Omicron and Delta variant of SARS‐CoV‐2: A comparative computational study of spike protein

  1. Suresh Kumar
  2. Thiviya S. Thambiraja
  3. Kalimuthu Karuppanan
  4. Gunasekaran Subramaniam

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Abstract

Emerging severe acute respiratory syndrome coronavirus type 2 (SARS‐CoV‐2) variants, especially those of concern, may have an impact on the virus's transmissibility and pathogenicity, as well as diagnostic equipment performance and vaccine effectiveness. Even though the SARS‐CoV‐2 Delta variant (B.1.617.2) emerged during India's second wave of infections, Delta variants have grown dominant internationally and are still evolving. On November 26, 2021, World Health Organization identified the variant B.1.1.529 as a variant of concern, naming it Omicron, based on evidence that Omicron contains numerous mutations that may influence its behavior. However, the mode of transmission and severity of the Omicron variant remains unknown. We used computational studies to examine the Delta and Omicron variants in this study and found that the Omicron variant had a higher affinity for human angiotensin‐converting enzyme 2 (ACE2) than the Delta variant due to a significant number of mutations in the SARS‐CoV‐2 receptor‐binding domain (RBD), indicating a higher potential for transmission. Based on docking studies, the Q493R, N501Y, S371L, S373P, S375F, Q498R, and T478K mutations contribute significantly to high binding affinity with human ACE2. In comparison to the Delta variant, both the entire spike protein and the RBD in Omicron include a high proportion of hydrophobic amino acids such as leucine and phenylalanine. These amino acids are located within the protein's core and are required for structural stability. We observed a disorder–order transition in the Omicron variant between spike protein RBD regions 468–473, and it may be significant in the influence of disordered residues/regions on spike protein stability and binding to ACE2. A future study might investigate the epidemiological and biological consequences of the Omicron variant.

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  1. Version published to 10.1002/jmv.27526
  2. ScreenIT

    SciScore for 10.1101/2021.12.02.470946: (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

    Experimental Models: Organisms/Strains
    SentencesResources
    Identification of Conserved Residues and Mutation: Clustal Omega 18 a bioinformatics programme, was used to align the Wuhan-Hu-1 (wild type) sequence with variants of delta and omicron sequences.
    Wuhan-Hu-1
    suggested: None
    Software and Algorithms
    SentencesResources
    Analysis of physicochemical parameter: The Wuhan-Hu-1 (wild type), delta, and omicron variant sequences were analysed using the ExPASy ProtParam online tool.
    ExPASy
    suggested: None
    Identification of Conserved Residues and Mutation: Clustal Omega 18 a bioinformatics programme, was used to align the Wuhan-Hu-1 (wild type) sequence with variants of delta and omicron sequences.
    Clustal Omega
    suggested: (Clustal Omega, RRID:SCR_001591)
    SIFT for prediction of the effect of nsSNPs on protein function: The Wild type, Delta, and Omicron variants are checked whether mutation impacts protein function through SIFT tool 22.
    SIFT
    suggested: (SIFT, RRID:SCR_012813)
    Prediction of disease-associated: VarSite 23 is a web server mapping known disease□associated variants from UniProt and ClinVar, together with natural variants from gnomAD, onto protein 3D structures in the Protein Data Bank.
    UniProt
    suggested: (UniProtKB, RRID:SCR_004426)
    ClinVar
    suggested: (ClinVar, RRID:SCR_006169)
    The SARS-CoV-2 RBD mutations were introduced using the Pymol mutagenesis wizard programme at the appropriate delta and omicron mutated positions for each residue and the whole RBD.
    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.

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

    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 10.1101/2021.12.02.470946 on bioRxiv