In silico prediction of linear B-cell epitopes for S1 protein of two Iranian ‎‎793/B isolates and their changes after 90 serial passaging‎

Document Type : Original Article

Authors

1 Department of Veterinary Research and Biotechnology, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and ‎Extension Organization, Mashhad, Iran

2 Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran

3 Department of Poultry Disease Research and Diagnosis, Razi Vaccine and Serum Research Institute, Karaj, Iran‎

Abstract

Neutralizing, serotype-specific, and hemagglutination-inhibiting antibodies against infectious bronchitis virus (IBV) are induced by epitopes in the S1 protein. Most changes in the virus genome due to mutation and recombination during serial passaging in embryonated chicken eggs occur in the S1 gene. In the current study, we tried to predict the potential linear B-cell epitopes of the S1 subunit of two Iranian 793/B isolates and then we analyzed their changes at passage level 90 due to mutations at this passage level. To predict linear B-cell epitopes of the S1 protein belonging to two Iranian 793/B isolates, we used two online epitope prediction programs called BepiPred and ABCpred. Some of the most important features of proteins including antigenicity, physicochemical properties, and secondary structure composition were analyzed. The predicted epitopes were studied between wild viruses and their passage level 90 viruses. We identified 15 potential linear B-cell epitopes among which six epitopes had the highest scores of physicochemical properties and antigenicity. Due to amino acid substitutions, seven predicted epitopes had different amino acid sequences at passage level 90. Among eight epitopes with no amino acid substitution at passage level 90, three epitopes had the highest scores. These three conserved epitopes including NH2-NQLGSCPLTGMI-COOH,NH2-GNFSDGFYPFTNSSLVKD-COOH,andNH2-GPIQGGC-COOHmight be strategic and potential candidates for use in designing epitope-based vaccine researches. In conclusion, based on scores of physicochemical properties and antigenicity, it seemed that the sequence of most epitopes in wild viruses might be more antigenic and immunogenic compared to their sequence in viruses of passage 90.

Keywords


  1. Liu S, Han Z, Chen J, et al. S1 gene sequence heterogeneity of a pathogenic infectious bronchitis virus strain and its embryo-passaged, attenuated derivatives. Avian Pathol 2007; 36(3): 231-234.
  2. Cook JK, Orbell SJ, Woods MA, et al. Breadth of protection of the respiratory tract provided by different live-attenuated infectious bronchitis vaccines against challenge with infectious bronchitis viruses of heterologous serotypes. Avian Pathol 1999; 28(5): 477-485.
  3. Schalk AF, Hawn MC. An apparently new respiratory disease of baby chicks. J Am Vet Med Assoc 1931; 78:413-422.
  4. Jackwood MW, Hilt DA, Callison SA, et al. Spike glycoprotein cleavage recognition site analysis of infectious bronchitis virus. Avian Dis 2001; 45(2):366-372.
  5. Casais R, Dove B, Cavanagh D, et al. Recombinant avian infectious bronchitis virus expressing a heterologous spike gene demonstrates that the spike protein is a determinant of cell tropism. J Virol 2003; 77(16): 9084-9089.
  6. Adzhar A, Gough RE, Haydon D, et al. Molecular analysis of the 793/B serotype of infectious bronchitis virus in Great Britain. Avian Pathol 2007; 26(3):625-640.
  7. Cavanagh D. Coronavirus avian infectious bronchitis virus. Vet Res 2007;38(2):281-297.
  8. Cavanagh D. Structural polypeptides of coronavirus IBV. J Gen Virol 1981;53(Pt 1):93-103.
  9. Andoh K, Ashikaga K, Suenaga K, et al. Identification of novel linear epitopes located in the infectious bronchitis virus spike s2 region. Avian Dis 2018; 62(2):210-217.
  10. Bijlenga G, Cook JKA, Gelb Jr J, et al. Development and use of the H strain of avian infectious bronchitis virus from the Netherlands as a vaccine: a review. Avian Pathol 2004;33(6):550-557.
  11. Cavanagh D, Picault JP, Gough R, et al. Variation in the spike protein of the 793/B type of infectious bronchitis virus, in the field and during alternate passage in chickens and embryonated eggs. Avian Pathol 2005; 34(1):20-25.
  12. Huang YP, Wang CH. Sequence changes of infectious bronchitis virus isolates in the 3' 7.3 kb of the genome after attenuating passage in embryonated eggs. Avian Pathol 2007;36(1):59-67.
  13. Britton P, Armesto M, Cavanagh D, et al. Modification of the avian coronavirus infectious bronchitis virus for vaccine development. Bioeng Bugs 2012;3(2): 112-117.
  14. Callison SA, Jackwood MW, Hilt DA. Molecular characterization of infectious bronchitis virus isolates foreign to the United States and comparison with United States isolates. Avian Dis 2001; 45(2):492-499.
  15. Momayez R, Pourbakhsh SA, Khodashenas M, et al. Isolation and identification of infectious bronchitis virus from commercial chickens. Arch Razi Ins 2002; 53: 1-10.
  16. Larsen JEP, Lund O, Nielsen M. Improved method for predicting linear B-cell epitopes. Immunome Res 2006;2: 2. doi: 10.1186/1745-7580-2-2.
  17. Ladman BS, Loupos AB, Gelb Jr J. Infectious bronchitis virus S1 gene sequence comparison is a better predictor of challenge of immunity in chickens than serotyping by virus neutralization. Avian Pathol 2008;35(2):127-133.
  18. Emini EA, Hughes JV, Perlow DS, et al. Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide. J Virol 1985; 55(3):836-839.
  19. Karplus PA, Schulz GE. Prediction of chain flexibility in proteins - A tool for the selection of peptide antigens. Naturwissenschaften 1985;72:212-213.
  20. Kyte J, Doolittle RF. A simple method for displaying the hydropathic character of a protein. J Mol Biol 1982;157(1):105-132.
  21. IEDB Analysis Resource. Available at: http://tools.immuneepitope.org/main/html/analysis_tools.html. ‎Accessed 03 September, 2018.‎
  22. Montassier HJ. Molecular epidemiology and evolution of avian infectious bronchitis virus. Rev Bras Cienc Avic [online] 2010;12(2):87-96.
  23. Tan L, Zhang Y, Liu F, et al. Infectious bronchitis virus poly-epitope-based vaccine protects chickens from acute infection. Vaccine 2016; 34(44): 5209-5216.
  24. Lin KY, Wang HC, Wang CH. Protective effect of vaccination in chicks with local infectious bronchitis viruses against field virus challenge. J Microbiol Immunol Infect 2005;38(1):25-30.
  25. Ignjatovic J, Sapats S. Identification of previously unknown antigenic epitopes on the S and N proteins of avian infectious bronchitis virus. Arch Virol 2005;150(9):1813-1831.
  26. Salarpour A, Toroghi R, Momayez R. Nucleotide sequence analysis of S1 gene among Iranian avian infectious brinchitis viruses isolated during 2001-2002. Arch Razi Ins 2019;74(1):21-31.
  27. Rowley MJ, O'Connor K, Wijeyewickrema L. Phage display for epitope determination: a paradigm for identifying receptor-ligand interaction. Biotechnol Annu Rev 2004;10:151-188.