The Essential Facts of Wuhan Novel Coronavirus Outbreak in China and Epitope-based Vaccine Designing against COVID-19

  1. Bishajit Sarkar
  2. Md. Asad Ullah
  3. Fatema Tuz Johora
  4. Masuma Afrin Taniya
  5. Yusha Araf

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Abstract

Wuhan Novel Coronavirus disease (COVID-19) outbreak has become a global outbreak which has raised the concern of scientific community to design and discover a definitive cure against this deadly virus which has caused deaths of numerous infected people upon infection and spreading. To date, no antiviral therapy or vaccine is available which can effectively combat the infection caused by this virus. This study was conducted to design possible epitope-based subunit vaccines against the SARS-CoV-2 virus using the approaches of reverse vaccinology and immunoinformatics. Upon continual computational experimentation three possible vaccine constructs were designed and one vaccine construct was selected as the best vaccine based on molecular docking study which is supposed to effectively act against SARS-CoV-2. Later, molecular dynamics simulation and in silico codon adaptation experiments were carried out in order to check biological stability and find effective mass production strategy of the selected vaccine. Hopefully, this study will contribute to uphold the present efforts of the researches to secure a definitive treatment against this lethal virus.

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  1. ScreenIT

    SciScore for 10.1101/2020.02.05.935072: (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
    , membrane glycoprotein (PubMed accession no: QHD43419.1), ORF3a protein (PubMed accession no: QHD43417.1) and surface glycoprotein (PubMed accession no: QHD43416.1) were downloaded from the NCBI (https://www.ncbi.nlm.nih.gov/) database in fasta format. 2.3. Antigenicity Prediction and Physicochemical Property Analysis of the Protein Sequences: The antigenicity of protein sequences was determined using an online tool called VaxiJen v2.0 (http://www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.htm).
    PubMed
    suggested: (PubMed, RRID:SCR_004846)
    https://www.ncbi.nlm.nih.gov/
    suggested: (GENSAT at NCBI - Gene Expression Nervous System Atlas, RRID:SCR_003923)
    Next, the selected antigenic protein sequences were analyzed by ExPASy’s online tool and ProtParam (https://web.expasy.org/protparam/) to determine their physicochemical properties i.e., the number of amino acids, theoretical pI, extinction co-efficient, aliphatic index and grand average of hydropathicity (GRAVY) etc. [109]. 2.4.
    ProtParam
    suggested: (ProtParam Tool, RRID:SCR_018087)
    For, the B-cell lymphocytic epitopes (BCL), with amino acid number of more than ten, were selected for analysis that were predicted using BepiPred linear epitope prediction method [112] [113]. 2.5. Transmembrane Topology, Antigenicity Prediction, Allergenicity and Toxicity Prediction of the Selected Epitopes: The epitopes selected in the previous step were then subjected to the transmembrane topology experiment using the transmembrane topology of protein helices determinant, TMHMM v2.0 server (http://www.cbs.dtu.dk/services/TMHMM/) [114].
    http://www.cbs.dtu.dk/services/TMHMM/
    suggested: (TMHMM Server, RRID:SCR_014935)
    After successful docking by PatchDock, the refinement and re-scoring of the docking results were carried out by the FireDock server (http://bioinfo3d.cs.tau.ac.il/FireDock/php.php).
    PatchDock
    suggested: (PatchDock, RRID:SCR_017589)
    The three vaccines differ from each other only in their adjuvant sequences. 2.10. Antigenicity, Allergenicity and Physicochemical Property Analysis of the Predicted Vaccines: The antigenicity of the constructed vaccines was predicted by the online server VaxiJen v2.0 (http://www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.htm) using the tumor model where the threshold was set at 0.4.
    VaxiJen
    suggested: (VaxiJen, RRID:SCR_018514)
    AlgPred (http://crdd.osdd.net/raghava/algpred/) and AllerTop v2.0 (https://www.ddg-pharmfac.net/AllerTOP/).
    AllerTop
    suggested: (AllerTop, RRID:SCR_018496)
    The secondary structures of the vaccine constructs were predicted using the PRISPRED 4.0 prediction method.
    PRISPRED
    suggested: None
    At first, the docking was performed by ClusPro 2.0 (https://cluspro.bu.edu/login.php).
    ClusPro
    suggested: (ClusPro, RRID:SCR_018248)
    The docked structures were visualized by PyMol tool [164]. 2.15. Molecular Dynamic Simulation: The molecular dynamics (MD) simulation study was of the best selected vaccine construct was carried out using the online MD simulation tool, iMODS (http://imods.chaconlab.org/).
    PyMol
    suggested: (PyMOL, RRID:SCR_000305)

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

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  2. Version published to 10.1101/2020.02.05.935072v2 on bioRxiv
  3. Version published to 10.1101/2020.02.05.935072v1 on bioRxiv