Identification and Characterization of Novel Mutants of Nsp13 Protein among Indian SARS-CoV-2 Isolates

  1. Deepa Kumari
  2. Namrata Kumari
  3. Sudhir Kumar
  4. Prabhat Kumar Sinha
  5. Shivendra Kumar Shahi
  6. Nihar Ranjan Biswas
  7. Abhay Kumar

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Abstract

SARS-CoV-2, the causative agent of COVID-19, has mutated rapidly, enabling it to adapt and evade the immune system of the host. Emerging SARS-CoV-2 variants with crucial mutations pose a global challenge in the context of therapeutic drugs and vaccines developing globally. There are currently no specific therapeutics or vaccines available to combat SARS-CoV-2 devastation. Concerning this, the current study aimed to identify and characterize the mutations found in the Nsp13 of SARS-CoV-2 in Indian isolates.

Methods:

In the present study, the Clustal omega tool was used for mutational analysis. The impact of mutations on protein stability, flexibility, and function was predicted using the DynaMut and PROVEAN tools. Furthermore, B-cell epitopes contributed by Nsp13 were identified using various predictive immunoinformatic tools.

Results:

Non-structural protein Nsp13 sequences from Indian isolates were analyzed by comparing them with the firstly reported Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) protein sequence in Wuhan, China. Out of 825 Nsp13 protein sequences, a total of 38 mutations were observed among Indian isolates. Our data showed that mutations in Nsp13 at various positions (H164Y, A237T, T214I, C309Y, S236I, P419S, V305E, G54S, H290Y, P53S, A308Y, and A308Y) have a significant impact on the protein's stability and flexibility. Moreover, the impact of Nsp13 mutations on protein function was predicted based on the PROVEAN score that indicated 15 mutants as neutral and 23 mutants as deleterious effects. Immunological parameters of Nsp13, such as antigenicity, allergenicity, and toxicity, were evaluated to predict the potential B-cell epitopes. The predicted peptide sequences were correlated with the observed mutants. Our predicted data showed that there are seven high-rank linear epitopes as well as 18 discontinuous B-cell epitopes based on immunoinformatic tools. Moreover, it was observed that out of the total 38 identified mutations among Indian SARS-CoV-2 Nsp13 protein, four mutant residues at positions 142 (E142), 245 (H245), 247 (V247), and 419 (P419) were localised in the predicted B cell epitopic region.

Conclusion:

Altogether, the results of the present in silico study might help to understand the impact of the identified mutations in Nsp13 protein on its stability, flexibility, and function.

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  1. Version published to 10.2174/18750362-v15-e2202100
  2. ScreenIT

    SciScore for 10.1101/2021.07.30.454406: (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
    Prediction of PROVEAN Score: To understand the effect of amino acid variations on the function of Nsp13, PROVEAN (Protein Variation effect Analyzer) tool was used [25].
    PROVEAN
    suggested: (PROVEAN, RRID:SCR_002182)
    Moreover, the Discontinuous Bcell epitopes were also predicted using Disco tope 2.0 webserver tool [30] at a threshold value of −6.6 followed by representing the identified epitopes in the three-dimensional structure of Nsp13 protein.
    Disco
    suggested: (DISCO, RRID:SCR_004586)

    Results from OddPub: Thank you for sharing your data.

    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

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  3. Version published to 10.1101/2021.07.30.454406 on bioRxiv