Genome based evolutionary lineage of SARS-CoV-2 towards the development of novel chimeric vaccine
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SciScore for 10.1101/2020.04.15.036285: (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) of the complete genome and protein sequences were performed using MAFFT v7.310 (Katoh & Standley, 2013) tool. MAFFTsuggested: (MAFFT, RRID:SCR_011811)Alignment position with more than 50% gaps was pruned from coronavirus genome using Phyutility 2.2.6 program (Smith & Dunn, 2008). Phyutilitysuggested: (Phyutility, RRID:SCR_018545)RAxML version 8.2.11 (Stamatakis, 2014) with the substitution model GTRGAMMAI was used using 1000 rapid bootstrap replicates. RAxMLsuggested: (RAxML, RRID:SCR_006086)MrBayes version 3.2.6 (Ronquist et al., 2012) with INVGAMMA model … SciScore for 10.1101/2020.04.15.036285: (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) of the complete genome and protein sequences were performed using MAFFT v7.310 (Katoh & Standley, 2013) tool. MAFFTsuggested: (MAFFT, RRID:SCR_011811)Alignment position with more than 50% gaps was pruned from coronavirus genome using Phyutility 2.2.6 program (Smith & Dunn, 2008). Phyutilitysuggested: (Phyutility, RRID:SCR_018545)RAxML version 8.2.11 (Stamatakis, 2014) with the substitution model GTRGAMMAI was used using 1000 rapid bootstrap replicates. RAxMLsuggested: (RAxML, RRID:SCR_006086)MrBayes version 3.2.6 (Ronquist et al., 2012) with INVGAMMA model was used for the corona virus genomes. MrBayessuggested: (MrBayes, RRID:SCR_012067)For the retrieval of the domain sequences of the stated protein sequences, InterPro database (https://www.ebi.ac.uk/interpro/) was utilized. InterProsuggested: (InterPro, RRID:SCR_006695)Finally, the Interactive Tree of Life (iTOL; EMBL, Heidelberg, Germany) was used for the visualization of the phylogenetic trees. EMBLsuggested: (ChEMBL, RRID:SCR_014042)After sequence retrieval from NCBI, the sequences were subjected to BLASTp analysis to find out the homologous protein sequences. BLASTpsuggested: (BLASTP, RRID:SCR_001010)Multiple sequence alignment was done by using Clustal Omega to identify the conserved regions (Sievers and Higgins, 2014). Clustal Omegasuggested: (Clustal Omega, RRID:SCR_001591)2.0 (http://www.cbs.dtu.dk/services/TMHMM/), while the antigenicity of the conserved regions was determined by VaxiJen v2.0 (Doytchinova and Flower, 2007a). 2.4. http://www.cbs.dtu.dk/services/TMHMM/suggested: (TMHMM Server, RRID:SCR_014935)Homologous sequence sets of the chosen antigenic proteins were retrieved form the NCBI database by utilizing BLASTp tool. NCBIsuggested: (NCBI, RRID:SCR_006472)The most potential vaccine among the three constructs was then determined by assessing the antigenicity and solubility of the vaccines via VaxiJen v2.0 (Doytchinova and Flower, 2007b) and Proso II server (Smialowski et al., 2006), respectively. 2.9. VaxiJensuggested: (VaxiJen, RRID:SCR_018514)Physicochemical characterization and secondary structure analysis: ProtParam tool (https://web.expasy.org/protparam/), provided by ExPASy server (Hasan et al., 2019c) was used to functionally characterize (Gasteiger et al., 2003) the vaccine constructs. ProtParamsuggested: (ProtParam Tool, RRID:SCR_018087)ExPASysuggested: NoneAlpha helix, beta sheet and coil structures of the vaccine constructs were analyzed through GOR4 secondary structure prediction method using Prabi (https://npsa-prabi.ibcp.fr/). Prabisuggested: (PRABI, RRID:SCR_010522)The iMod server determined the stability of construct V3 by comparing the essential dynamics to the normal modes of protein (Aalten et al, 1997; Wuthrich et al., 1980). iModsuggested: (IMOD, RRID:SCR_003297)Protein-protein interaction study: Patchdock server was prioritized for docking between different HLA alleles and the putative vaccine molecules. Patchdocksuggested: (PatchDock, RRID:SCR_017589)SnapGene tool was utilized for in silico restriction cloning (Solanki and Tiwari, 2018). SnapGenesuggested: (SnapGene, RRID:SCR_015052)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: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.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: Please consider improving the rainbow (“jet”) colormap(s) used on page 50. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.
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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