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In-silico Evaluation of the Capsid Proteins of Fmdv as Potential Vaccine Candidates

F. M. N. Hassan
Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna-9208, Banglades

Md. Shaifur Rahman
Tissue Banking and Biomaterial Research Unit, Atomic Energy Research Establishment, BAEC, Dhaka-1349, Bangladesh

K. M. T. Rahman
Research and Development Division, Incepta Vaccine Limited, Dhaka, Bangladesh

Sharmin S. Sumi
Department of Biochemistry, University of Alberta,Edmonton, Alberta, Canada T6G 2H7

Md. F. Islam
Department of Biochemistry, University of Saskatchewan, Saskatoon, S7N 5E5 Canada

Md. Badrul Alam
Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna-9208, Bangladesh

Md. Giasuddin
Bangladesh Livestock Research Institute (BLRI), Savar, Dhaka -1341, Bangladesh

Khondoker M. Hossain
Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna-9208, Bangladesh

Abstract/ Executive Summary:

In this study, the capsid proteins of four major serotypes of Foot and Mouth Disease Virus (FMDV) were assessed as the vaccine candidates. Different protein sequences regarding FMDV capsid of O, A, Asia 1 and C type were identified from NCBI Genome Database and UniprotKB. Phylogenetic tree of the four serotypes was developed using ClustalW software. HMMTOP, RANKPEP, Swiss-Model and Vaxign software were used for comparing the capsid proteins in terms of their feasibility as vaccine candidates. The virus and viral serotype were identified from the cultured disease sample using RT-PCR. Our results revealed that different capsid proteins of the four serotypes vary in their suitability to be considered as peptide vaccine components. Viral protein 1 (VP1) for Asia 1 serotype represented the best result as a vaccine candidate. The VP1 region of Asia 1 serotype amplified based on the result of dry lab analysis. Our findings provide a future indication of multivalent vaccine development against FMDV.

Keywords: Reverse Vaccinology, FMDV, Capsid Protein, Viral Protein, Vaccine Candidate

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End Date:

Program Area: Animal Health and Management

Commodity: Diseases

Objectives:

To compare and analyze the capsid proteins (VP0, VP1, VP2, VP3 and VP4) of different Eurasian serotypes (O, A, Asia 1, C; UniprotKB entry P03305 P49303, E9KMQ6, P15072 respectively) of FMDV through computational approach in order to evaluate their feasibility as vaccine candidates.

Methodology:

At first the genome polyprotein sequences of four serotypes of FMDV were identified from NCBI Genome Database. Multiple sequence alignment of the genome polyproteins of four serotypes of FMDV was done by ClustalW to determine the mutations among the serotypes. Maximum likelihood method was used for phylogenetic tree construction from MEGA software in which boot strapped value was 1000. The serotypes under study show very close phylogenetic relationship with approximately 90% sequence similarity among them and some observable point mutations. Phylogenetic tree acts as harbinger to find out the ancestral relationship between different types of viruses. In this research Phylogenetic tree analysis depicts that four types of virus are closely related to each other. So it will act as quintessence to develop single type of vaccine to unfold the intricateness of these viruses. Amino acid sequence of the proteins of FMDV was identified from UniprotKB. HMMTOP was used to determine the number of transmembrane (TM) helix, topology of the antigenic proteins and feasibility of molecule cloning of the antigenic proteins. Epitope binding sites against specific MHC (major histocompatibility complex) for each antigen were determined by RANKPEP. Determination of the adhesion probability (which denotes to binding capacity of antigen to host surface) against specific MHC molecule of each antigen was done by Vaxign. The antigenic proteins were compared based on all the parameters under study (related to immunogenecity and antigenecity) to identify the better vaccine candidates. At last the structures of each antigen were also predicted based on homology modeling by SWISS-MODEL (structure not shown in this article).

Cell culture: Baby hamster kidney cells (BHK-21) (American Type Culture Collection, ATCC, Rockville, MD, USA) were cultured and maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% heat-inactivated fetal bovine serum (Gibco Life Technologies, USA), 100 U/ml penicillin, 2 mM L-glutamine, and 100 μg/ml streptomycin. Determination of cellular morphology upon FMDV infection BHK-21 cells (1.6 x 105) were grown onto 60 mm tissue culture plate. Cells were challenged with the viral sample collected from suspected FMD Virus infected cattle from Savar Military Firm, Dhaka Bangladesh. After 72 hours, images were taken under an inverted microscope with a magnification of 10X. Reverse transcription-polymerase chain reaction (RT-PCR) assay BHK-21 cells were challenged with the viral sample using established protocol of Virology Lab of Animal Health Research Division of Bangladesh Livestock Research Institute (BLRI). RNA was extracted by using Qiagen RNeasy kit and RT-PCR was done by Superscript III RT-PCR kit. The oligonucleotide primers for the detection of FMDV and FMDV serotypes were used from the 2B and VP1 (1D) regions of the viral genome as published.

Source of Information: Computational Biology and Bioinformatics, 2015; 3(1): 6-20, ISSN: 2330-8265 (Print); ISSN: 2330-8281 (Online),doi: 10.11648/j.cbb.20150301.12

Article Link (Online Journal): http://www.sciencepublishinggroup.com/journal/paperinfo?journalid=112&doi=10.11648/j.cbb.20150301.12

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Achievement/Findings:

The present study mainly focused on genomic based approach of vaccine development known as reverse vaccinology. In the dry lab study, the capsid proteins of different serotypes of FMDV showed different levels of feasibility that are to be considered as peptide vaccine components. Since the idea of producing single peptide vaccine can be replaced by the concept of multivalent vaccine. The wet lab study identified the Asia 1 ser FMDV in the samples of suspected animals.

Knowledge Management: Journal