SARS-CoV-2 Variants Show a Gradual Declining Pathogenicity and Pro-Inflammatory Cytokine Stimulation, an Increasing Antigenic and Anti-Inflammatory Cytokine Induction, and Rising Structural Protein Instability: A Minimal Number Genome-Based Approach

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1. Version published to 10.1007/s10753-022-01734-w

   Oct 10, 2022
2. 

   ScreenIT

   Feb 21, 2022

   SciScore for 10.1101/2022.02.15.480592: (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

   Software and Algorithms
   Sentences	Resources
   Multiple sequence alignment (MSA) was performed using Clustal Omega [26], and the mutations were identified based on the RefSeq Wuhan (wild-type) sequence.	Clustal Omega suggested: (Clustal Omega, RRID:SCR_001591) RefSeq suggested: (RefSeq, RRID:SCR_003496)
   Jalview V.2 [27] was used to visualize the MSA results.	Jalview suggested: (Jalview, RRID:SCR_006459)
   For antigenic property analysis, amino acid sequences of each of these proteins from each variant were used, and the VaxiJen v2.0 server [32] with the threshold of 0.4 was applied.	VaxiJen suggested: (VaxiJen, RRID:SCR_018514)
   Identification of …

   SciScore for 10.1101/2022.02.15.480592: (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

   Software and Algorithms
   Sentences	Resources
   Multiple sequence alignment (MSA) was performed using Clustal Omega [26], and the mutations were identified based on the RefSeq Wuhan (wild-type) sequence.	Clustal Omega suggested: (Clustal Omega, RRID:SCR_001591) RefSeq suggested: (RefSeq, RRID:SCR_003496)
   Jalview V.2 [27] was used to visualize the MSA results.	Jalview suggested: (Jalview, RRID:SCR_006459)
   For antigenic property analysis, amino acid sequences of each of these proteins from each variant were used, and the VaxiJen v2.0 server [32] with the threshold of 0.4 was applied.	VaxiJen suggested: (VaxiJen, RRID:SCR_018514)
   Identification of immune-associated human proteins that interact with ORF8, M, and N of SARS-CoV-2: The interacting human protein partners of ORF8, M, and N proteins of SARS-CoV-2 as described by Gordon et al. [38] and Enrichr-based Gene set enrichment analysis (GSEA) [39] were used.	Gene set enrichment analysis suggested: (Gene Set Enrichment Analysis, RRID:SCR_003199)
   To investigate the immune-modulating pathway for each of these SARS-CoV-2 proteins, we used the corresponding interacting human proteins in Enrichr.	Enrichr suggested: (Enrichr, RRID:SCR_001575)
   For human Stomatin (hSTOM) (UniProtKB: P27105), AlphaFold based structure AF-P27105-F1 available in UniProt was used.	UniProt suggested: (UniProtKB, RRID:SCR_004426)
   The 3D models of M and N were obtained by using the RaptorX server [42], followed by the GalaxyRefine server [43].	GalaxyRefine suggested: (GalaxyRefine, RRID:SCR_018531)
   The SAVES v6.0 server (https://saves.mbi.ucla.edu	SAVES suggested: (SAVES, RRID:SCR_018219)
   The UCSF Chimera X program [47] was used for 3D structure analysis and protein-protein 2D interaction maps were generated using LigPlot+ v.2.2 [48].	LigPlot+ suggested: (LigPlot+, RRID:SCR_018249)
   We also used the commercial version of Schrödinger Platform (https://www.schrodinger.com) for a second line validation.	https://www.schrodinger.com suggested: (Schrodinger, RRID:SCR_014879)

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   Results from OddPub: Thank you for sharing your data.

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   Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

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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.
   • No funding statement was detected.
   • No protocol registration statement was detected.

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   Results from scite Reference Check: We found no unreliable references.

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3. 

   Version published to 10.1101/2022.02.15.480592v2 on bioRxiv

   Feb 18, 2022
4. 

   Version published to 10.1101/2022.02.15.480592v1 on bioRxiv

   Feb 16, 2022