 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.	Fiji suggested: (Fiji, RRID:SCR_002285)

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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:

   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...

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

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3. 

   Version published to 10.1101/2022.01.13.22269205v1 on medRxiv

   Jan 13, 2022