Design of Peptide Vaccine for COVID19: CD8+ and CD4+ T cell epitopes from SARS-CoV-2 open-reading-frame protein variants

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   ScreenIT

   Sep 27, 2021

   SciScore for 10.1101/2021.09.21.461301: (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

   Experimental Models: Cell Lines
   Sentences	Resources
   Retrieval of variant sequences: The lineages of variants of concern, UK B.1.1.7 [38], South African B.1.351 [39], Brazilian P.1 [40] and Indian B.1.617.2 [41], were used to identify the most prevalent mutations for nsp3, nsp12, ORF3a and ORF9b that would be present in at least 75% of the sequences [42] (Table 1).	B.1.617.2 suggested: None
   Experimental Models: Organisms/Strains
   Sentences	Resources
   Two common mouse strains to study COVID-19 vaccines, C57BL/6 and BALB/CJ, were used in mouse HLA affinity predictions.	C57BL/6 suggested: None
   Software and Algorithms
   Sentences	Resources
   Retrieval of …

   SciScore for 10.1101/2021.09.21.461301: (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

   Experimental Models: Cell Lines
   Sentences	Resources
   Retrieval of variant sequences: The lineages of variants of concern, UK B.1.1.7 [38], South African B.1.351 [39], Brazilian P.1 [40] and Indian B.1.617.2 [41], were used to identify the most prevalent mutations for nsp3, nsp12, ORF3a and ORF9b that would be present in at least 75% of the sequences [42] (Table 1).	B.1.617.2 suggested: None
   Experimental Models: Organisms/Strains
   Sentences	Resources
   Two common mouse strains to study COVID-19 vaccines, C57BL/6 and BALB/CJ, were used in mouse HLA affinity predictions.	C57BL/6 suggested: None
   Software and Algorithms
   Sentences	Resources
   Retrieval of SARS-CoV-2 sequence: The reference protein sequences of SARS-CoV-2 Wuhan isolate were retrieved from NCBI database using accession number NC_045512.	NCBI suggested: (NCBI, RRID:SCR_006472)
   Antigenicity, allergenicity and toxicity evaluation: Antigenicity was evaluated by VaxiJen 2.0 [47] server with a threshold of 0.4, allergenicity by AllerTop v2.0 [48] and toxicity by ToxinPred [49].	VaxiJen suggested: (VaxiJen, RRID:SCR_018514) AllerTop suggested: (AllerTop, RRID:SCR_018496)
   Hence, various chemical and physical parameters associated with the vaccine were predicted in this study using ProtParam tool on ExPASy [50].	ProtParam suggested: (ProtParam Tool, RRID:SCR_018087) ExPASy suggested: None
   The native peptides from the RCSB structures were replaced with our predicted epitopes using PyMol.	PyMol suggested: (PyMOL, RRID:SCR_000305)

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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:

   A limitation of current studies relates to mutational spectra of SARS-CoV-2 that is constantly changing. This poses a risk to the vaccine candidates to no longer being viable to offer protection against newly formed variants. To overcome this, we selected the most prevalent variants of concern and their most common mutations in nsp3, nsp12, ORF3a and ORF9b proteins across all identified sequences to date. The selected proteins may carry some important mutations that increase the transmissibility and survival of the virus, like the nonsynonymous mutation P323L in nsp12 which has possibly affected the catalytic activity of the nsp12 protein, therefore altering the binding capability with other cofactors, such as nsp7 and nsp8 proteins [65]. However, studies have reported generally low mutation rates in these proteins which increase the efficiency of the proposed multi-epitope vaccine candidates in the long term [66]. Another challenge with peptide vaccines is that peptides can be easily degraded by peptidases which causes a lower T cell response. The present study addresses this issue by calculating the half-life of the top common epitopes to make sure that the vaccine construct is not degraded early in blood.

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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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   Version published to 10.1101/2021.09.21.461301 on bioRxiv

   Sep 22, 2021