Trachea transcriptome analysis in SPF broiler chickens infected with avian infectious bronchitis
Subject Areas :
Veterinary Clinical Pathology
Seyed Hossein Zamzam
1
,
Arash Ghalyanchilangeroudi
2
,
Ali Reza Khosravi
3
1 - PhD Student in Virology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran.
2 - Professor, Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran.
3 - Professor, Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran.
Received: 2021-12-05
Accepted : 2022-01-31
Published : 2021-10-23
Keywords:
",
Avian infection bronchitis virus",
transcriptome",
RNA-Seq",
Trachea ",
Abstract :
Avian infectious bronchitis (IB) is an acute and highly contagious disease of the upper-respiratory tract caused by the infectious bronchitis virus (IBV). The virus is a member of the Coronaviridae family and has numerous serotypes and strains. Rapid replication combined with high mutation rate and recombination are the main causes of the observed high diversity.Feed conversion and average daily gain are affected in broilers, and infection is often followed by secondary bacterial infections. In layers, IBV causes a reduction in egg production.Today, IB is one of the most economically important diseases in the poultry industry. Transcriptional profiles of trachea tissue of the infected group (IBV) were studied with control group to evaluate changes in transcriptome profile at the early stages of infection. After the challenge of SPF chickens with IBV IS-1494 like (GI-23, the trachea tissue was used for RNA extraction, and changes in the transcriptome were investigated by Illumina RNA-seq technique. Up-regulated and down-regulated differentially expressed genes (DEGs) in the transcriptome of trachea were identified. Gene ontology category, KEGG pathway were analyzed to identify relationships among differentially expressed genes. In general, the numbers of up-regulated genes were higher than of down-regulated genes in experimental group. In the experimental group, a more severe immune response occurred; an important up-regulated genes in this group’s was Toll-like receptor signaling pathway, apoptotic pathway, MAPK signaling pathway. Results of this study could provide a general overview of transcriptome changes in the trachea at the early stage of infection with avian infectious bronchitis (IBV) virus.
References:
Ariaans, M. P., Matthijs, M. G., van Haarlem, D., van de Haar, P., van Eck, J. H., Hensen, E. J. and Vervelde, L. (2008), "The role of phagocytic cells in enhanced susceptibility of broilers to colibacillosis after infectious bronchitis virus infection", Veterinary Immunology and Immunopathology, Vol. 123 No. 3-4, pp. 240-250.
Awad, F., Chhabra, R., Baylis, M. and Ganapathy, K. (2014), "An overview of infectious bronchitis virus in chickens", World's Poultry Science Journal, Vol. 70 No. 2, pp. 375-384.
Barjesteh, N., O'Dowd, K. and Vahedi, S. M. (2020), "Antiviral responses against chicken respiratory infections: Focus on avian influenza virus and infectious bronchitis virus", Cytokine, Vol. 127, p. 154961.
Chen, S., Cheng, A. and Wang, M. (2013), "Innate sensing of viruses by pattern recognition receptors in birds", Veterinary research, Vol. 44 No. 1, pp. 1-12.
Chhabra, R., Chantrey, J. and Ganapathy, K. (2015), "Immune responses to virulent and vaccine strains of infectious bronchitis viruses in chickens", Viral immunology, Vol. 28 No. 9, pp. 478-488.
Cong, F., Liu, X., Han, Z., Shao, Y., Kong, X. and Liu, S. (2013), "Transcriptome analysis of chicken kidney tissues following coronavirus avian infectious bronchitis virus infection", BMC genomics, Vol. 14 1, pp. 1-13.
Cook, J. K., Jackwood, M. and Jones, R. (2012), "The long view: 40 years of infectious bronchitis research", Avian Pathology, Vol. 41 No. 3, pp. 239-250.
Feizi, A. and Kaboli, K. (2012), "Comparative survey on ascites syndrome incidence rate in broiler chickens infected and non-infected by infectious bronchitis", Veterinary Clinical Pathology The Quarterly Scientific Journal, Vol. 6 No. 2 (22) Summer, pp. 1561-1571.
Fulton, R., Thacker, H., Reed, W. and DeNicola, D. (1997), "Effect of Cytoxan®-Induced Heteropenia on the Response of Specific-Pathogen-Free Chickens to Infectious Bronchitis", Avian diseases, pp. 511-518.
Ganapathy, K., Wilkins, M., Forrester, A., Lemiere, S., Cserep, T., McMullin, P. and Jones, R. (2012), "QX-like infectious bronchitis virus isolated from cases of proventriculitis in commercial broilers in England", The Veterinary record, Vol. 171 No. 23, p. 597.
Garceau, V., Smith, J., Paton, I. R., Davey, M., Fares, M. A., Sester, D. P., Burt, D. W. and Hume, D. A. (2010), "Pivotal Advance: Avian colony‐stimulating factor 1 (CSF‐1), interleukin‐34 (IL‐34), and CSF‐1 receptor genes and gene products", Journal of leukocyte biology, Vol. 87 No. 5, pp. 753-764.
Gholami-Ahangaran, M., Shoushtari, A., Doosti, A., Fathi Hafshejani, E. and Zia-Jahromi, N. (2012), "Detection of infectious bronchitis virus (4/91 type) in broiler chickens in Chahrmahal-va-bakhtiyari province", Veterinary Clinical Pathology The Quarterly Scientific Journal, Vol. 6 No. 2 (22) Summer, pp. 1543-1547.
Guillot, L., Le Goffic, R., Bloch, S., Escriou, N., Akira, S., Chignard, M. and Si-Tahar, M. (2005), "Involvement of toll-like receptor 3 in the immune response of lung epithelial cells to double-stranded RNA and influenza A virus", Journal of Biological Chemistry, Vol. 280 No. 7, pp. 5571-5580.
Guo, X., Rosa, A. J., Chen, D.-G. and Wang, X. (2008), "Molecular mechanisms of primary and secondary mucosal immunity using avian infectious bronchitis virus as a model system", Veterinary immunology and immunopathology, Vol. 121 No. 3-4, pp. 332-343.
Hay, S. and Kannourakis, G. (2002), "A time to kill: viral manipulation of the cell death program", Journal of General Virology, Vol. 83 No. 7, pp. 1547-1564.
He, H., Genovese, K. J. and Kogut, M. H. (2011), "Modulation of chicken macrophage effector function by TH1/TH2 cytokines", Cytokine, Vol. 53 No. 3, pp. 363-369.
Holmes, H. and Darbyshire, J. (1978), "Induction of chicken interferon by avian infectious bronchitis virus", Research in veterinary science, Vol. 25 2, pp. 178-181.
Huang, D. W., Sherman, B. T. and Lempicki, R. A. (2009), "Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists", Nucleic acids research, Vol. 37 No. 1, pp. 1-13.
Hynes, N. E., Ingham, W., Lim, W. A., Marshall, C. J., Massagué, J. and Pawson, T. (2013), "Signalling change: signal transduction through the decades", Nature reviews Molecular cell biology, Vol. 14 No. 6, pp. 393-398.
Jackwood, M. W., Hall, D. and Handel, A. (2012), "Molecular evolution and emergence of avian gammacoronaviruses", Infection, Genetics and Evolution, Vol. 12 No. 6, pp. 1305-1311.
Jackwood, M. W. and Wit, S. d. (2020), Infectious Bronchitis, Diseases of poultry.
Jordan, B. (2017), "Vaccination against infectious bronchitis virus: a continuous challenge", Veterinary microbiology, Vol. 206, pp. 137-143.
Kameka, A. M., Haddadi, S., Kim, D. S., Cork, S. C. and Abdul-Careem, M. F. (2014), "Induction of innate immune response following infectious bronchitis corona virus infection in the respiratory tract of chickens", Virology, Vol. 450, pp. 114-121.
Kanehisa, M., Sato, Y., Furumichi, M., Morishima, K. and Tanabe, M. (2019), "New approach for understanding genome variations in KEGG", Nucleic acids research, Vol. 47 D1, pp. D590-D595.
Khatri, M. and Sharma, J. M. (2006), "Infectious bursal disease virus infection induces macrophage activation via p38 MAPK and NF-κB pathways", Virus research, Vol. 118 No. 1-2, pp. 70-77.
Le Goffic, R., Pothlichet, J., Vitour, D., Fujita, T., Meurs, E., Chignard, M. and Si-Tahar, M. (2007), "Cutting Edge: Influenza A virus activates TLR3-dependent inflammatory and RIG-I-dependent antiviral responses in human lung epithelial cells", The Journal of Immunology, Vol. 178 No. 6, pp. 3368-3372.
Li, F. Q., Tam, J. P. and Liu, D. X. (2007), "Cell cycle arrest and apoptosis induced by the coronavirus infectious bronchitis virus in the absence of p53", Virology, Vol. 365 No. 2, pp. 435-445.
Liu, H., Yang, X., Zhang, Z., Li, J., Zou, W., Zeng, F. and Wang, H. (2017), "Comparative transcriptome analysis reveals induction of apoptosis in chicken kidney cells associated with the virulence of nephropathogenic infectious bronchitis virus", Microbial pathogenesis, Vol. 113, pp. 451-459.
Liu, P., Jamaluddin, M., Li, K., Garofalo, R. P., Casola, A. and Brasier, A. R. (2007), "Retinoic acid-inducible gene I mediates early antiviral response and Toll-like receptor 3 expression in respiratory syncytial virus-infected airway epithelial cells", Journal of virology, Vol. 81 No. 3, pp. 1401-1411.
Mahdavi, S., Zakeri, A. and Mehmannavaz, Y. (2014), "Comparison of serum antibody titer of 8 types of commercial live infectious bronchitis vaccine in broiler chickens", Veterinary Clinical Pathology The Quarterly Scientific Journal, Vol. 8 No. 2 (30) Summer, pp. 473-479.
Matsumoto, M. and Seya, T. (2008), "TLR3: interferon induction by double-stranded RNA including poly (I: C)", Advanced drug delivery reviews, Vol. 60 No. 7, pp. 805-812.
Matthijs, M. G., Ariaans, P., Dwars, R. M., van Eck, J. H., Bouma, A., Stegeman, A. and Vervelde, L. (2009), "Course of infection and immune responses in the respiratory tract of IBV infected broilers after superinfection with E. coli", Veterinary immunology and immunopathology, Vol. 127 No. 1-2, pp. 77-84.
Meir, R., Krispel, S., Simanov, L., Eliahu, D., Maharat, O. and Pitcovski, J. (2012), "Immune responses to mucosal vaccination by the recombinant S1 and N proteins of infectious bronchitis virus", Viral immunology, Vol. 25 1, pp. 55-62.
Miettinen, M., Sareneva, T., Julkunen, I. and Matikainen, S. (2001), "IFNs activate toll-like receptor gene expression in viral infections", Genes & Immunity, Vol. 2 No. 6, pp. 349-355.
Najafi, H., Langeroudi, A. G., Hashemzadeh, M., Karimi, V., Madadgar, O., Ghafouri, S. A., Maghsoudlo, H. and Farahani, R. K. (2016), "Molecular characterization of infectious bronchitis viruses isolated from broiler chicken farms in Iran, 2014-2015", Archives of virology, Vol. 161 No. 1, pp. 53-62.
Nawab, , An, L., Wu, J., Li, G., Liu, W., Zhao, Y., Wu, Q. and Xiao, M. (2019), "Chicken toll-like receptors and their significance in immune response and disease resistance", International reviews of immunology, Vol. 38 No. 6, pp. 284-306.
Paul, M. S., Brisbin, J. T., Abdul-Careem, M. F. and Sharif, S. (2013), "Immunostimulatory properties of Toll-like receptor ligands in chickens", Veterinary immunology and immunopathology, Vol. 152 No. 3-4, pp. 191-199.
Raj, G. D. and Jones, R. (1997), "Infectious bronchitis virus: immunopathogenesis of infection in the chicken", Avian Pathology, Vol. 26 No. 4, pp. 677-706.
Reed, L. J. and Muench, H. (1938), "A simple method of estimating fifty per cent endpoints", American journal of epidemiology, Vol. 27 No. 3, pp. 493-497.
Wang, X., Rosa, A. J., Oliverira, H. N., Rosa, G. J., Guo, X., Travnicek, M. and Girshick, T. (2006), "Transcriptome of local innate and adaptive immunity during early phase of infectious bronchitis viral infection", Viral immunology, Vol. 19 No. 4, 768-774.
Wu, Z. and Kaiser, P. (2011), "Antigen presenting cells in a non-mammalian model system, the chicken", Immunobiology, Vol. 216 No. 11, pp. 1177-1183.
Xu, P., Liu, P., Zhou, C., Shi, Y., Wu, Q., Yang, Y., Li, G., Hu, G. and Guo, X. (2019), "A Multi-omics study of chicken infected by nephropathogenic infectious bronchitis virus", Viruses, Vol. 11 No. 11, p. 1070.
Zhang, W. and Liu, H. T. (2002), "MAPK signal pathways in the regulation of cell proliferation in mammalian cells", Cell research, Vol. 12 No. 1, pp. 9-18.
_||_
Ariaans, M. P., Matthijs, M. G., van Haarlem, D., van de Haar, P., van Eck, J. H., Hensen, E. J. and Vervelde, L. (2008), "The role of phagocytic cells in enhanced susceptibility of broilers to colibacillosis after infectious bronchitis virus infection", Veterinary Immunology and Immunopathology, Vol. 123 No. 3-4, pp. 240-250.
Awad, F., Chhabra, R., Baylis, M. and Ganapathy, K. (2014), "An overview of infectious bronchitis virus in chickens", World's Poultry Science Journal, Vol. 70 No. 2, pp. 375-384.
Barjesteh, N., O'Dowd, K. and Vahedi, S. M. (2020), "Antiviral responses against chicken respiratory infections: Focus on avian influenza virus and infectious bronchitis virus", Cytokine, Vol. 127, p. 154961.
Chen, S., Cheng, A. and Wang, M. (2013), "Innate sensing of viruses by pattern recognition receptors in birds", Veterinary research, Vol. 44 No. 1, pp. 1-12.
Chhabra, R., Chantrey, J. and Ganapathy, K. (2015), "Immune responses to virulent and vaccine strains of infectious bronchitis viruses in chickens", Viral immunology, Vol. 28 No. 9, pp. 478-488.
Cong, F., Liu, X., Han, Z., Shao, Y., Kong, X. and Liu, S. (2013), "Transcriptome analysis of chicken kidney tissues following coronavirus avian infectious bronchitis virus infection", BMC genomics, Vol. 14 1, pp. 1-13.
Cook, J. K., Jackwood, M. and Jones, R. (2012), "The long view: 40 years of infectious bronchitis research", Avian Pathology, Vol. 41 No. 3, pp. 239-250.
Feizi, A. and Kaboli, K. (2012), "Comparative survey on ascites syndrome incidence rate in broiler chickens infected and non-infected by infectious bronchitis", Veterinary Clinical Pathology The Quarterly Scientific Journal, Vol. 6 No. 2 (22) Summer, pp. 1561-1571.
Fulton, R., Thacker, H., Reed, W. and DeNicola, D. (1997), "Effect of Cytoxan®-Induced Heteropenia on the Response of Specific-Pathogen-Free Chickens to Infectious Bronchitis", Avian diseases, pp. 511-518.
Ganapathy, K., Wilkins, M., Forrester, A., Lemiere, S., Cserep, T., McMullin, P. and Jones, R. (2012), "QX-like infectious bronchitis virus isolated from cases of proventriculitis in commercial broilers in England", The Veterinary record, Vol. 171 No. 23, p. 597.
Garceau, V., Smith, J., Paton, I. R., Davey, M., Fares, M. A., Sester, D. P., Burt, D. W. and Hume, D. A. (2010), "Pivotal Advance: Avian colony‐stimulating factor 1 (CSF‐1), interleukin‐34 (IL‐34), and CSF‐1 receptor genes and gene products", Journal of leukocyte biology, Vol. 87 No. 5, pp. 753-764.
Gholami-Ahangaran, M., Shoushtari, A., Doosti, A., Fathi Hafshejani, E. and Zia-Jahromi, N. (2012), "Detection of infectious bronchitis virus (4/91 type) in broiler chickens in Chahrmahal-va-bakhtiyari province", Veterinary Clinical Pathology The Quarterly Scientific Journal, Vol. 6 No. 2 (22) Summer, pp. 1543-1547.
Guillot, L., Le Goffic, R., Bloch, S., Escriou, N., Akira, S., Chignard, M. and Si-Tahar, M. (2005), "Involvement of toll-like receptor 3 in the immune response of lung epithelial cells to double-stranded RNA and influenza A virus", Journal of Biological Chemistry, Vol. 280 No. 7, pp. 5571-5580.
Guo, X., Rosa, A. J., Chen, D.-G. and Wang, X. (2008), "Molecular mechanisms of primary and secondary mucosal immunity using avian infectious bronchitis virus as a model system", Veterinary immunology and immunopathology, Vol. 121 No. 3-4, pp. 332-343.
Hay, S. and Kannourakis, G. (2002), "A time to kill: viral manipulation of the cell death program", Journal of General Virology, Vol. 83 No. 7, pp. 1547-1564.
He, H., Genovese, K. J. and Kogut, M. H. (2011), "Modulation of chicken macrophage effector function by TH1/TH2 cytokines", Cytokine, Vol. 53 No. 3, pp. 363-369.
Holmes, H. and Darbyshire, J. (1978), "Induction of chicken interferon by avian infectious bronchitis virus", Research in veterinary science, Vol. 25 2, pp. 178-181.
Huang, D. W., Sherman, B. T. and Lempicki, R. A. (2009), "Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists", Nucleic acids research, Vol. 37 No. 1, pp. 1-13.
Hynes, N. E., Ingham, W., Lim, W. A., Marshall, C. J., Massagué, J. and Pawson, T. (2013), "Signalling change: signal transduction through the decades", Nature reviews Molecular cell biology, Vol. 14 No. 6, pp. 393-398.
Jackwood, M. W., Hall, D. and Handel, A. (2012), "Molecular evolution and emergence of avian gammacoronaviruses", Infection, Genetics and Evolution, Vol. 12 No. 6, pp. 1305-1311.
Jackwood, M. W. and Wit, S. d. (2020), Infectious Bronchitis, Diseases of poultry.
Jordan, B. (2017), "Vaccination against infectious bronchitis virus: a continuous challenge", Veterinary microbiology, Vol. 206, pp. 137-143.
Kameka, A. M., Haddadi, S., Kim, D. S., Cork, S. C. and Abdul-Careem, M. F. (2014), "Induction of innate immune response following infectious bronchitis corona virus infection in the respiratory tract of chickens", Virology, Vol. 450, pp. 114-121.
Kanehisa, M., Sato, Y., Furumichi, M., Morishima, K. and Tanabe, M. (2019), "New approach for understanding genome variations in KEGG", Nucleic acids research, Vol. 47 D1, pp. D590-D595.
Khatri, M. and Sharma, J. M. (2006), "Infectious bursal disease virus infection induces macrophage activation via p38 MAPK and NF-κB pathways", Virus research, Vol. 118 No. 1-2, pp. 70-77.
Le Goffic, R., Pothlichet, J., Vitour, D., Fujita, T., Meurs, E., Chignard, M. and Si-Tahar, M. (2007), "Cutting Edge: Influenza A virus activates TLR3-dependent inflammatory and RIG-I-dependent antiviral responses in human lung epithelial cells", The Journal of Immunology, Vol. 178 No. 6, pp. 3368-3372.
Li, F. Q., Tam, J. P. and Liu, D. X. (2007), "Cell cycle arrest and apoptosis induced by the coronavirus infectious bronchitis virus in the absence of p53", Virology, Vol. 365 No. 2, pp. 435-445.
Liu, H., Yang, X., Zhang, Z., Li, J., Zou, W., Zeng, F. and Wang, H. (2017), "Comparative transcriptome analysis reveals induction of apoptosis in chicken kidney cells associated with the virulence of nephropathogenic infectious bronchitis virus", Microbial pathogenesis, Vol. 113, pp. 451-459.
Liu, P., Jamaluddin, M., Li, K., Garofalo, R. P., Casola, A. and Brasier, A. R. (2007), "Retinoic acid-inducible gene I mediates early antiviral response and Toll-like receptor 3 expression in respiratory syncytial virus-infected airway epithelial cells", Journal of virology, Vol. 81 No. 3, pp. 1401-1411.
Mahdavi, S., Zakeri, A. and Mehmannavaz, Y. (2014), "Comparison of serum antibody titer of 8 types of commercial live infectious bronchitis vaccine in broiler chickens", Veterinary Clinical Pathology The Quarterly Scientific Journal, Vol. 8 No. 2 (30) Summer, pp. 473-479.
Matsumoto, M. and Seya, T. (2008), "TLR3: interferon induction by double-stranded RNA including poly (I: C)", Advanced drug delivery reviews, Vol. 60 No. 7, pp. 805-812.
Matthijs, M. G., Ariaans, P., Dwars, R. M., van Eck, J. H., Bouma, A., Stegeman, A. and Vervelde, L. (2009), "Course of infection and immune responses in the respiratory tract of IBV infected broilers after superinfection with E. coli", Veterinary immunology and immunopathology, Vol. 127 No. 1-2, pp. 77-84.
Meir, R., Krispel, S., Simanov, L., Eliahu, D., Maharat, O. and Pitcovski, J. (2012), "Immune responses to mucosal vaccination by the recombinant S1 and N proteins of infectious bronchitis virus", Viral immunology, Vol. 25 1, pp. 55-62.
Miettinen, M., Sareneva, T., Julkunen, I. and Matikainen, S. (2001), "IFNs activate toll-like receptor gene expression in viral infections", Genes & Immunity, Vol. 2 No. 6, pp. 349-355.
Najafi, H., Langeroudi, A. G., Hashemzadeh, M., Karimi, V., Madadgar, O., Ghafouri, S. A., Maghsoudlo, H. and Farahani, R. K. (2016), "Molecular characterization of infectious bronchitis viruses isolated from broiler chicken farms in Iran, 2014-2015", Archives of virology, Vol. 161 No. 1, pp. 53-62.
Nawab, , An, L., Wu, J., Li, G., Liu, W., Zhao, Y., Wu, Q. and Xiao, M. (2019), "Chicken toll-like receptors and their significance in immune response and disease resistance", International reviews of immunology, Vol. 38 No. 6, pp. 284-306.
Paul, M. S., Brisbin, J. T., Abdul-Careem, M. F. and Sharif, S. (2013), "Immunostimulatory properties of Toll-like receptor ligands in chickens", Veterinary immunology and immunopathology, Vol. 152 No. 3-4, pp. 191-199.
Raj, G. D. and Jones, R. (1997), "Infectious bronchitis virus: immunopathogenesis of infection in the chicken", Avian Pathology, Vol. 26 No. 4, pp. 677-706.
Reed, L. J. and Muench, H. (1938), "A simple method of estimating fifty per cent endpoints", American journal of epidemiology, Vol. 27 No. 3, pp. 493-497.
Wang, X., Rosa, A. J., Oliverira, H. N., Rosa, G. J., Guo, X., Travnicek, M. and Girshick, T. (2006), "Transcriptome of local innate and adaptive immunity during early phase of infectious bronchitis viral infection", Viral immunology, Vol. 19 No. 4, 768-774.
Wu, Z. and Kaiser, P. (2011), "Antigen presenting cells in a non-mammalian model system, the chicken", Immunobiology, Vol. 216 No. 11, pp. 1177-1183.
Xu, P., Liu, P., Zhou, C., Shi, Y., Wu, Q., Yang, Y., Li, G., Hu, G. and Guo, X. (2019), "A Multi-omics study of chicken infected by nephropathogenic infectious bronchitis virus", Viruses, Vol. 11 No. 11, p. 1070.
Zhang, W. and Liu, H. T. (2002), "MAPK signal pathways in the regulation of cell proliferation in mammalian cells", Cell research, Vol. 12 No. 1, pp. 9-18.
