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.
| Published in | Computational Biology and Bioinformatics (Volume 3, Issue 1) |
| DOI | 10.11648/j.cbb.20150301.12 |
| Page(s) | 6-20 |
| Creative Commons |
This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited. |
| Copyright |
Copyright © The Author(s), 2015. Published by Science Publishing Group |
Reverse Vaccinology, FMDV, Capsid Protein, Viral Protein 1, Vaccine Candidate
| [1] | Raju S, Uma Maheshwari Rao: Current development strategies for vaccines and the role of reverse vaccinology. PHRC 2010,2(4): 339-346. |
| [2] | Grammatikos, Alexandros P, Mantadakis, Elpis, Falagas, Matthew E: Meta-analyses on pediatric infections and vaccines.Infectious Disease Clinics of North America 2009, 23 (2): 431–57. |
| [3] | RinoRappuoli: Reverse vaccinology.Current Opinion in Microbiology2000, 3: 445–450. |
| [4] | Martinez-Salas E, Saiz M, Sobrino F: "Foot-and-Mouth Disease Virus". Animal Viruses: Molecular Biology 2008,Caister Academic Press. pp. 1–38. |
| [5] | Belsham GJ: Translation and replication of FMDV RNA in ‘Foot and Mouth Disease Virus. Curr Top MicrobiolImmunol. 2005, 288: 43–70. |
| [6] | Coetzer JAW, Thomsen GR, Tustin RC, Kriek NPJ: Infectious diseases of livestock with special reference to Southern Africa. Cape Town: Oxford University Press; 1994. Foot-and-mouth disease. |
| [7] | Alexandersen S, Zhang Z, Donaldson AI and Garland AJM: The pathogenesis and diagnosis of Foot and Mouth Disease.J. Comp. Pathol. 2003c, 129:1–36. |
| [8] | Carrillo C, Tulman ER, Delhon G, Lu Z, Carreno A, Vagnozzi A, Kutish GF, Rock DL: Comparative genomics of Foot and Mouth Disease. J Virol. 2005, 70: 6487–6504. |
| [9] | Grubman MJ: Development of novel strategies to control Foot-and-Mouth Disease: Marker vaccines and antivirals.Biologicals2005, 33 (4): 227–234. |
| [10] | Balinda SN et al: Phylogenetic analyses of the polyproteincoding sequences of serotype O Foot-and-Mouth Disease Viruses in East Africa: Evidence for interserotypic recombination.Virol J. 2010,7 (199): 3-9. |
| [11] | Domingo E, Escarmısa C, Martinez MA, Martinez-Salas E, Mateu MG: Foot-and-Mouth Disease Virus populations are quasispecies. Curr Top MicrobiolImmunol. 1992, 176: 33–47. |
| [12] | Domingo E, Pariente N, Airaksinen A, Gonzalez-Lopez C, S S, Herrera M, Grande-Perez A, Lowenstein PR, Manrubia SC, Lazaro E, Escarm'ısa C: Foot-and-Mouth Disease Virus: Exploring pathways towards virus extinction. Curr Top MicrobiolImmunol. 2005, 288:149–173. |
| [13] | Jackson AL, O'Neill H, Maree F, Blignaut B, Carillo C, Rodriguez L, Haydon DT: Mosaic structure of Foot-and-Mouth Disease Virus genomes. J Gen Virol. 2007, 88: 487–492. |
| [14] | Parida S: Accination against Foot-and-Mouth Disease Virus: Strategies and effectiveness.Expert Rev. Vaccines 2009, 8(3): 347–365. |
| [15] | Kahn S:Vaccination against Foot-and-Mouth Disease: The implications for Canada.Can Vet J. 2002, 43:349–354. |
| [16] | Zhang L: Research in advance for FMD novel vaccines.Virology Journal 2011, 8: 268. |
| [17] | Thompson JD, Higgins DG. and Gibson TJ: CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignments through sequence weighting, position specific gap penalties and weight matrix choice.Nucl. Acids Res. 1994, 22: 4673-4680. |
| [18] | The UniProt Consortium: Reorganizing the protein space at the universal protein resource (UniProt).Nucleic Acids Research 40 (Database issue) 2012: D71–D75. |
| [19] | Tusnády GE and Simon I: Principles governing amino acid composition of integral membrane proteins: applications to topology prediction.J. Mol. Biol. 1998, 283:489-506. |
| [20] | Tusnády GE and Simon I: The HMMTOP transmembrane topology prediction server. Bioinformatics 2001, 17: 849-850. |
| [21] | Reche PA, Glutting JP, Reinherz EL: Prediction of MHC class I binding peptides using profile motifs. Human Immunology 2002,63: 701-709. |
| [22] | Reche PA, Glutting JP, Zhang H and Reinherz EL: Enhancement to the RANKPEP resource for the prediction of peptide binding to MHC molecules using profiles. Immunogenetics2004, 56: 405-419. |
| [23] | He Y, Xiang Z, and Mobley HLT Vaxign: The first web-based vaccine design program for reverse vaccinology and applications for vaccine development.Journal of Biomedicine and Biotechnology 2010, 2010: 1-15 |
| [24] | Schwede T, Kopp J, Guex N, Peitsch MC: SWISS-MODEL: An automated protein homology-modeling server. Nucleic Acids Research 2003, 31(13): 3381–3385. |
| [25] | Arnold K, Bordoli L, Kopp J, and Schwede T: The SWISS-MODEL Workspace: A web-based environment for protein structure homology modelling. Bioinformatics 2006, 22: 195-201. |
| [26] | Arnold K, Bordoli L, Kopp J, and Schwede T: The SWISS-MODEL Workspace: A web-based environment for protein structure homology modelling. Bioinformatics 2009, 22 (2): 195-201. |
| [27] | Vangrysperre W and De Clercq K: Rapid and sensitive polymerase chain reaction based detection and typing of Foot and Mouth Disease Virus in clinical samples and cell culture isolates, combined with a simultaneous differentiation with other and/ or symptomatically related viruses.Arch. Virol. 1996,141: 331–344. |
| [28] | Reche PA, Reinherz EL: Prediction of peptide-MHC binding using profiles. Methods Mol Biol. 2007, 409: 185-200. |
| [29] | U.S.F Tambunan and A.A. Parikesit: In silico analysis of envelope Dengue Virus-2 and envelope Dengue Virus-3 protein as the backbone of Dengue Virus tetravalent vaccine by using homology modeling method.OnLine Journal of Biological Sciences 2009, 9 (1): 6-16. |
| [30] | Benkert P, Biasini M, Schwede T: Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics 2011, 27(3): 343-50. |
| [31] | Xiang Z, He Y: Vaxign: A web-based vaccine target design program for reverse vaccinology. ProcediainVaccinology 2009, 1(1): 23-29. |
| [32] | Knowles NJ, Samuel AR: Molecular epidemiology of Foot-and-Mouth Disease Virus. Virus Res. 2003, 91: 65–80. |
| [33] | Pfaff E, Mussgay M, Bóhm HO, Schultz GE and Schaller H: Antibodies against a preselected peptide recognize and neutralize Foot and Mouth Disease Virus.EMBO J. 1982, 1: 869-874. |
APA Style
F. M. N. Hassan, Md. Shaifur Rahman, K. M. T. Rahman, Sharmin S. Sumi, Md. F. Islam, et al. (2015). In-Silico Evaluation of the Capsid Proteins of FMDV as Potential Vaccine Candidates. Computational Biology and Bioinformatics, 3(1), 6-20. https://doi.org/10.11648/j.cbb.20150301.12
ACS Style
F. M. N. Hassan; Md. Shaifur Rahman; K. M. T. Rahman; Sharmin S. Sumi; Md. F. Islam, et al. In-Silico Evaluation of the Capsid Proteins of FMDV as Potential Vaccine Candidates. Comput. Biol. Bioinform. 2015, 3(1), 6-20. doi: 10.11648/j.cbb.20150301.12
AMA Style
F. M. N. Hassan, Md. Shaifur Rahman, K. M. T. Rahman, Sharmin S. Sumi, Md. F. Islam, et al. In-Silico Evaluation of the Capsid Proteins of FMDV as Potential Vaccine Candidates. Comput Biol Bioinform. 2015;3(1):6-20. doi: 10.11648/j.cbb.20150301.12
Share This Article
Twitter
Linked In
Facebook
Copy
Download@article{10.11648/j.cbb.20150301.12,
author = {F. M. N. Hassan and Md. Shaifur Rahman and K. M. T. Rahman and Sharmin S. Sumi and Md. F. Islam and Md. Badrul Alam and Md. Giasuddin and Khondoker M. Hossain},
title = {In-Silico Evaluation of the Capsid Proteins of FMDV as Potential Vaccine Candidates},
journal = {Computational Biology and Bioinformatics},
volume = {3},
number = {1},
pages = {6-20},
doi = {10.11648/j.cbb.20150301.12},
url = {https://doi.org/10.11648/j.cbb.20150301.12},
eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.cbb.20150301.12},
abstract = {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.},
year = {2015}
}
TY - JOUR T1 - In-Silico Evaluation of the Capsid Proteins of FMDV as Potential Vaccine Candidates AU - F. M. N. Hassan AU - Md. Shaifur Rahman AU - K. M. T. Rahman AU - Sharmin S. Sumi AU - Md. F. Islam AU - Md. Badrul Alam AU - Md. Giasuddin AU - Khondoker M. Hossain Y1 - 2015/03/09 PY - 2015 N1 - https://doi.org/10.11648/j.cbb.20150301.12 DO - 10.11648/j.cbb.20150301.12 T2 - Computational Biology and Bioinformatics JF - Computational Biology and Bioinformatics JO - Computational Biology and Bioinformatics SP - 6 EP - 20 PB - Science Publishing Group SN - 2330-8281 UR - https://doi.org/10.11648/j.cbb.20150301.12 AB - 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. VL - 3 IS - 1 ER -
Information
Email: