Mapping SARS-CoV-2 Antibody Epitopes in COVID-19 Patients with a Multi-Coronavirus Protein Microarray

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1. Version published to 10.1128/spectrum.01416-21

   Oct 31, 2021
2. 

   ScreenIT

   Jan 16, 2021

   SciScore for 10.1101/2021.01.14.21249690: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	Consent: These samples were from participants in prior Mayo Clinic vaccine studies who had provided informed consent for future use of their biospecimens.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Microarrays were probed with sera and antibody binding detected by incubation with fluorochrome-conjugated goat anti-human IgG or IgA or IgM (Jackson ImmunoResearch, West Grove, PA, USA or Bethyl Laboratories, Inc., Montgomery, TX, USA).	anti-human IgG suggested: None IgA suggested: None
   Samples were tested for …

   SciScore for 10.1101/2021.01.14.21249690: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	Consent: These samples were from participants in prior Mayo Clinic vaccine studies who had provided informed consent for future use of their biospecimens.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Microarrays were probed with sera and antibody binding detected by incubation with fluorochrome-conjugated goat anti-human IgG or IgA or IgM (Jackson ImmunoResearch, West Grove, PA, USA or Bethyl Laboratories, Inc., Montgomery, TX, USA).	anti-human IgG suggested: None IgA suggested: None
   Samples were tested for SARS-CoV-2 specific antibodies and the presence of neutralizing antibodies as described below.	SARS-CoV-2 suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Protein microarray analysis of serum samples: The first generation multi-coronavirus protein microarray, produced by Antigen Discovery, Inc. (ADI, Irvine, CA, USA), included 935 full-length coronavirus proteins, overlapping 100, 50 and 30 aa protein fragments and overlapping 13-20 aa peptides from SARS-CoV-2 (WA-1), SARS-CoV, MERS-CoV, HCoV-NL63 and HCoV-OC43.	HCoV-NL63 suggested: RRID:CVCL_RW88)
   All these coronavirus proteins were produced in Escherichia coli except the SARS-CoV-2 and SARS-CoV S proteins, which were made in Sf9 insect cells and the SARS-CoV-2 RBD, made in HEK-293 cells.	HEK-293 suggested: CLS Cat# 300192/p777_HEK293, RRID:CVCL_0045)
   27 Vero cell suspensions (ATCC CCL-81) were prepared at 2.2 – 2.5 × 105 cells/mL in DMEM (Thermo Fisher, catalog 11965118) + 10% fetal bovine serum (FBS, defined, Hyclone catalog SH30070.03, heat-inactivated 56°C for 30 min) + 2X antibiotic-antimycotic (Thermo Fisher catalog 15240062) + 2X penicillin-streptomycin (Thermo Fisher catalog 15140122) immediately before use.	Vero suggested: None
   Software and Algorithms
   Sentences	Resources
   Data visualization was performed using the circlize (37), ComplexHeatmap (38), ggplot2, heatmap2 and corrplot (39) packages in R.	ComplexHeatmap suggested: (ComplexHeatmap, RRID:SCR_017270) ggplot2 suggested: (ggplot2, RRID:SCR_014601)

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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:

   Limitations of our study are the small sample size and the inclusion of only convalescent samples. Despite these limitations, we were able to identify clear differences in the antibody response from COVID-19 patients and healthy, non-exposed controls. The ideal dataset to further investigate associations between preexisting antibody to specific epitopes and protection from severe disease would be longitudinal, with at least a pre-exposure sample, an acute sample, and a convalescent sample from each subject. Inclusion of samples from COVID-19 patients with a range of clinical symptoms will also provide an important comparison. In upcoming projects, we are seeking to analyze these types of samples paired with detailed clinical data on disease outcomes ranging from asymptomatic to fatal to further improve our understanding of the complex role antibodies play in SARS-CoV-2 infection. It may also prove interesting to test convalescent plasma samples, especially given the variable results on efficacy that have been reported in the literature (27-30). An assay providing more granular detail on the humoral response in these samples, such as the protein microarray described here, may provide valuable insights into what is happening during these convalescent plasma trials.

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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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3. 

   Version published to 10.1101/2021.01.14.21249690v1 on medRxiv

   Jan 15, 2021