In silico detection of SARS-CoV-2 specific B-cell epitopes and validation in ELISA for serological diagnosis of COVID-19

Article activity feed

1. Version published to 10.1038/s41598-021-83730-y

   Feb 22, 2021
2. 

   ScreenIT

   Jun 9, 2020

   SciScore for 10.1101/2020.05.22.111526: (What is this?)

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

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   We then added 100 μL per well of anti-IgG-HRP (Rockland anti-human-IgG(H+L) goat antibody horseradish peroxidase (HRP) conjugated, Cat# 609-1302) (diluted in same buffer as the sera/plasma), and incubated 1 hr at room temp while shaking.	anti-IgG-HRP (Rockland anti-human-IgG(H+L) goat suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   The spike protein was expressed using transient transfection in Thermo Expi HEK293 mammalian cells per IPD protocol, harvested after 3 days incubation at 33°C, and clarified using PDAD (Sigma-Aldrich #409014).	HEK293 suggested: None
   Software and Algorithms
   Sentence…

   SciScore for 10.1101/2020.05.22.111526: (What is this?)

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

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   We then added 100 μL per well of anti-IgG-HRP (Rockland anti-human-IgG(H+L) goat antibody horseradish peroxidase (HRP) conjugated, Cat# 609-1302) (diluted in same buffer as the sera/plasma), and incubated 1 hr at room temp while shaking.	anti-IgG-HRP (Rockland anti-human-IgG(H+L) goat suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   The spike protein was expressed using transient transfection in Thermo Expi HEK293 mammalian cells per IPD protocol, harvested after 3 days incubation at 33°C, and clarified using PDAD (Sigma-Aldrich #409014).	HEK293 suggested: None
   Software and Algorithms
   Sentences	Resources
   The comprehensive database of endemic human coronavirus (HCoV) protein sequences was built from 3 sources: NCBI, UniProtKB and ViPR.	ViPR suggested: (vipR, RRID:SCR_010685)
   The UniProtKB and NCBI Identical Protein Groups databases were searched by the NCBI taxonomy identifiers for human coronaviruses strains HKU1, 229E, OC43 and NL63.	NCBI Identical Protein Groups suggested: None
   Although NCBI, UniProtKB and ViPR datasets overlap, we found that each contained unique sequences: 1 for NCBI, 12 for ViPR and 51 for UniProtKB.	UniProtKB suggested: (UniProtKB, RRID:SCR_004426)
   The combined dataset of 15,188 sequences was reduced to 1,740 after redundancy elimination and clustering with CD-HIT to remove 100% overlapping fragments21.	CD-HIT suggested: (CD-HIT, RRID:SCR_007105)
   The unique sequences were aligned to the reference genome with MAFFT experimental version 7.463 using options ‘--auto --addfragments’24,25.	MAFFT suggested: (MAFFT, RRID:SCR_011811)
   The spike protein was expressed using transient transfection in Thermo Expi HEK293 mammalian cells per IPD protocol, harvested after 3 days incubation at 33°C, and clarified using PDAD (Sigma-Aldrich #409014).	Thermo Expi suggested: None
   A third group of negative controls were 29 serum specimens from the Department of Laboratory Medicine that tested negative for COVID-19 in the Abbott Architect SARS-CoV-2 IgG Assay30.	Abbott Architect suggested: (Abbott ARCHITECT i1000sr System, RRID:SCR_019328)

   ---

   Results from OddPub: Thank you for sharing your code and data.

   ---

   Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

   This is a known limitation of the predictor which achieves high specificity at a high sensitivity cost. Nonetheless, strong signals were observed for the nucleoprotein, consistent with several recent studies2,7. Second, we assessed the level of sequence conservation of each SARS-CoV-2 epitope compared to endemic human coronaviruses (HCoVs) strains HKU1, 229E, OC43 and NL63. For this purpose, a comprehensive database of endemic HCoVs protein sequences was built from 3 different sources: NCBI, UniProt and ViPR (Table S2). Prior to performing the comparison, each epitope was trimmed to 15 residues to avoid length bias. Trimmed epitopes were scanned using a sliding window against the endemic HCoV sequences. The average pairwise identity between the epitope and aligned residues was recorded at each position. Conservation was defined as the maximal value obtained after scanning was completed. Conservation levels ranged between 40-100% with large local variations (Figure S1 B). Perhaps unsurprisingly, the most conserved epitopes were located in enzymes that perform essential functions in viral replication, such as the nsp12 RNA-dependent RNA polymerase, and are thus likely to be conserved across species (Figure 2). For proteins with less conserved epitopes overall, the average masked large local differences. In particular, the nucleoprotein contained epitopes in both the N-terminal RNA-binding and C-terminal dimerization domains, but only the C-terminus includes highly conserved, no...

   ---

   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.

   ---

   Read the original source
3. 

   Version published to 10.1101/2020.05.22.111526v3 on bioRxiv

   Jun 2, 2020
4. 

   Version published to 10.1101/2020.05.22.111526v2 on bioRxiv

   May 25, 2020
5. 

   Version published to 10.1101/2020.05.22.111526v1 on bioRxiv

   May 23, 2020