Sequence Analysis and B Cell Epitope Prediction of Duck Hepatitis A Virus 1 VP1 Gene

Abstract:

Molecular characterization and phylogenetic analysis of the DHAV-1 VP1 gene, structure and biological function of the VP1 protein were analyzed by using the programs of the DNAstar software ,MEGA software and other bioinformatics software on the line. The nucleotide sequence homologies among and the amino acids homologies of the VP1 gene of DHAV H stain with other 13 DHAV-1 strains in the GenBank were 92.54%-99.86% and 93.75%-99.57%.The putative secondary structure of the VP1 protein contained 10.08% H(alpha helix), 38.24% E(beta-sheet), 51.68%L(loop/coil), Protein can be classified as mixed. The results showed that the B cell epitopes of the VP1 protein were located at the C-terminal 131-136, and 209-218 regions according to Kyte-Doolitte method, Emini method,Karlus-Schulz method, and Jameson-Wolf method implemented in Protean program of DNAStar 7.The VP1 protein in the surface of the virus most exposed, it is to decide the major components of the effects of the virus of Picornaviridae. The VP1 protein of DHAV is a good biomaterial for vaccine research, and genetic and phylogenetic analyses of the VP1 and the B cell epitope prediction can help us to develop multi-epitope vaccine against DHAV variant viruses infections.

• Periodical: Advanced Materials Research (Volume 647)
• Pages: 214-219
• DOI: https://doi.org/10.4028/www.scientific.net/AMR.647.214
• Online since: January 2013
• Authors: Xing Jian Wen, An Chun Cheng, Ming Shu Wang
• Keywords: B-Cell Epitopes, DHAV, Duck Hepatitis A Virus, Multi-Epitope Vaccine, VP1

References

[1] Information on http: /www. oie. int.

[2] R. Gough, M. Collins, E. Borland, and L. Keymer: The Veterinary Record, vol. 114 (1984), p.279.

DOI: 10.1136/vr.114.11.279-a

[3] R. Gough, E. Borland, I. Keymer, and J. Stuart: Avian pathology, vol. 14 (1985), p.227.

[4] A. M. Q. King, E. Lefkowitz, M. J. Adams, and E. B. Carstens: Virus taxonomy: ninth report of the International Committee on Taxonomy of Viruses(Elsevier Inc , UK 2011).

[5] D. Todd, V. J. Smyth, N. Ball, B. M. Donnelly, M. Wylie, N. J. Knowles, and B. Adair: Avian pathology, vol. 38 (2009), p.21.

[6] P. Levine and J. Fabricant: Cornell Veterinarian, vol. 40 (1950), p.71.

[7] C. H. Tseng, N. J. Knowles, and H. J. Tsai: Virus research, vol. 123 (2007), p.190.

[8] Information on http: /www. picornastudygroup. com.

[9] T. E. Toth: Avian diseases, vol. 13, (1969) No. 4, p.834.

[10] McNulty, M.S. Picornaviridae. In: Jordan, F., Pattison, M., Alexander,D., Faragher, T. (Eds. ): Poultry Diseases(fifth ed. )(WB Saunders, London 2001), p.305.

[11] Woolcock, P.R. Duck hepatitis. In: Saif, Y.M., Barnes, H.J., Glisson, J.R., Fadly, A.M., McDougald, L.R., Swayne, D.E. (Eds. ): Diseases of Poultry(11th ed)(Iowa State Press, Ames, IA 2003), p.343.

[12] C. Ding and D. Zhang: Virology, vol. 361 (2007), p.9.

[13] P. W. Mason, M. J. Grubman, and B. Baxt: Virus research, vol. 91 (2003), p.9.

[14] M. C. Kim, Y. K. Kwon, S. J. Joh, A. M. Lindberg, J. H. Kwon, J. H. Kim, and S. J. Kim：Journal of general virology, vol. 87 (2006), p.3307.

[15] C. Carrillo, A. Wigdorovitz, J. Oliveros, P. Zamorano, A. Sadir, N. Gomez, J. Salinas, J. Escribano, and M. Borca: Journal of virology, vol. 72 (1998), p.1688.

DOI: 10.1128/jvi.72.2.1688-1690.1998

[16] F. Brown: Seminars in Virology, Vol. 6 (1995), p.243.

[17] M. S. Oberste, K. Maher, D. R. Kilpatrick, and M. A. Pallansch: Journal of virology, vol. 73 (1999), p. (1941).

[18] J. L. Bittle, R. A. Houghten, H. Alexander, T. M. Shinnick, J. G. Sutcliffe, and R. A. Lerner: Nature, vol. 298 (1982) , p.30.

[19] E. Pfaff, M. Mussgay, H. Böhm, G. Schulz, and H. Schaller: The EMBO journal, vol. 1 (1982), p.869.

[20] K. Strohmaier, R. Franze, and K. Adam: The Journal of general virology, vol. 59 (1982), p.295.

[21] M. G. Rossmann, E. Arnold, J. W. Erickson, E. A. Frankenberger, J. P. Griffith, H. J. Hecht, J. E. Johnson, G. Kamer, M. Luo, and A. G. Mosser: Nature, vol. 317 (1985), p.145.

DOI: 10.1038/317145a0

[22] J. Felsenstein: Evolution, (1985), p.783.

[23] R. D. M. Page: Comp Appl Biol Sci, vol. 12(1996), p.357.

[24] F. Wright: Gene, vol. 87 (1990), p.23.

[25] A. Fuglsang: Molecular biology and evolution, vol. 23 (2006), p.1345.

[26] O. Gascuel and J. Golmard: Computer applications in the biosciences: CABIOS, vol. 4 (1988), p.357.

[27] P. Y. Chou and G. D. Fasman: Biochemistry, vol. 13 (1974), p.222.

[28] C. H. Tseng and H. J. Tsai: Virus research, vol. 126 (2007), p.19.

[29] M. C. Kim, Y. K. Kwon, S. J. Joh, S. J. Kim, C. Tolf, J. H. Kim, H. W. Sung, A. M. Lindberg, and J. H. Kwon: Archives of virology, vol. 152 (2007), p. (2059).

DOI: 10.1007/s00705-007-1023-0

[30] Y. Fu, M. Pan, X. Wang, Y. Xu, H. Yang, and D. Zhang: Veterinary microbiology, vol. 131 (2008), p.247.

[31] M. S. Oberste, K. Maher, and M. A. Pallansch: Journal of virology, vol. 76 (2002), p.1244.

[32] M. S. Oberste, K. Maher, and M. A. Pallansch: Virology, vol. 314 (2003), p.283.