{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T18:55:10Z","timestamp":1767984910246,"version":"3.49.0"},"reference-count":42,"publisher":"Springer Science and Business Media LLC","issue":"3","license":[{"start":{"date-parts":[[2022,3,17]],"date-time":"2022-03-17T00:00:00Z","timestamp":1647475200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2022,3,17]],"date-time":"2022-03-17T00:00:00Z","timestamp":1647475200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Virus Genes"],"published-print":{"date-parts":[[2022,6]]},"DOI":"10.1007\/s11262-022-01893-w","type":"journal-article","created":{"date-parts":[[2022,3,17]],"date-time":"2022-03-17T18:35:02Z","timestamp":1647542102000},"page":"203-213","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Comparative trachea transcriptome analysis in SPF broiler chickens infected with avian infectious bronchitis and avian influenza viruses"],"prefix":"10.1007","volume":"58","author":[{"given":"Seyed Hossein","family":"Zamzam","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9044-1659","authenticated-orcid":false,"given":"Arash","family":"Ghalyanchilangeroudi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ali Reza","family":"Khosravi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2022,3,17]]},"reference":[{"issue":"3","key":"1893_CR1","doi-asserted-by":"publisher","first-page":"239","DOI":"10.1080\/03079457.2012.680432","volume":"41","author":"JK Cook","year":"2012","unstructured":"Cook JK, Jackwood M, Jones R (2012) The long view: 40 years of infectious bronchitis research. Avian Pathol 41(3):239\u2013250","journal-title":"Avian Pathol"},{"issue":"6","key":"1893_CR2","doi-asserted-by":"publisher","first-page":"1271","DOI":"10.3382\/ps\/pew068","volume":"95","author":"KE Hassan","year":"2016","unstructured":"Hassan KE, Shany SA, Ali A, Dahshan A-HM, Azza A, El-Kady MF (2016) Prevalence of avian respiratory viruses in broiler flocks in Egypt. Poult Sci 95(6):1271\u20131280","journal-title":"Poult Sci"},{"issue":"3","key":"1893_CR3","doi-asserted-by":"publisher","first-page":"444","DOI":"10.3382\/ps.2007-00415","volume":"87","author":"D Roussan","year":"2008","unstructured":"Roussan D, Haddad R, Khawaldeh G (2008) Molecular survey of avian respiratory pathogens in commercial broiler chicken flocks with respiratory diseases in Jordan. Poult Sci 87(3):444\u2013448","journal-title":"Poult Sci"},{"issue":"2","key":"1893_CR4","first-page":"39","volume":"13","author":"S Seifi","year":"2012","unstructured":"Seifi S, Asasi K, Mohammadi A (2012) An experimental study on broiler chicken co-infected with the specimens containing avian influenza (H9subtype) and infectious bronchitis (4\/91 strain) viruses. Iran J Vet Res 13(2):39","journal-title":"Iran J Vet Res"},{"issue":"11","key":"1893_CR5","doi-asserted-by":"publisher","first-page":"1318","DOI":"10.1016\/j.vaccine.2014.01.006","volume":"32","author":"I Fernandez-Siurob","year":"2014","unstructured":"Fernandez-Siurob I, Retana M, Tellez G, Arroyo-Navarro L, Ba\u00f1uelos-Hernandez B, Castellanos-Huerta I (2014) Assessment of viral interference using a chemical receptor blocker against avian influenza and establishment of protection levels in field outbreaks. Vaccine 32(11):1318\u20131322","journal-title":"Vaccine"},{"issue":"1","key":"1893_CR6","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1080\/03079450802632049","volume":"38","author":"SAE Rahman","year":"2009","unstructured":"Rahman SAE, El-Kenawy A, Neumann U, Herrler G, Winter C (2009) Comparative analysis of the sialic acid binding activity and the tropism for the respiratory epithelium of four different strains of avian infectious bronchitis virus. Avian Pathol 38(1):41\u201345","journal-title":"Avian Pathol"},{"issue":"9","key":"1893_CR7","doi-asserted-by":"publisher","first-page":"618","DOI":"10.1038\/nrmicro2852","volume":"10","author":"AJ Westermann","year":"2012","unstructured":"Westermann AJ, Gorski SA, Vogel J (2012) Dual RNA-seq of pathogen and host. Nat Rev Microbiol 10(9):618\u2013630","journal-title":"Nat Rev Microbiol"},{"key":"1893_CR8","doi-asserted-by":"publisher","first-page":"114","DOI":"10.1016\/j.virol.2013.12.001","volume":"450","author":"AM Kameka","year":"2014","unstructured":"Kameka AM, Haddadi S, Kim DS, Cork SC, Abdul-Careem MF (2014) Induction of innate immune response following infectious bronchitis corona virus infection in the respiratory tract of chickens. Virology 450:114\u2013121","journal-title":"Virology"},{"issue":"1","key":"1893_CR9","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1080\/03079450701774850","volume":"37","author":"K Zaffuto","year":"2008","unstructured":"Zaffuto K, Estevez C, Afonso C (2008) Primary chicken tracheal cell culture system for the study of infection with avian respiratory viruses. Avian Pathol 37(1):25\u201331","journal-title":"Avian Pathol"},{"issue":"3\u20134","key":"1893_CR10","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1016\/j.vetimm.2012.11.012","volume":"151","author":"L Vervelde","year":"2013","unstructured":"Vervelde L, Matthijs M, Van Haarlem D, de Wit J, Jansen C (2013) Rapid NK-cell activation in chicken after infection with infectious bronchitis virus M41. Vet Immunol Immunopathol 151(3\u20134):337\u2013341","journal-title":"Vet Immunol Immunopathol"},{"issue":"2","key":"1893_CR11","doi-asserted-by":"publisher","first-page":"269","DOI":"10.1016\/S0195-5616(98)82005-6","volume":"28","author":"SA Kruth","year":"1998","unstructured":"Kruth SA (1998) Biological response modifiers: interferons, interleukins, recombinant products, liposomal products. Vet Clin N Am 28(2):269\u2013295","journal-title":"Vet Clin N Am"},{"issue":"3","key":"1893_CR12","doi-asserted-by":"publisher","first-page":"479","DOI":"10.1089\/vim.2006.0109","volume":"20","author":"M Asif","year":"2007","unstructured":"Asif M, Lowenthal JW, Ford ME, Schat KA, Kimpton WG, Bean AG (2007) Interleukin-6 expression after infectious bronchitis virus infection in chickens. Viral Immunol 20(3):479\u2013486","journal-title":"Viral Immunol"},{"issue":"3\u20134","key":"1893_CR13","doi-asserted-by":"publisher","first-page":"332","DOI":"10.1016\/j.vetimm.2007.09.016","volume":"121","author":"X Guo","year":"2008","unstructured":"Guo X, Rosa AJ, Chen D-G, Wang X (2008) Molecular mechanisms of primary and secondary mucosal immunity using avian infectious bronchitis virus as a model system. Vet Immunol Immunopathol 121(3\u20134):332\u2013343","journal-title":"Vet Immunol Immunopathol"},{"issue":"9","key":"1893_CR14","doi-asserted-by":"publisher","first-page":"478","DOI":"10.1089\/vim.2015.0027","volume":"28","author":"R Chhabra","year":"2015","unstructured":"Chhabra R, Chantrey J, Ganapathy K (2015) Immune responses to virulent and vaccine strains of infectious bronchitis viruses in chickens. Viral Immunol 28(9):478\u2013488","journal-title":"Viral Immunol"},{"key":"1893_CR15","doi-asserted-by":"publisher","DOI":"10.1007\/s00705-021-05322-5","author":"H Ghobadian Diali","year":"2022","unstructured":"Ghobadian Diali H, Hosseini H, Fallah Mehrabadi MH, Yahyaraeyat R, Ghalyanchilangeroudi A (2022) Evaluation of viral load and transcriptome changes in tracheal tissue of two hybrids of commercial broiler chickens infected with avian infectious bronchitis virus: a comparative study. Adv Virol. https:\/\/doi.org\/10.1007\/s00705-021-05322-5","journal-title":"Adv Virol"},{"issue":"04","key":"1893_CR16","doi-asserted-by":"publisher","first-page":"457","DOI":"10.4149\/av_2020_413","volume":"64","author":"S Hashemi","year":"2020","unstructured":"Hashemi S, Ghalyanchilangeroudi A, Hosseini SM, Sheikhi N (2020) Comparative trachea transcriptome analysis between avian infectious bronchitis virus and avian pathogenic E. coli individual infection and co-infection in SPF chickens. Acta Virol 64(04):457\u2013469. https:\/\/doi.org\/10.4149\/av_2020_413","journal-title":"Acta Virol"},{"key":"1893_CR17","doi-asserted-by":"publisher","DOI":"10.1186\/1743-422x-10-279","author":"P Massin","year":"2013","unstructured":"Massin P, Deleage C, Oger A, Briand F-X, Quenault H, Blanchard Y (2013) Differential cellular gene expression in duck trachea infected with a highly or low pathogenic H5N1 avian influenza virus. Virol J. https:\/\/doi.org\/10.1186\/1743-422x-10-279","journal-title":"Virol J"},{"issue":"1","key":"1893_CR18","first-page":"53","volume":"161","author":"H Najafi","year":"2016","unstructured":"Najafi H, Langeroudi AG, Hashemzadeh M, Karimi V, Madadgar O, Ghafouri SA, Maghsoudlo H, Farahani RK (2016) Molecular characterization of infectious bronchitis viruses isolated from broiler chicken farms in Iran, 2014\u20132015. Adv Virol 161(1):53\u201362","journal-title":"Adv Virol"},{"issue":"6","key":"1893_CR19","doi-asserted-by":"publisher","first-page":"1737","DOI":"10.1007\/s11250-019-01809-1","volume":"51","author":"MHF Mehrabadi","year":"2019","unstructured":"Mehrabadi MHF, Ghalyanchilangeroudi A, Ghafouri SA, Malekan M, Ziafati Z, Hosseini H, Mousavi FS, Jabbarifakhr M, Aghaeean L (2019) Full-genome characterization and genetic analysis of a H9N2 virus in commercial broilers in Iran, 2017. Trop Anim Health Prod 51(6):1737\u20131749","journal-title":"Trop Anim Health Prod"},{"issue":"3","key":"1893_CR20","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1093\/oxfordjournals.aje.a118408","volume":"27","author":"LJ Reed","year":"1938","unstructured":"Reed LJ, Muench H (1938) A simple method of estimating fifty per cent endpoints. Am J Epidemiol 27(3):493\u2013497","journal-title":"Am J Epidemiol"},{"issue":"1","key":"1893_CR21","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","volume":"29","author":"A Dobin","year":"2013","unstructured":"Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29(1):15\u201321","journal-title":"Bioinformatics"},{"issue":"1","key":"1893_CR22","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/nar\/gkn923","volume":"37","author":"DW Huang","year":"2009","unstructured":"Huang DW, Sherman BT, Lempicki RA (2009) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37(1):1\u201313","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"1893_CR23","doi-asserted-by":"publisher","first-page":"D590","DOI":"10.1093\/nar\/gky962","volume":"47","author":"M Kanehisa","year":"2019","unstructured":"Kanehisa M, Sato Y, Furumichi M, Morishima K, Tanabe M (2019) New approach for understanding genome variations in KEGG. Nucleic Acids Res 47(D1):D590\u2013D595","journal-title":"Nucleic Acids Res"},{"issue":"3\u20134","key":"1893_CR24","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1016\/j.vetimm.2012.10.013","volume":"152","author":"MS Paul","year":"2013","unstructured":"Paul MS, Brisbin JT, Abdul-Careem MF, Sharif S (2013) Immunostimulatory properties of Toll-like receptor ligands in chickens. Vet Immunol Immunopathol 152(3\u20134):191\u2013199","journal-title":"Vet Immunol Immunopathol"},{"issue":"1","key":"1893_CR25","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13567-020-00874-x","volume":"44","author":"S Chen","year":"2013","unstructured":"Chen S, Cheng A, Wang M (2013) Innate sensing of viruses by pattern recognition receptors in birds. Vet Res 44(1):1\u201312","journal-title":"Vet Res"},{"issue":"7","key":"1893_CR26","doi-asserted-by":"publisher","first-page":"5571","DOI":"10.1074\/jbc.M410592200","volume":"280","author":"L Guillot","year":"2005","unstructured":"Guillot L, Le Goffic R, Bloch S, Escriou N, Akira S, Chignard M, 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. J Biol Chem 280(7):5571\u20135580","journal-title":"J Biol Chem"},{"issue":"6","key":"1893_CR27","doi-asserted-by":"publisher","first-page":"3368","DOI":"10.4049\/jimmunol.178.6.3368","volume":"178","author":"R Le Goffic","year":"2007","unstructured":"Le Goffic R, Pothlichet J, Vitour D, Fujita T, Meurs E, Chignard M, Si-Tahar M (2007) Cutting edge: influenza A virus activates TLR3-dependent inflammatory and RIG-I-dependent antiviral responses in human lung epithelial cells. J Immunol 178(6):3368\u20133372","journal-title":"J Immunol"},{"issue":"1\u20132","key":"1893_CR28","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1016\/j.vetimm.2011.05.031","volume":"148","author":"AJ Karpala","year":"2012","unstructured":"Karpala AJ, Lowenthal JW, Bean AG (2012) Identifying innate immune pathways of the chicken may lead to new antiviral therapies. Vet Immunol Immunopathol 148(1\u20132):100\u2013109","journal-title":"Vet Immunol Immunopathol"},{"issue":"6","key":"1893_CR29","doi-asserted-by":"publisher","first-page":"2900","DOI":"10.1128\/JVI.05738-11","volume":"86","author":"S Jensen","year":"2012","unstructured":"Jensen S, Thomsen AR (2012) Sensing of RNA viruses: a review of innate immune receptors involved in recognizing RNA virus invasion. J Virol 86(6):2900\u20132910","journal-title":"J Virol"},{"key":"1893_CR30","doi-asserted-by":"publisher","first-page":"154961","DOI":"10.1016\/j.cyto.2019.154961","volume":"127","author":"N Barjesteh","year":"2020","unstructured":"Barjesteh N, O\u2019Dowd K, Vahedi SM (2020) Antiviral responses against chicken respiratory infections: Focus on avian influenza virus and infectious bronchitis virus. Cytokine 127:154961","journal-title":"Cytokine"},{"issue":"7138","key":"1893_CR31","doi-asserted-by":"publisher","first-page":"916","DOI":"10.1038\/nature05732","volume":"446","author":"MU Gack","year":"2007","unstructured":"Gack MU, Shin YC, Joo C-H, Urano T, Liang C, Sun L, Takeuchi O, Akira S, Chen Z, Inoue S (2007) TRIM25 RING-finger E3 ubiquitin ligase is essential for RIG-I-mediated antiviral activity. Nature 446(7138):916\u2013920","journal-title":"Nature"},{"issue":"1\u20132","key":"1893_CR32","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1016\/j.virusres.2005.11.015","volume":"118","author":"M Khatri","year":"2006","unstructured":"Khatri M, Sharma JM (2006) Infectious bursal disease virus infection induces macrophage activation via p38 MAPK and NF-\u03baB pathways. Virus Res 118(1\u20132):70\u201377","journal-title":"Virus Res"},{"key":"1893_CR33","doi-asserted-by":"publisher","first-page":"511","DOI":"10.2307\/1592139","volume":"41","author":"R Fulton","year":"1997","unstructured":"Fulton R, Thacker H, Reed W, DeNicola D (1997) Effect of cytoxan\u00ae-induced heteropenia on the response of specific-pathogen-free chickens to infectious bronchitis. Avian Dis 41:511\u2013518","journal-title":"Avian Dis"},{"issue":"1\u20132","key":"1893_CR34","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1016\/j.vetimm.2008.09.016","volume":"127","author":"MG Matthijs","year":"2009","unstructured":"Matthijs MG, Ariaans MP, Dwars RM, van Eck JH, Bouma A, Stegeman A, Vervelde L (2009) Course of infection and immune responses in the respiratory tract of IBV infected broilers after superinfection with E. coli. Vet Immunol Immunopathol 127(1\u20132):77\u201384","journal-title":"Vet Immunol Immunopathol"},{"issue":"3\u20134","key":"1893_CR35","doi-asserted-by":"publisher","first-page":"240","DOI":"10.1016\/j.vetimm.2008.02.003","volume":"123","author":"MP Ariaans","year":"2008","unstructured":"Ariaans MP, Matthijs MG, van Haarlem D, van de Haar P, van Eck JH, Hensen EJ, Vervelde L (2008) The role of phagocytic cells in enhanced susceptibility of broilers to colibacillosis after infectious bronchitis virus infection. Vet Immunol Immunopathol 123(3\u20134):240\u2013250","journal-title":"Vet Immunol Immunopathol"},{"issue":"3","key":"1893_CR36","doi-asserted-by":"publisher","first-page":"363","DOI":"10.1016\/j.cyto.2010.12.009","volume":"53","author":"H He","year":"2011","unstructured":"He H, Genovese KJ, Kogut MH (2011) Modulation of chicken macrophage effector function by TH1\/TH2 cytokines. Cytokine 53(3):363\u2013369","journal-title":"Cytokine"},{"issue":"1","key":"1893_CR37","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1089\/vim.2010.0064","volume":"24","author":"TM Crowley","year":"2011","unstructured":"Crowley TM, Haring VR, Moore R (2011) Chicken anemia virus: an understanding of the in-vitro host response over time. Viral Immunol 24(1):3\u20139","journal-title":"Viral Immunol"},{"issue":"7","key":"1893_CR38","doi-asserted-by":"publisher","first-page":"1547","DOI":"10.1099\/0022-1317-83-7-1547","volume":"83","author":"S Hay","year":"2002","unstructured":"Hay S, Kannourakis G (2002) A time to kill: viral manipulation of the cell death program. J Gen Virol 83(7):1547\u20131564","journal-title":"J Gen Virol"},{"issue":"2","key":"1893_CR39","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1016\/j.virol.2007.04.015","volume":"365","author":"FQ Li","year":"2007","unstructured":"Li FQ, Tam JP, Liu DX (2007) Cell cycle arrest and apoptosis induced by the coronavirus infectious bronchitis virus in the absence of p53. Virology 365(2):435\u2013445","journal-title":"Virology"},{"issue":"1","key":"1893_CR40","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2164-14-743","volume":"14","author":"F Cong","year":"2013","unstructured":"Cong F, Liu X, Han Z, Shao Y, Kong X, Liu S (2013) Transcriptome analysis of chicken kidney tissues following coronavirus avian infectious bronchitis virus infection. BMC Genomics 14(1):1\u201313","journal-title":"BMC Genomics"},{"issue":"7","key":"1893_CR41","doi-asserted-by":"publisher","first-page":"805","DOI":"10.1016\/j.addr.2007.11.005","volume":"60","author":"M Matsumoto","year":"2008","unstructured":"Matsumoto M, Seya T (2008) TLR3: interferon induction by double-stranded RNA including poly (I: C). Adv Drug Deliv Rev 60(7):805\u2013812","journal-title":"Adv Drug Deliv Rev"},{"key":"1893_CR42","doi-asserted-by":"publisher","first-page":"110","DOI":"10.1016\/j.vetmic.2017.02.015","volume":"203","author":"Q Huang","year":"2017","unstructured":"Huang Q, Wang K, Pan L, Qi K, Liu H, Chen H (2017) Co-infection of H9N2 subtype avian influenza virus and infectious bronchitis virus decreases SP-A expression level in chickens. Vet Microbiol 203:110\u2013116","journal-title":"Vet Microbiol"}],"container-title":["Virus Genes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s11262-022-01893-w.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s11262-022-01893-w\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s11262-022-01893-w.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,4,29]],"date-time":"2022-04-29T11:16:41Z","timestamp":1651231001000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s11262-022-01893-w"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,3,17]]},"references-count":42,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2022,6]]}},"alternative-id":["1893"],"URL":"https:\/\/doi.org\/10.1007\/s11262-022-01893-w","relation":{},"ISSN":["0920-8569","1572-994X"],"issn-type":[{"value":"0920-8569","type":"print"},{"value":"1572-994X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,3,17]]},"assertion":[{"value":"2 November 2021","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"2 March 2022","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 March 2022","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"All the authors approved the final manuscript for publication. In addition, the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interest"}},{"value":"No humans were used in the present study. Ethical considerations were observed following the principles of the University of Tehran under sterile conditions. In addition, the study protocol was approved by the Ethics Committee of Tehran University of Medical Sciences (code: UT1397612).","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethical approval"}}]}}