Abstract
Infectious bronchitis virus (IBV) continues to circulate worldwide, with a significant impact on the poultry industry and affecting both vaccinated and unvaccinated flocks. Several studies have focused on the hypervariable regions (HVRs) of the spike gene (S1); however, genetic and bioinformatics studies of the whole S1 gene are limited. In this study, the whole S1 gene of five Egyptian IBVs was genetically analyzed. Phylogenetic analysis revealed that the Egyptian IBVs are clustered within two distinct groups: the classic group resembling the GI-1 genotype (vaccine strains) and the variant group (field strains) of the GI-23 genotype. The variant genotype was divided into two distinct subgroups (Egy/var I and Egy/var II) resembling the Israeli variants IS/1494 and IS885 strain, respectively. Significant amino acid sequence differences between the two subgroups, especially in the epitope sites, were identified. A deletion at position 63 and an I69A/S substitution mutation associated with virus tropism were detected in the receptor-binding sites. The deduced amino acid sequence of HVRs of the variant subgroups indicated different genetic features in comparison to the classic vaccine group (H120 lineage). The Egyptian variant IBVs also contained additional N-glycosylation sites compared to the classical viruses. Recombination analysis gave evidence for distinct patterns of origin by recombination throughout the S1 gene, suggesting that the recent virus IBV-EG/1586CV-2015 emerged as a recombinant of two viruses from the variant groups Egy/var I and Egy/var II, providing another example of intra-genotypic recombination among IBVs and the first example of recombination within the GI-23 genotype. Our data suggest that both mutation and recombination may be contributing to the emergence of IBV variants. Moreover, we found that the commercially used vaccines are genotypically distant from the circulating field strains. Hence, continuous follow-up of the current vaccine strategy is highly recommended for better control and prevention of infectious bronchitis virus in the poultry sector in Egypt.
Similar content being viewed by others
References
King AM, Lefkowitz E, Adams MJ, Carsten EB (2011) Ninth report of the International Committee on Taxonomy of Viruses
Cavanagh D (2003) Severe acute respiratory syndrome vaccine development: experiences of vaccination against avian infectious bronchitis coronavirus. Avian Pathol J WVPA 32:567–582
Spaan W, Cavanagh D, Horzinek MC (1988) Coronaviruses: structure and genome expression. J Gen Virol 69(Pt 12):2939–2952
Cavanagh D (2007) Coronavirus avian infectious bronchitis virus. Vet Res 38:281–297
Wickramasinghe IN, de Vries RP, Grone A, de Haan CA, Verheije MH (2011) Binding of avian coronavirus spike proteins to host factors reflects virus tropism and pathogenicity. J Virol 85:8903–8912
Belouzard S, Millet JK, Licitra BN, Whittaker GR (2012) Mechanisms of coronavirus cell entry mediated by the viral spike protein. Viruses 4:1011–1033
Moore KM, Jackwood MW, Hilt DA (1997) Identification of amino acids involved in a serotype and neutralization specific epitope within the s1 subunit of avian infectious bronchitis virus. Arch Virol 142:2249–2256
Cavanagh D, Davis PJ, Mockett AP (1988) Amino acids within hypervariable region 1 of avian coronavirus IBV (Massachusetts serotype) spike glycoprotein are associated with neutralization epitopes. Virus Res 11:141–150
Koch G, Hartog L, Kant A, van Roozelaar DJ (1990) Antigenic domains on the peplomer protein of avian infectious bronchitis virus: correlation with biological functions. J Gen Virol 71(Pt 9):1929–1935
Promkuntod N, van Eijndhoven RE, de Vrieze G, Grone A, Verheije MH (2014) Mapping of the receptor-binding domain and amino acids critical for attachment in the spike protein of avian coronavirus infectious bronchitis virus. Virology 448:26–32
Valastro V, Holmes EC, Britton P, Fusaro A, Jackwood MW, Cattoli G, Monne I (2016) S1 gene-based phylogeny of infectious bronchitis virus: An attempt to harmonize virus classification. Infect Genet Evol 39:349–364
Jackwood MW (2012) Review of infectious bronchitis virus around the world. Avian Dis 56:634–641
Adzhar A, Gough RE, Haydon D, Shaw K, Britton P, Cavanagh D (1997) Molecular analysis of the 793/B serotype of infectious bronchitis virus in Great Britain. Avian Pathol J WVPA 26:625–640
Hewson KA, Noormohammadi AH, Devlin JM, Browning GF, Schultz BK, Ignjatovic J (2014) Evaluation of a novel strain of infectious bronchitis virus emerged as a result of spike gene recombination between two highly diverged parent strains. Avian Pathol J WVPA 43:249–257
Li K, Schuler T, Chen Z, Glass GE, Childs JE, Plagemann PG (2000) Isolation of lactate dehydrogenase-elevating viruses from wild house mice and their biological and molecular characterization. Virus Res 67:153–162
Abd El Rahman S, Hoffmann M, Lueschow D, Eladl A, Hafez HM (2015) Isolation and characterization of new variant strains of infectious bronchitis virus in Northern Egypt. Adv Anim Vet Sci 3:362–371
Abdel-Moneim AS, Madbouly HM, Gelb J, Ladman BS (2002) Isolation and identification of Egypt/Beni-Suef/01 a novel genotype of infectious bronchitis virus. Vet Med J Giza Egypt 50:1065–1078
Abdel-Moneim AS, Afifi MA, El-Kady MF (2012) Emergence of a novel genotype of avian infectious bronchitis virus in Egypt. Arch Virol 157:2453–2457
Callison SA, Hilt DA, Boynton TO, Sample BF, Robison R, Swayne DE, Jackwood MW (2006) Development and evaluation of a real-time Taqman RT-PCR assay for the detection of infectious bronchitis virus from infected chickens. J Virol Methods 138:60–65
Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772–780
Hall T (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98
Minh BQ, Nguyen MA, von Haeseler A (2013) Ultrafast approximation for phylogenetic bootstrap. Mol Biol Evol 30:1188–1195
Selim K, Arafa AS, Hussein HA, El-Sanousi AA (2013) Molecular characterization of infectious bronchitis viruses isolated from broiler and layer chicken farms in Egypt during 2012. Int J Vet Sci Med 1:102–108
Zhang Y, Wang HN, Wang T, Fan WQ, Zhang AY, Wei K, Tian GB, Yang X (2010) Complete genome sequence and recombination analysis of infectious bronchitis virus attenuated vaccine strain H120. Virus Genes 41:377–388
Han Z, Zhang T, Xu Q, Gao M, Chen Y, Wang Q, Zhao Y, Shao Y, Li H, Kong X, Liu S (2016) Altered pathogenicity of a tl/CH/LDT3/03 genotype infectious bronchitis coronavirus due to natural recombination in the 5’-17 kb region of the genome. Virus Res 213:140–148
Jackwood MW, Boynton TO, Hilt DA, McKinley ET, Kissinger JC, Paterson AH, Robertson J, Lemke C, McCall AW, Williams SM, Jackwood JW, Byrd LA (2010) Emergence of a group 3 coronavirus through recombination. Virology 398:98–108
Martin DP, Murrell B, Golden M, Khoosal A, Muhire B (2015) RDP4: detection and analysis of recombination patterns in virus genomes. Virus Evol 1(1):vev003. doi:10.1093/ve/vev003
Casais R, Dove B, Cavanagh D, Britton P (2003) Recombinant avian infectious bronchitis virus expressing a heterologous spike gene demonstrates that the spike protein is a determinant of cell tropism. J Virol 77:9084–9089
Acknowledgments
The authors are grateful to colleagues and co-workers from the National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Dokki, Giza, Egypt, for their technical assistance. The authors acknowledge Ceva Santé Animale, Egypt.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare no conflict of interest.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Zanaty, A., Naguib, M.M., El-Husseiny, M.H. et al. The sequence of the full spike S1 glycoprotein of infectious bronchitis virus circulating in Egypt reveals evidence of intra-genotypic recombination. Arch Virol 161, 3583–3587 (2016). https://doi.org/10.1007/s00705-016-3042-1
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00705-016-3042-1