Identification of immunodominant linear epitopes from SARS-CoV-2 patient plasma
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
Abstract
Article activity feed
-
-
SciScore for 10.1101/2020.06.15.20131391: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IACUC: Plasma specimens from COVID-19 and healthy patients: Anonymized leftovers of whole blood-EDTA were used for this method evaluation, in accordance with our institution’s ethical committee and national regulations. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Sequence alignment: Sequence alignment was done using Clustal Omega [46]. Clustal Omegasuggested: (Clustal Omega, RRID:SCR_001591)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 …
SciScore for 10.1101/2020.06.15.20131391: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IACUC: Plasma specimens from COVID-19 and healthy patients: Anonymized leftovers of whole blood-EDTA were used for this method evaluation, in accordance with our institution’s ethical committee and national regulations. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Sequence alignment: Sequence alignment was done using Clustal Omega [46]. Clustal Omegasuggested: (Clustal Omega, RRID:SCR_001591)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:One limitation of epitope mapping with a peptide array is that it is restricted to linear epitopes. Antibodies binding to the RBD have been shown to participate in interactions spanning multiple peptide fragments. Indeed, we did not observe a strong response to linear peptides in the RBD. A control experiment with AI334/CR3022 antibody [25, 70] showed only weak binding to 367-378 peptide sequence of the RBD. To validate the results observed on the microarray, a peptide (655-672) was synthesized as a biotin conjugate for pull-down and ELISA experiments. The sequence corresponding to 655-672-biotin and a scrambled version of the biotinylated peptide were individually immobilized on agarose streptavidin beads. Beads were exposed to serum from patients that were either positive or negative for that epitope based on the microarray data and subsequently treated with anti-Human-IgG-FITC. The fluorescence of the beads was quantified by confocal microscopy (Fig 5A). As can be seen in Fig 5B-E, the beads with 655-672 peptide and positive serum sample showed higher fluorescence than the ones with either negative serum or using the scrambled peptide. To further probe the binding of 655-672 peptide to antibodies of SARS-CoV-2 positive patients, the same 655-672 biotinylated peptide was used in an ELISA assay (Fig 6A). Three SARS-CoV-2 positive samples showing strong 655-672 signal (Samples 7, 8 and 9) and three SARS-CoV-2 negative samples (Samples 14, 15 and 17) were analyzed showing clea...
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.
-
