American Journal of Infectious Diseases and Microbiology
ISSN (Print): 2328-4056 ISSN (Online): 2328-4064 Website: Editor-in-chief: Maysaa El Sayed Zaki
Open Access
Journal Browser
American Journal of Infectious Diseases and Microbiology. 2019, 7(1), 43-56
DOI: 10.12691/ajidm-7-1-6
Open AccessArticle

Novel Multi Epitopes Vaccine Candidates against Vesicular Stomatitis Virus through Reverse Vaccinology

Walla Hasab Elrasoul Makki1, 2, Yassir A. Almofti1, , Khoubieb Ali Abd-elrahman3 and Sanaa Bashir1, 2

1Department of Molecular Biology and Bioinformatics, College of Veterinary Medicine, University of Bahri, Khartoum- Sudan

2Department of Botany, Faculty of Science, University of Khartoum, Khartoum- Sudan

3Department of pharmaceutical technology, College of Pharmacy, University of Medical Science and Technology (MUST) Khartoum- Sudan

Pub. Date: October 18, 2019

Cite this paper:
Walla Hasab Elrasoul Makki, Yassir A. Almofti, Khoubieb Ali Abd-elrahman and Sanaa Bashir. Novel Multi Epitopes Vaccine Candidates against Vesicular Stomatitis Virus through Reverse Vaccinology. American Journal of Infectious Diseases and Microbiology. 2019; 7(1):43-56. doi: 10.12691/ajidm-7-1-6


Vesicular stomatitis (VS) is a disease of horses, cattle and swine caused by vesicular stomatitis virus (VSV). The virus belongs to the genus Vesiculovirus of the family Rhabdoviridae. The disease has no treatment or vaccine. Therefore the aim of this study was to design multi-epitopes vaccine against vesicular stomatitis New Jersey virus using peptides of the glycoprotein to stimulate protective immune response. A total of 46 sequences of the Glycoprotein of VSV were retrieved from NCBI database. Sequences were aligned to determine the conservancy and to predict epitopes using IEDB analysis resource. Six epitopes were predicted as promising B cell epitopes since they fulfilled the criteria of surface accessibility, antigenicity and proposed as most probable B cell epitope. These epitopes were 393-VLKTKQGYK-401, 147-PHSVKVDEY-155, 454-SKNPVEL-460, 240-CRKPGYKL-247, 427-HPHIE-431 and 505-PIYKS-509. For T cell; four epitopes 86-FRWYGPKYI-94, 184-FTSSDGESV-192, 189-GESVCSQLF-197 and 108-CLEAIKAYK-116 were proposed as MHC-I epitopes since they interacted with the highest numbers of alleles and with high binding affinity. For MHC-II four epitopes namely 241LKNDLWFQI255, 86FRWYGPKYI94, 184FTSSDGESV192, and 18IEIVFPQHT26 were proposed as peptide vaccine since they interacted with high affinity to MHC-II alleles. It is noteworthy the epitopes 86-FRWYGPKYI-94, 184-FTSSDGESV-192 were found interacting with both MHC-I and MHC-II. Thus they further used for docking with the equine haplotype molecules (ELA-A3) where they demonstrated lowest binding energy to the equine MHC class I molecule haplotype. To our knowledge there is no epitope based vaccine for the Vesicular stomatitis New Jersey Virus (VSV-NJ) via reverse vaccinology. In this study, twelve epitopes were proposed eliciting both humeral and cell mediated immunity and predicted to act as a promising peptide vaccine against VSV. Clinical trial is required to proof these epitopes as an efficient vaccine against vesicular stomatitis virus.

Vesicular stomatitis Virus (VSV) Epitope Peptide vaccine Immune epitope database (IEDB) NCBI

Creative CommonsThis work is licensed under a Creative Commons Attribution 4.0 International License. To view a copy of this license, visit


Figure of 8


[1]  Alvarado JF, Dolz G, Herrero MV, McCluskey B, Salman M. Comparison of the serum neutralization test and a competitive enzyme-linked immunosorbent assay for the detection of antibodies to vesicular stomatitis virus New Jersey and vesicular stomatitis virus Indiana. Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc. 2002; 14(3): 240-2.
[2]  Cornish TE, Stallknecht DE, Brown CC, Seal BS, Howerth EW. Pathogenesis of experimental vesicular stomatitis virus (New Jersey serotype) infection in the deer mouse (Peromyscus maniculatus). Veterinary pathology. 2001; 38(4): 396-406.
[3]  Reis JL, Rodriguez LL, Mead DG, Smoliga G, Brown CC. Lesion development and replication kinetics during early infection in cattle inoculated with Vesicular stomatitis New Jersey virus via scarification and black fly (Simulium vittatum) bite. Veterinary pathology. 2011; 48(3): 547-57.
[4]  Smith PF, Howerth EW, Carter D, Gray EW, Noblet R, Smoliga G, et al. Domestic cattle as a non-conventional amplifying host of vesicular stomatitis New Jersey virus. Medical and veterinary entomology. 2011; 25(2): 184-91.
[5]  Lee HS, Heo EJ, Jeoung HY, Ko HR, Kweon CH, Youn HJ, et al. Enzyme-linked immunosorbent assay using glycoprotein and monoclonal antibody for detecting antibodies to vesicular stomatitis virus serotype New Jersey. Clinical and vaccine immunology : CVI. 2009; 16(5): 667-71.
[6]  Scherer CF, O'Donnell V, Golde WT, Gregg D, Estes DM, Rodriguez LL. Vesicular stomatitis New Jersey virus (VSNJV) infects keratinocytes and is restricted to lesion sites and local lymph nodes in the bovine, a natural host. Veterinary research. 2007; 38(3): 375-90.
[7]  Arshed MJ, Magnuson RJ, Triantis J, Abubakar M, Van Campen H, Salman M. Comparison of RNA extraction methods to augment the sensitivity for the differentiation of vesicular stomatitis virus Indiana1 and New Jersey. Journal of clinical laboratory analysis. 2011; 25(2): 95-9.
[8]  Fowler VL, Howson EL, Madi M, Mioulet V, Caiusi C, Pauszek SJ, et al. Development of a reverse transcription loop-mediated isothermal amplification assay for the detection of vesicular stomatitis New Jersey virus: Use of rapid molecular assays to differentiate between vesicular disease viruses. Journal of virological methods. 2016; 234: 123-31.
[9]  Rainwater-Lovett K, Pauszek SJ, Kelley WN, Rodriguez LL. Molecular epidemiology of vesicular stomatitis New Jersey virus from the 2004-2005 US outbreak indicates a common origin with Mexican strains. The Journal of general virology. 2007; 88(Pt 7): 2042-51.
[10]  Smith PF, Howerth EW, Carter D, Gray EW, Noblet R, Berghaus RD, et al. Host predilection and transmissibility of vesicular stomatitis New Jersey virus strains in domestic cattle (Bos taurus) and swine (Sus scrofa). BMC veterinary research. 2012; 8: 183.
[11]  Killmaster LF, Stallknecht DE, Howerth EW, Moulton JK, Smith PF, Mead DG. Apparent disappearance of Vesicular Stomatitis New Jersey Virus from Ossabaw Island, Georgia. Vector borne and zoonotic diseases. 2011; 11(5): 559-65.
[12]  Rasmussen TB, Uttenthal A, Fernandez J, Storgaard T. Quantitative multiplex assay for simultaneous detection and identification of Indiana and New Jersey serotypes of vesicular stomatitis virus. Journal of clinical microbiology. 2005; 43(1): 356-62.
[13]  Velazquez-Salinas L, Isa P, Pauszek SJ, Rodriguez LL. Complete Genome Sequences of Two Vesicular Stomatitis Virus Isolates Collected in Mexico. Genome announcements. 2017; 5(37).
[14]  Martinez I, Barrera JC, Rodriguez LL, Wertz GW. Recombinant vesicular stomatitis (Indiana) virus expressing New Jersey and Indiana glycoproteins induces neutralizing antibodies to each serotype in swine, a natural host. Vaccine. 2004; 22(29-30): 4035-43.
[15]  Wu K, Kim GN, Kang CY. Expression and processing of human immunodeficiency virus type 1 gp160 using the vesicular stomatitis virus New Jersey serotype vector system. The Journal of general virology. 2009; 90(Pt 5): 1135-40.
[16]  Georgel P, Jiang Z, Kunz S, Janssen E, Mols J, Hoebe K, et al. Vesicular stomatitis virus glycoprotein G activates a specific antiviral Toll-like receptor 4-dependent pathway. Virology. 2007; 362(2): 304-13.
[17]  Kim IS, Jenni S, Stanifer ML, Roth E, Whelan SP, van Oijen AM, et al. Mechanism of membrane fusion induced by vesicular stomatitis virus G protein. Proceedings of the National Academy of Sciences of the United States of America. 2017; 114(1): E28-E36.
[18]  Bachmann MF, Kundig TM, Kalberer CP, Hengartner H, Zinkernagel RM. Formalin inactivation of vesicular stomatitis virus impairs T-cell- but not T-help-independent B-cell responses. Journal of virology. 1993; 67(7): 3917-22.
[19]  House JA HC, Dubourget P, Lombard M. Protective immunity in cattle vaccinated with a commercial scale, inactivated, bivalent vesicular stomatitis vaccine. Vaccine. 2003: 1932-7.
[20]  J.D. Cantlon PWG, R.A. Bowen. Immune responses in mice, cattle and horses to a DNA vaccine for vesicular stomatitis. Vaccine. 2000; 18: 2368-74.
[21]  Flanagan EB, Zamparo JM, Ball LA, Rodriguez LL, Wertz GW. Rearrangement of the genes of vesicular stomatitis virus eliminates clinical disease in the natural host: new strategy for vaccine development. Journal of virology. 2001; 75(13): 6107-14.
[22]  Ruth E. Soria-Guerra RN-G, Dania O. Govea-Alonso, Sergio Rosales-Mendoza. An overview of bioinformatics tools for epitope prediction: Implications on vaccine development. Journal of Biomedical Informatics. 2014:1-9.
[23]  Doytchinova APaI. T-cell epitope vaccine design by immunoinformatics. Open Biology. 2013:1-13.
[24]  Bette Korber ML, Karina Yusim. Immunoinformatics Comes of Age. PLoS Computational Biology. 2006; 2(6): 484-92.
[25]  Jonathan M. Gershoni AR-B, Dror D. Siman-Tov, Natalia Tarnovitski Freund and, Weiss Y. Epitope Mapping The First Step in Developing Epitope-Based Vaccines. Biodrugs. 2007: 145-56.
[26]  Usman Sumo Friend Tambunan FRPS, Arli Aditya Parikesit and Djati Kerami. Vaccine Design for H5N1 Based on B- and T-cell Epitope Predictions. Bioinformatics and Biology Insights. 2016: 27-35.
[27]  Perla Carlos V, Sébastien Holbert, Felipe Ascencio, Kris Huygen, Gracia Gomez-Anduro, MaximeBranger, MarthaReyes-Becerril, Carlos Angulo. In silico epitope analysis of unique and membrane associated proteins from Mycobacteriumavium subsp. paratuberculosis for immunogenicity and vaccine evaluation. Journal of Theoretical Biology. 2015:1-9.
[28]  Malaz Abdelbagi TH, Mohammed Shihabeldin, Sanaa Bashir, Elkhaleel Ahmed, Elmoez Mohamed, Shawgi Hafiz, Abdah Abdelmonim, Tassneem Hamid, Shimaa Awad, Ahmed Hamdi, Khoubieb Ali and Mohammed A. Hassan. Immunoinformatics Prediction of Peptide-Based Vaccine Against African Horse Sickness Virus. Immunome Research. 2017; 13(2): 1-14.
[29]  Ahmed Hamdi Abu-haraz KAA-e, Mojahid Salah Ibrahim, Waleed Hassan Hussien, Mohammed Siddig Mohammed, Marwan Mustafa Badawi and Mohamed Ahmed Salih. Multi Epitope Peptide Vaccine Prediction against Sudan Ebola Virus Using Immuno-Informatics Approaches. Advanced Techniques in Biology & Medicine. 2017; 5(1): 1-21.
[30]  Ren JCTaEC. Immunoinformatics: Current trends and future directions. Drug Discovery Today. 2009; 14.
[31]  De NTaRK. Immunoinformatics: an integrated scenario. Immunology. 2010:153-68.
[32]  Kumar, S., G. Stecher, and K. Tamura, MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular biology and evolution, 2016. 33(7): p. 1870-1874.
[33]  Tom Hall Ib, Carlsbad, Ca. BioEdit: An important software for molecular biology. GERF Bulletin of Biosciences. 2011: 60-1.
[34]  Bourne JVPaPE. Antibody-protein interactions: benchmark datasets and prediction tools evaluation. BMC Structural Biology. 2007: 1-19.
[35]  Jens Erik Pontoppidan Larsen OLaMN. Improved method for predicting linear B-cell epitopes. Immunome Research. 2006: 1-7.
[36]  EMILIO A. EMINI JVH, ' DEBRA S. PERLOW, AND JOSHUA BOGER. Induction of Hepatitis A Virus-Neutralizing Antibody by a Virus- Specific Synthetic Peptide. JOURNAL OF VIROLOGY,. 1985; 55: 836-9.
[37]  Tongaonkar ASKaPC. A semi-empirical method for prediction of antigenic determinants on protein antigens. FEBS 09210. 1990; 276: 172-4.
[38]  MORTEN NIELSEN CL, PEDER WORNING, SANNE LISE LAUEMØLLER, KASPER LAMBERTH, SØREN BUUS SØREN BRUNAK, AND OLE LUND. Reliable prediction of T-cell epitopes using neural networks with novel sequence representations. Protein Science. 2003:12:1007-17.
[39]  Rebecca L. Tallmadge JAC, Donald C. Miller, and Douglas F. Antczak. Analysis of MHC class I genes across horse MHC haplotypes. Immunogenetics. 2010: 159-72.
[40]  Claus Lundegaard OLaMN. Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers. bioinformatics. 2008; 24: 1397-8.
[41]  Gabor Szalai DFA, Heinz Gerber , Sandor Lazary. Molecular cloning and characterization of horse DQB cDNA. Immunogenetics. 1994; 40: 458.
[42]  Lund MNaO. NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction. BMC Bioinformatics. 2009:1-10.
[43]  ERIC F. PETTERSEN TDG, CONRAD C. HUANG, GREGORY S. COUCH, DANIEL M. GREENBLATT, ELAINE C. MENG, THOMAS E. FERRIN. UCSF Chimera—A Visualization System for Exploratory Research and Analysis. J Comput Chem. 2004; 25: 1605-12.
[44]  Julien Maupetit PDaPT. PEP-FOLD: an online resource for de novo peptide structure prediction. Nucleic acids research. 2009; 37: 498-503.
[45]  PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic acids research. 2005; 33: 363-7.
[46]  Groot ASD. Immunomics: discovering new targets for vaccines and therapeutics. Drug Discovery Today. 2006; 11: 203-9.
[47]  Immuno-informatics: Mining genomes for vaccine components. Immunology and Cell Biology 2002; 80: 255-69.
[48]  Anne S. De Groot MA, Elizabeth M. McClaine, Leonard Moise, William D. Martin. Immunoinformatic comparison of T-cell epitopes contained in novel swine-origin influenza A (H1N1) virus with epitopes in 2008-2009 conventional influenza vaccine. Vaccine. 2009; 27 5740-7.
[49]  Jiandong Shi1 JZ, Sijin Li1, Jing Sun, Yumei Teng, Meini Wu, Jianfan Li, Yanhan Li, Ningzhu Hu, Haixuan Wang, Yunzhang Hu. Epitope-Based Vaccine Target Screening against Highly Pathogenic MERS-CoV: An In Silico Approach Applied to Emerging Infectious Diseases. PloS one. 2015: 1-16.
[50]  Omar Hashim Ahmed AA, Sahar Obi, Khoubieb Ali Abd_elrahman, Ahmed Hamdi and Mohammed A. Hassan. Immunoinformatic Approach for Epitope-Based Peptide Vaccine against Lagos Rabies Virus Glycoprotein G. Immunome Research. 2017: 1-8.
[51]  Kenth Gustafsson LA. Structure and polymorphism of horse MHC class II DRB genes: convergent evolution in the antigen binding site. lmmunogenetics 1994; 39: 355-8.
[52]  Brinkmeyer-Langford CL, Childers WJM, C. P and L. C. Skow. A conserved segmental duplication within ELA. Animal Genetics 2010: 186-95.