Molecular basis of the logical evolution of the novel coronavirus SARS-CoV-2: A comparative analysis

  1. Abhisek Dwivedy
  2. Krushna Chandra Murmu
  3. Mohammed Ahmad
  4. Punit Prasad
  5. Bichitra Kumar Biswal
  6. Palok Aich

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Abstract

A novel disease, COVID-19, is sweeping the world since end of 2019. While in many countries, the first wave is over, but the pandemic is going through its next phase with a significantly higher infectability. COVID-19 is caused by the novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) that seems to be more infectious than any other previous human coronaviruses. To understand any unique traits of the virus that facilitate its entry into the host, we compared the published structures of the viral spike protein of SARS-CoV-2 with other known coronaviruses to determine the possible evolutionary pathway leading to the higher infectivity. The current report presents unique information regarding the amino acid residues that were a) conserved to maintain the binding with ACE2 (Angiotensin-converting enzyme 2), and b) substituted to confer an enhanced binding affinity and conformational flexibility to the SARS-CoV-2 spike protein. The present study provides novel insights into the evolutionary nature and molecular basis of higher infectability and perhaps the virulence of SARS-CoV-2.

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  1. ScreenIT

    SciScore for 10.1101/2020.12.03.409458: (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
    The sequences were aligned using Clustal Omega (Sievers and Higgins, 2014) and a maximum likelihood phylogenetic tree was generated using the NEXUS algorithm (Giribet, 2005).
    Clustal Omega
    suggested: (Clustal Omega, RRID:SCR_001591)
    Two structure alignments were performed at the FATCAT web server (Veeramalai et al., 2008) using both flexible and rigid body algorithms.
    FATCAT
    suggested: (FATCAT, RRID:SCR_014631)
    Pymol 2.3 was used for structural visualizations (DeLano, 2020).
    Pymol
    suggested: (PyMOL, RRID:SCR_000305)
    The sequences were aligned using MEGA X software (Kumar et al., 2018) with MUSCLE (Edgar, 2004) as the alignment algorithm using the default parameters.
    MEGA X
    suggested: None
    MUSCLE
    suggested: (MUSCLE, RRID:SCR_011812)
    The phylogenetic trees were generated using the R-package “ggtree” of Bioconductor including the genera and host of the respective coronavirus (Yu et al., 2017).
    Bioconductor
    suggested: (Bioconductor, RRID:SCR_006442)
    The ancestry and substitution analysis were performed using MEGA X. 2.3 Dendrogram comparison analysis: Aligned amino acid and nucleotide sequences were assigned the same names in both the alignments for comparison.
    MEGA
    suggested: (Mega BLAST, RRID:SCR_011920)

    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.
    • 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

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  2. Version published to 10.1101/2020.12.03.409458v1 on bioRxiv