A Bioinformatics Approach for the Prediction of Immunogenic Properties and Structure of the SARS-COV-2 B.1.617.1 Variant Spike Protein.

Vijay Kumar Srivastava,Gazal Bhargava,Sanket Kaushik,Anupam Jyoti,Ajay Jain,Juhi Saxena

doi:10.1155/2021/7251119

Vijay Kumar Srivastava, Gazal Bhargava + Show 4 more

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https://doi.org/10.1155/2021/7251119

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Abstract

Background B.1.617.1, a variant of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causing respiratory illness is responsible for the second wave of COVID-19 and associated with a high incidence of infectivity and mortality. To mitigate the B.1.617.1 variant of SARS-CoV-2, deciphering the protein structure and immunological responses by employing bioinformatics tools for data mining and analysis is pivotal. Objectives Here, an in silico approach was employed for deciphering the structure and immune function of the subunit of spike (S) protein of SARS-CoV-2 B.1.617.1 variant. Methods The partial amino acid sequence of SARS-CoV-2 B.1.617.1 variant S protein was analyzed, and its putative secondary and tertiary structure was predicted. Immunogenic analyses including B- and T-cell epitopes, interferon-gamma (IFN-γ) response, chemokine, and protective antigens for SARS-CoV 2 S proteins were predicted using appropriate tools. Results B.1.617.1 variant S protein sequence was found to be highly stable and amphipathic. ABCpred and CTLpred analyses led to the identification of two potential antigenic B cell and T cell epitopes with starting amino acid positions at 60 and 82 (for B cell epitopes) and 54 and 98 (for T cell epitopes) having prediction scores > 0.8. Further, RAMPAGE tool was used for determining the allowed and disallowed regions of the three-dimensional predicted structure of SARS-CoV-2 B.1.617.1 variant S protein. Conclusion Together, the in silico analysis revealed the predicted structure of partial S protein, immunogenic properties, and possible regions for S protein of SARS-CoV-2 and provides a valuable prelude for engineering the targeted vaccine or drug against B.1.617.1 variant of SARS-CoV-2.

Highlights

Coronaviruses (CoVs), belonging to the family Coronaviridae, are enveloped nonsegmented, single-stranded positive-sense RNA viruses and infect humans and various animals [1]
Six different species of CoVs infecting humans, all belonging to betacoronavirus, have been identified, i.e., human coronavirus (HCoV) 229E, HCoVOC43, SARS-CoV, HCoV-NL63, HCoV-HKU1, and Middle East respiratory syndrome coronavirus (MERS-CoV)
In 2012, the Middle East respiratory syndrome (MERS) was first identified in Saudi Arabia infecting ~2500 of which more than 800 resulted in death and rapidly spread in 27 countries across the globe [5]. Both SARS-CoV and MERS-CoV are zoonotic, and in human, they infect the upper respiratory tract causing common cold as well as lower respiratory tract resulting in bronchitis, whooping cough, and pneumonia [4, 5], and till to date, there is no approved therapeutic molecule for the treatment

Summary

Introduction

Coronaviruses (CoVs), belonging to the family Coronaviridae, are enveloped nonsegmented, single-stranded positive-sense RNA viruses and infect humans and various animals (bats, birds, camels, cats, dogs, and mice) [1]. In 2012, the Middle East respiratory syndrome (MERS) was first identified in Saudi Arabia infecting ~2500 of which more than 800 resulted in death and rapidly spread in 27 countries across the globe [5]. Both SARS-CoV and MERS-CoV are zoonotic, and in human, they infect the upper respiratory tract causing common cold as well as lower respiratory tract resulting in bronchitis, whooping cough, and pneumonia [4, 5], and till to date, there is no approved therapeutic molecule for the treatment. The in silico analysis revealed the predicted structure of partial S protein, immunogenic properties, and possible regions for S protein of SARS-CoV-2 and provides a valuable prelude for engineering the targeted vaccine or drug against B.1.617.1 variant of SARS-CoV-2

Methods

Results

Conclusion