Genome based evolutionary lineage of SARS-CoV-2 towards the development of novel chimeric vaccine

  1. Mst Rubaiat Nazneen Akhand
  2. Kazi Faizul Azim
  3. Syeda Farjana Hoque
  4. Mahmuda Akther Moli
  5. Bijit Das Joy
  6. Hafsa Akter
  7. Ibrahim Khalil Afif
  8. Nadim Ahmed
  9. Mahmudul Hasan

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Abstract

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  1. Version published to 10.1016/j.meegid.2020.104517
  2. ScreenIT

    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
    SentencesResources
    Multiple sequence alignment (MSA) of the complete genome and protein sequences were performed using MAFFT v7.310 (Katoh & Standley, 2013) tool.
    MAFFT
    suggested: (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).
    Phyutility
    suggested: (Phyutility, RRID:SCR_018545)
    RAxML version 8.2.11 (Stamatakis, 2014) with the substitution model GTRGAMMAI was used using 1000 rapid bootstrap replicates.
    RAxML
    suggested: (RAxML, RRID:SCR_006086)
    MrBayes version 3.2.6 (Ronquist et al., 2012) with INVGAMMA model was used for the corona virus genomes.
    MrBayes
    suggested: (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.
    InterPro
    suggested: (InterPro, RRID:SCR_006695)
    Finally, the Interactive Tree of Life (iTOL; EMBL, Heidelberg, Germany) was used for the visualization of the phylogenetic trees.
    EMBL
    suggested: (ChEMBL, RRID:SCR_014042)
    After sequence retrieval from NCBI, the sequences were subjected to BLASTp analysis to find out the homologous protein sequences.
    BLASTp
    suggested: (BLASTP, RRID:SCR_001010)
    Multiple sequence alignment was done by using Clustal Omega to identify the conserved regions (Sievers and Higgins, 2014).
    Clustal Omega
    suggested: (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.
    NCBI
    suggested: (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.
    VaxiJen
    suggested: (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.
    ProtParam
    suggested: (ProtParam Tool, RRID:SCR_018087)
    ExPASy
    suggested: None
    Alpha 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/).
    Prabi
    suggested: (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).
    iMod
    suggested: (IMOD, RRID:SCR_003297)
    Protein-protein interaction study: Patchdock server was prioritized for docking between different HLA alleles and the putative vaccine molecules.
    Patchdock
    suggested: (PatchDock, RRID:SCR_017589)
    SnapGene tool was utilized for in silico restriction cloning (Solanki and Tiwari, 2018).
    SnapGene
    suggested: (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.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  3. Version published to 10.1101/2020.04.15.036285v1 on bioRxiv