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Genome based Evolutionary study of SARS-CoV-2 towards the Prediction of Epitope Based Chimeric Vaccine

Mst Rubaiat Nazneen Akhand, Kazi Faizul Azim, Syeda Farjana Hoque, Mahmuda Akther Moli, Bijit Das Joy, Hafsa Akter, Ibrahim Khalil Afif, Nadim Ahmed, Mahmudul Hasan
doi: https://doi.org/10.1101/2020.04.15.036285
Mst Rubaiat Nazneen Akhand
1Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet-3100, Bangladesh
2Department of Biochemistry and Chemistry, Sylhet Agricultural University, Sylhet-3100, Bangladesh
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Kazi Faizul Azim
1Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet-3100, Bangladesh
3Department of Microbial Biotechnology, Sylhet Agricultural University, Sylhet-3100, Bangladesh
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Syeda Farjana Hoque
1Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet-3100, Bangladesh
4Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet-3100
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Mahmuda Akther Moli
1Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet-3100, Bangladesh
4Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet-3100
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Bijit Das Joy
1Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet-3100, Bangladesh
2Department of Biochemistry and Chemistry, Sylhet Agricultural University, Sylhet-3100, Bangladesh
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Hafsa Akter
1Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet-3100, Bangladesh
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Ibrahim Khalil Afif
5Department of Genetic Engineering and Biotechnology, Noakhali Science and Technology University, Noakhali, Bangladesh
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Nadim Ahmed
1Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet-3100, Bangladesh
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Mahmudul Hasan
1Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet-3100, Bangladesh
4Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet-3100
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  • For correspondence: mhasan.pib@sau.ac.bd
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Abstract

SARS-CoV-2 is known to infect the neurological, respiratory, enteric, and hepatic systems of human and has already become an unprecedented threat to global healthcare system. COVID-19, the most serious public condition caused by SARS-CoV-2 leads the world to an uncertainty alongside thousands of regular death scenes. Unavailability of specific therapeutics or approved vaccine has made the recovery of COVI-19 more troublesome and challenging. The present in silico study aimed to predict a novel chimeric vaccines by simultaneously targeting four major structural proteins via the establishment of ancestral relationship among different strains of coronaviruses. Conserved regions from the homologous protein sets of spike glycoprotein (S), membrane protein (M), envelope protein and nucleocapsid protein (N) were identified through multiple sequence alignment. The phylogeny analyses of whole genome stated that four proteins (S, E, M and N) reflected the close ancestral relation of SARS-CoV-2 to SARS-COV-1 and bat coronavirus. Numerous immunogenic epitopes (both T cell and B cell) were generated from the common fragments which were further ranked on the basis of antigenicity, transmembrane topology, conservancy level, toxicity and allergenicity pattern and population coverage analysis. Top putative epitopes were combined with appropriate adjuvants and linkers to construct a novel multiepitope subunit vaccine against COVID-19. The designed constructs were characterized based on physicochemical properties, allergenicity, antigenicity and solubility which revealed the superiority of construct V3 in terms safety and efficacy. Essential molecular dynamics and Normal Mode analysis confirmed minimal deformability of the refined model at molecular level. In addition, disulfide engineering was investigated to accelerate the stability of the protein. Molecular docking study ensured high binding affinity between construct V3 and HLA cells, as well as with different host receptors. Microbial expression and translational efficacy of the constructs were checked using pET28a(+) vector of E. coli strain K12. The development of preventive measures to combat COVID-19 infections might be aided the present study. However, the in vivo and in vitro validation might be ensured with wet lab trials using model animals for the implementation of the presented data.

  • SARS-CoV-2
  • COVID-19
  • Chimeric Vaccine
  • Evolutionary Relationship
  • Normal Mode Analysis
  • Molecular Docking
  • Restriction cloning

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted April 15, 2020.
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Genome based Evolutionary study of SARS-CoV-2 towards the Prediction of Epitope Based Chimeric Vaccine
Mst Rubaiat Nazneen Akhand, Kazi Faizul Azim, Syeda Farjana Hoque, Mahmuda Akther Moli, Bijit Das Joy, Hafsa Akter, Ibrahim Khalil Afif, Nadim Ahmed, Mahmudul Hasan
bioRxiv 2020.04.15.036285; doi: https://doi.org/10.1101/2020.04.15.036285
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Genome based Evolutionary study of SARS-CoV-2 towards the Prediction of Epitope Based Chimeric Vaccine
Mst Rubaiat Nazneen Akhand, Kazi Faizul Azim, Syeda Farjana Hoque, Mahmuda Akther Moli, Bijit Das Joy, Hafsa Akter, Ibrahim Khalil Afif, Nadim Ahmed, Mahmudul Hasan
bioRxiv 2020.04.15.036285; doi: https://doi.org/10.1101/2020.04.15.036285

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