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

Deepa Kumari1, Namrata Kumari2, Sudhir Kumar3, Prabhat Kumar Sinha4, Shivendra Kumar Shahi4, Nihar Ranjan Biswas4, Abhay Kumar1, *
1 Department of Microbiology, Molecular Genomics Laboratory, Indira Gandhi Institute of Medical Sciences, Patna, India
2 Department of Microbiology, Indira Gandhi Institute of Medical Sciences, Patna, India
3 Department of General Medicine, Indira Gandhi Institute of Medical Sciences, Patna, India
4 Indira Gandhi Institute of Medical Sciences, Patna, India

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© 2022 Kumari et al.

open-access license: This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International Public License (CC-BY 4.0), a copy of which is available at: This license permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

* Address correspondence to this author at the Department of Microbiology, Molecular Genomics Laboratory, IGIMS, Patna-800014, Bihar, India; E-mail:



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.


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.


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.


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.

Keywords: SARS-CoV-2, Nsp13, COVID-19, B-cell epitopes, Immunoinformatics, Novel mutants.