Microarray-Based Detection of Antibodies against SARS-CoV-2 Proteins, Common Respiratory Viruses and Type I Interferons

Article activity feed

1. Version published to 10.3390/v13122553

   Dec 20, 2021
2. 

   ScreenIT

   Dec 17, 2021

   SciScore for 10.1101/2021.12.13.21267509: (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	not detected.
   Power Analysis	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   After incubation (usually overnight, 37°C), intermediate washing (PBS with 0.01% Tween 20 (Sigma–Aldrich, St. Louis, MO, USA), 20 min), rinsing and drying, the microarrays were treated with a mixture of fluorescently labeled antibodies (5 µg/mL; F(ab’) 2-goat anti-human IgG-Cy5, and 5 µg/mL, goat anti-IgM-Cy3; 50 µL in total) in PBS buffer with 0.14% polyvinyl alcohol, 0.14% polyvinylpyrrolidone and 1% BSA (Sigma–Aldrich, St. Louis, MO, USA).	anti-human IgG-Cy5 suggested: None anti-IgM-Cy3 suggested: None
   For …

   SciScore for 10.1101/2021.12.13.21267509: (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	not detected.
   Power Analysis	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   After incubation (usually overnight, 37°C), intermediate washing (PBS with 0.01% Tween 20 (Sigma–Aldrich, St. Louis, MO, USA), 20 min), rinsing and drying, the microarrays were treated with a mixture of fluorescently labeled antibodies (5 µg/mL; F(ab’) 2-goat anti-human IgG-Cy5, and 5 µg/mL, goat anti-IgM-Cy3; 50 µL in total) in PBS buffer with 0.14% polyvinyl alcohol, 0.14% polyvinylpyrrolidone and 1% BSA (Sigma–Aldrich, St. Louis, MO, USA).	anti-human IgG-Cy5 suggested: None anti-IgM-Cy3 suggested: None
   For anti-SARS-CoV-2 antibodies, In/Iref ratios for the corresponding groups of microarray elements were obtained upon analysis with samples from 22 prepandemic individuals, and three standard deviations above these ratios were taken as the cutoff values.	anti-SARS-CoV-2 suggested: None
   The cutoff values for selecting positive signals were In/Iref ≥2.2 for IgG antibodies and In/Iref ≥3.8 for IgM antibodies.	IgG suggested: None IgM suggested: None
   Software and Algorithms
   Sentences	Resources
   (MedCalc Software bv, Ostend, Belgium; https://www.medcalc.org; 2020).	MedCalc suggested: (MedCalc, RRID:SCR_015044)

   ---

   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:

   Although IgM antibodies can be a sign of recent infection, IgM assays have limitations. First, IgM antibodies are released only at specific time points. In addition, they have lower affinity for viral antigens than IgG antibodies. Thus, the performance of IgM assays can vary and demonstrate low sensitivity, as shown in different studies [33]. In the studied cohort of COVID-19 ICU patients, IgM-class antibodies against more than two different viruses were found simultaneously in 10.5% of the samples. Anti-type I IFN antibodies are highly specific for APS-1 patients [16]. In addition, pre-existing autoantibodies against IFN-α and IFN-ω can be prognostic markers for severe COVID-19 [3]. The specificity of a microarray assay for anti-type I IFN antibodies was previously confirmed for a slightly different assay [13]. In this study, the presence of autoantibodies against type I IFNs in the cohort of critically ill COVID-19 ICU patients was detected in 10.5% of the samples. Using serum samples from APS-1 patients with known recent exposure to SARS-CoV-2, we tried to assess the changes in the levels of autoantibodies against type I IFNs in these patients compared with unexposed patients. All included APS-1 patients who contracted SARS-CoV-2 developed only mild / moderate COVID-19 symptoms and did not receive immunosuppressive therapy. Consistent with previous studies [34], similarly high levels of antibodies against type I IFNs were detected in the prepandemic (2019) and 2021 samples...

   ---

   Results from TrialIdentifier: No clinical trial numbers were referenced.

   ---

   Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

   ---

   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.

   ---

   Read the original source
3. 

   Version published to 10.1101/2021.12.13.21267509v1 on medRxiv

   Dec 14, 2021