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K.; Sung, H. W.; Kwon, H. M. title: S1 glycoprotein gene analysis of infectious bronchitis viruses isolated in Korea date: 2003-11-13 journal: Arch Virol DOI: 10.1007/s00705-003-0225-3 sha: doc_id: 4810 cord_uid: g0y7ied0 file: cache/cord-264716-igl25jhg.json key: cord-264716-igl25jhg authors: Koo, B.S.; Lee, H.R.; Jeon, E.O.; Han, M.S.; Min, K.C.; Lee, S.B.; Mo, I.P. title: Molecular survey of enteric viruses in commercial chicken farms in Korea with a history of enteritis date: 2013-11-01 journal: Poult Sci DOI: 10.3382/ps.2013-03280 sha: doc_id: 264716 cord_uid: igl25jhg file: cache/cord-255619-5h3l6nh6.json key: cord-255619-5h3l6nh6 authors: Kuo, Shu-Ming; Kao, Hsiao-Wei; Hou, Ming-Hon; Wang, Ching-Ho; Lin, Siou-Hong; Su, Hong-Lin title: Evolution of infectious bronchitis virus in Taiwan: Positively selected sites in the nucleocapsid protein and their effects on RNA-binding activity date: 2013-03-23 journal: Vet Microbiol DOI: 10.1016/j.vetmic.2012.10.020 sha: doc_id: 255619 cord_uid: 5h3l6nh6 file: cache/cord-269024-re0hyolh.json key: cord-269024-re0hyolh authors: Bande, Faruku; Arshad, Siti Suri; Hair Bejo, Mohd; Kadkhodaei, Saeid; Omar, Abdul Rahman title: Prediction and In Silico Identification of Novel B-Cells and T-Cells Epitopes in the S1-Spike Glycoprotein of M41 and CR88 (793/B) Infectious Bronchitis Virus Serotypes for Application in Peptide Vaccines date: 2016-09-07 journal: Adv Bioinformatics DOI: 10.1155/2016/5484972 sha: doc_id: 269024 cord_uid: re0hyolh file: cache/cord-256859-7ixegm72.json key: cord-256859-7ixegm72 authors: Liu, S. W.; Zhang, Q. X.; Chen, J. D.; Han, Z. X.; Liu, X.; Feng, L.; Shao, Y. H.; Rong, J. G.; Kong, X. G.; Tong, G. Z. title: Genetic diversity of avian infectious bronchitis coronavirus strains isolated in China between 1995 and 2004 date: 2006-01-09 journal: Arch Virol DOI: 10.1007/s00705-005-0695-6 sha: doc_id: 256859 cord_uid: 7ixegm72 file: cache/cord-003208-lwirkob3.json key: cord-003208-lwirkob3 authors: Yan, Liping; Hu, Jianhua; Lei, Jing; Shi, Zhiyu; Xiao, Qian; Bi, Zhenwei; Yao, Lu; Li, Yuan; Chen, Yuqing; Fang, An; Li, Hui; Song, Suquan; Liao, Min; Zhou, Jiyong title: Novel protein chip for the detection of antibodies against infectious bronchitis virus date: 2018-09-17 journal: BMC Vet Res DOI: 10.1186/s12917-018-1586-x sha: doc_id: 3208 cord_uid: lwirkob3 file: cache/cord-009487-7xb4huyz.json key: cord-009487-7xb4huyz authors: GODWIN, IR; CHAFFEY, GA title: Simple rapid method of rumen cannulation date: 2008-03-10 journal: Aust Vet J DOI: 10.1111/j.1751-0813.1988.tb14467.x sha: doc_id: 9487 cord_uid: 7xb4huyz file: cache/cord-280442-jtvez46y.json key: cord-280442-jtvez46y authors: Wu, Xuan; Song, Zengxu; Zhai, Xiwen; Zuo, Lei; Mei, Xueran; Xiang, Rong; Kang, Zhuangzhuang; Zhou, Long; Wang, Hongning title: Simultaneous and visual detection of infectious bronchitis virus and Newcastle disease virus by multiple LAMP and lateral flow dipstick date: 2019-11-01 journal: Poultry Science DOI: 10.3382/ps/pez372 sha: doc_id: 280442 cord_uid: jtvez46y file: cache/cord-007648-tm0hn0hz.json key: cord-007648-tm0hn0hz authors: Mockett, A.P.Adrian title: Envelope proteins of avian infectious bronchitis virus: Purification and biological properties date: 2002-12-20 journal: J Virol Methods DOI: 10.1016/0166-0934(85)90138-7 sha: doc_id: 7648 cord_uid: tm0hn0hz file: cache/cord-257064-iafm3pcc.json key: cord-257064-iafm3pcc authors: Kint, Joeri; Maier, Helena Jane; Jagt, Erik title: Quantification of Infectious Bronchitis Coronavirus by Titration In Vitro and In Ovo date: 2014-12-18 journal: Coronaviruses DOI: 10.1007/978-1-4939-2438-7_9 sha: doc_id: 257064 cord_uid: iafm3pcc file: cache/cord-260042-cs0wp99n.json key: cord-260042-cs0wp99n authors: Khan, Samiullah; Roberts, Juliet; Wu, Shu-Biao title: Genes involved in mitochondrial biogenesis and function may not show synchronised responses to mitochondria in shell gland of laying chickens under infectious bronchitis virus challenge date: 2019-04-01 journal: BMC Mol Cell Biol DOI: 10.1186/s12860-019-0190-7 sha: doc_id: 260042 cord_uid: cs0wp99n file: cache/cord-265681-ab8j4o1u.json key: cord-265681-ab8j4o1u authors: Boroomand, Zahra; Asasi, Keramat; Mohammadi, Ali title: Pathogenesis and Tissue Distribution of Avian Infectious Bronchitis Virus Isolate IRFIBV32 (793/B Serotype) in Experimentally Infected Broiler Chickens date: 2012-04-01 journal: ScientificWorldJournal DOI: 10.1100/2012/402537 sha: doc_id: 265681 cord_uid: ab8j4o1u file: cache/cord-010608-eaa2znom.json key: cord-010608-eaa2znom authors: Butt, Salman L.; Erwood, Eric C.; Zhang, Jian; Sellers, Holly S.; Young, Kelsey; Lahmers, Kevin K.; Stanton, James B. title: Real-time, MinION-based, amplicon sequencing for lineage typing of infectious bronchitis virus from upper respiratory samples date: 2020-03-05 journal: J Vet Diagn Invest DOI: 10.1177/1040638720910107 sha: doc_id: 10608 cord_uid: eaa2znom file: cache/cord-256444-grw5s2pf.json key: cord-256444-grw5s2pf authors: Lai, Michael M.C.; Cavanagh, David title: The Molecular Biology of Coronaviruses date: 1997-12-31 journal: Advances in Virus Research DOI: 10.1016/s0065-3527(08)60286-9 sha: doc_id: 256444 cord_uid: grw5s2pf file: cache/cord-258379-v3lceirh.json key: cord-258379-v3lceirh authors: Liu, D. X.; Inglis, S. C. title: Association of the infectious bronchitis virus 3c protein with the virion envelope date: 1991-12-31 journal: Virology DOI: 10.1016/0042-6822(91)90572-s sha: doc_id: 258379 cord_uid: v3lceirh file: cache/cord-276550-1in7m56w.json key: cord-276550-1in7m56w authors: Abdel-Moneim, Ahmed S; El-Kady, Magdy F; Ladman, Brian S; Gelb, Jack title: S1 gene sequence analysis of a nephropathogenic strain of avian infectious bronchitis virus in Egypt date: 2006-09-20 journal: Virol J DOI: 10.1186/1743-422x-3-78 sha: doc_id: 276550 cord_uid: 1in7m56w file: cache/cord-278324-eqqvwwh6.json key: cord-278324-eqqvwwh6 authors: Wang, Huanan; Cong, Feng; Guan, Jianchi; Xiao, Li; Zhu, Yujun; Lian, Yuexiao; Huang, Ren; Chen, Meili; Guo, Pengju title: Development of a sensitive and specific xMAP assay for detection of antibodies against infectious laryngotracheitis and bronchitis viruses date: 2018-09-21 journal: Virol J DOI: 10.1186/s12985-018-1048-x sha: doc_id: 278324 cord_uid: eqqvwwh6 file: cache/cord-252048-ftbjsoup.json key: cord-252048-ftbjsoup authors: McKinley, Enid T.; Jackwood, Mark W.; Hilt, Deborah A.; Kissinger, Jessica C.; Robertson, Jon S.; Lemke, Cornelia; Paterson, Andrew H. title: Attenuated live vaccine usage affects accurate measures of virus diversity and mutation rates in avian coronavirus infectious bronchitis virus date: 2011-04-22 journal: Virus Res DOI: 10.1016/j.virusres.2011.04.006 sha: doc_id: 252048 cord_uid: ftbjsoup file: cache/cord-000924-wwuqxx1r.json key: cord-000924-wwuqxx1r authors: Yan, Fang; Zhao, Yujun; Hu, Yongting; Qiu, Jianyang; Lei, Wenxin; Ji, Wenhui; Li, Xuying; Wu, Qian; Shi, Xiumin; Li, Zhong title: Protection of chickens against infectious bronchitis virus with a multivalent DNA vaccine and boosting with an inactivated vaccine date: 2013-03-24 journal: J Vet Sci DOI: 10.4142/jvs.2013.14.1.53 sha: doc_id: 924 cord_uid: wwuqxx1r file: cache/cord-265499-pbf11zy1.json key: cord-265499-pbf11zy1 authors: Dove, Brian K.; You, Jae‐Hwan; Reed, Mark L.; Emmett, Stevan R.; Brooks, Gavin; Hiscox, Julian A. title: Changes in nucleolar morphology and proteins during infection with the coronavirus infectious bronchitis virus date: 2006-03-03 journal: Cell Microbiol DOI: 10.1111/j.1462-5822.2006.00698.x sha: doc_id: 265499 cord_uid: pbf11zy1 file: cache/cord-266585-jfjrk9gy.json key: cord-266585-jfjrk9gy authors: Fang, Shouguo; Chen, Bo; Tay, Felicia P.L.; Ng, Beng Sern; Liu, Ding Xing title: An arginine-to-proline mutation in a domain with undefined functions within the helicase protein (Nsp13) is lethal to the coronavirus infectious bronchitis virus in cultured cells date: 2007-02-05 journal: Virology DOI: 10.1016/j.virol.2006.08.020 sha: doc_id: 266585 cord_uid: jfjrk9gy file: cache/cord-253695-tjdw2uta.json key: cord-253695-tjdw2uta authors: Winter, Christine; Herrler, Georg; Neumann, Ulrich title: Infection of the tracheal epithelium by infectious bronchitis virus is sialic acid dependent date: 2007-12-28 journal: Microbes Infect DOI: 10.1016/j.micinf.2007.12.009 sha: doc_id: 253695 cord_uid: tjdw2uta file: cache/cord-022187-7c3wz6c6.json key: cord-022187-7c3wz6c6 authors: Liu, Shengwang; Kong, Xiangang title: A new genotype of nephropathogenic infectious bronchitis virus circulating in vaccinated and non-vaccinated flocks in China date: 2010-10-19 journal: Avian Pathol DOI: 10.1080/0307945042000220697 sha: doc_id: 22187 cord_uid: 7c3wz6c6 file: cache/cord-255141-55ho9av4.json key: cord-255141-55ho9av4 authors: Abolnik, Celia title: Genomic and single nucleotide polymorphism analysis of infectious bronchitis coronavirus date: 2015-04-03 journal: Infect Genet Evol DOI: 10.1016/j.meegid.2015.03.033 sha: doc_id: 255141 cord_uid: 55ho9av4 file: cache/cord-285052-aql0vrzv.json key: cord-285052-aql0vrzv authors: Kamble, Nitin Machindra; Pillai, Aravind S.; Gaikwad, Satish S.; Shukla, Sanjeev Kumar; Khulape, Sagar Aashok; Dey, Sohini; Mohan, C. Madhan title: Evolutionary and bioinformatic analysis of the spike glycoprotein gene of H120 vaccine strain protectotype of infectious bronchitis virus from India date: 2016-02-12 journal: Biotechnol Appl Biochem DOI: 10.1002/bab.1298 sha: doc_id: 285052 cord_uid: aql0vrzv file: cache/cord-255870-gmq5zs2d.json key: cord-255870-gmq5zs2d authors: Liu, Shengwang; Zhang, Qingxia; Chen, Jianfei; Han, Zongxi; Shao, Yuhao; Kong, Xiangang; Tong, Guangzhi title: Identification of the avian infectious bronchitis coronaviruses with mutations in gene 3 date: 2008-04-15 journal: Gene DOI: 10.1016/j.gene.2008.01.004 sha: doc_id: 255870 cord_uid: gmq5zs2d file: cache/cord-284501-5i0w74q4.json key: cord-284501-5i0w74q4 authors: Armesto, Maria; Cavanagh, Dave; Britton, Paul title: The Replicase Gene of Avian Coronavirus Infectious Bronchitis Virus Is a Determinant of Pathogenicity date: 2009-10-09 journal: PLoS One DOI: 10.1371/journal.pone.0007384 sha: doc_id: 284501 cord_uid: 5i0w74q4 file: cache/cord-273366-xd84f8ct.json key: cord-273366-xd84f8ct authors: Brownsword, Matthew J.; Doyle, Nicole; Brocard, Michèle; Locker, Nicolas; Maier, Helena J. title: Infectious Bronchitis Virus Regulates Cellular Stress Granule Signaling date: 2020-05-14 journal: Viruses DOI: 10.3390/v12050536 sha: doc_id: 273366 cord_uid: xd84f8ct file: cache/cord-263785-0iift8zy.json key: cord-263785-0iift8zy authors: Zhang, Xiaorong; Liao, Kai; Chen, Shuqin; Yan, Kun; Du, Xubin; Zhang, Chengcheng; Guo, Mengjiao; Wu, Yantao title: Evaluation of the reproductive system development and egg-laying performance of hens infected with TW I-type infectious bronchitis virus date: 2020-07-31 journal: Vet Res DOI: 10.1186/s13567-020-00819-4 sha: doc_id: 263785 cord_uid: 0iift8zy file: cache/cord-002407-25cawzi0.json key: cord-002407-25cawzi0 authors: Nogales, Aitor; Martínez-Sobrido, Luis title: Reverse Genetics Approaches for the Development of Influenza Vaccines date: 2016-12-22 journal: Int J Mol Sci DOI: 10.3390/ijms18010020 sha: doc_id: 2407 cord_uid: 25cawzi0 file: cache/cord-277804-ujabzic4.json key: cord-277804-ujabzic4 authors: Yuk, Seong-su; Kwon, Jung-Hoon; Noh, Jin-Yong; Hong, Woo-tack; Gwon, Gyeong-Bin; Jeong, Jei-Hyun; Jeong, Sol; Youn, Ha-Na; Heo, Yong-Hwan; Lee, Joong-Bok; Park, Seung-Yong; Choi, In-Soo; Song, Chang-Seon title: Comparison between dot-immunoblotting assay and clinical sign determination method for quantifying avian infectious bronchitis virus vaccine by titration in embryonated eggs date: 2016-01-21 journal: J Virol Methods DOI: 10.1016/j.jviromet.2016.01.008 sha: doc_id: 277804 cord_uid: ujabzic4 file: cache/cord-001768-8vljd5cv.json key: cord-001768-8vljd5cv authors: Awad, Faez; Forrester, Anne; Baylis, Matthew; Lemiere, Stephane; Ganapathy, Kannan title: Protection conferred by live infectious bronchitis vaccine viruses against variant Middle East IS/885/00-like and IS/1494/06-like isolates in commercial broiler chicks date: 2015-09-09 journal: Vet Rec Open DOI: 10.1136/vetreco-2014-000111 sha: doc_id: 1768 cord_uid: 8vljd5cv file: cache/cord-004680-u3cnsdl8.json key: cord-004680-u3cnsdl8 authors: Lin, Z.; Kato, A.; Kudou, Y.; Umeda, K.; Ueda, S. title: Typing of recent infectious bronchitis virus isolates causing nephritis in chicken date: 1991 journal: Arch Virol DOI: 10.1007/bf01310957 sha: doc_id: 4680 cord_uid: u3cnsdl8 file: cache/cord-285942-mb1xwdqw.json key: cord-285942-mb1xwdqw authors: Feng, K. Y.; Chen, T; Zhang, X; Shao, G. M.; Cao, Y; Chen, D. K.; Lin, W. C.; Chen, F; Xie, Q. 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Alaraji, Furkan; Abdulwahab, Husam Muhsen; Khudhair, Yahia Ismail title: Sequencing and phylogenetic analysis of infectious bronchitis virus variant strain from an outbreak in egg-layer flocks in Baghdad, Iraq date: 2020-07-16 journal: Vet World DOI: 10.14202/vetworld.2020.1358-1362 sha: doc_id: 259959 cord_uid: qzd3hf8y file: cache/cord-268788-jcu3pasy.json key: cord-268788-jcu3pasy authors: Thor, Sharmi W.; Hilt, Deborah A.; Kissinger, Jessica C.; Paterson, Andrew H.; Jackwood, Mark W. title: Recombination in Avian Gamma-Coronavirus Infectious Bronchitis Virus date: 2011-09-23 journal: Viruses DOI: 10.3390/v3091777 sha: doc_id: 268788 cord_uid: jcu3pasy file: cache/cord-257999-apg4uhhq.json key: cord-257999-apg4uhhq authors: Ababneh, Mustafa; Dalab, Abd Elhafeed; Alsaad, Saad; Al-Zghoul, Mohammad title: Presence of Infectious Bronchitis Virus Strain CK/CH/LDL/97I in the Middle East date: 2012-04-11 journal: ISRN Vet Sci DOI: 10.5402/2012/201721 sha: doc_id: 257999 cord_uid: apg4uhhq file: cache/cord-269150-d1sgnxc0.json key: cord-269150-d1sgnxc0 authors: Tan, Yong Wah; Hong, Wanjin; Liu, Ding Xiang title: Binding of the 5′-untranslated region of coronavirus RNA to zinc finger CCHC-type and RNA-binding motif 1 enhances viral replication and transcription date: 2012-02-22 journal: Nucleic Acids Res DOI: 10.1093/nar/gks165 sha: doc_id: 269150 cord_uid: d1sgnxc0 file: cache/cord-260799-kx6hfpu0.json key: cord-260799-kx6hfpu0 authors: Mahmood, Zana H.; Sleman, Rizgar R.; Uthman, Aumaid U. title: Isolation and molecular characterization of Sul/01/09 avian infectious bronchitis virus, indicates the emergence of a new genotype in the Middle East date: 2011-05-12 journal: Vet Microbiol DOI: 10.1016/j.vetmic.2010.12.015 sha: doc_id: 260799 cord_uid: kx6hfpu0 file: cache/cord-259505-7hiss0j3.json key: cord-259505-7hiss0j3 authors: Kong, Qingming; Xue, Chunyi; Ren, Xiangpeng; Zhang, Chengwen; Li, Linlin; Shu, Dingming; Bi, Yingzuo; Cao, Yongchang title: Proteomic analysis of purified coronavirus infectious bronchitis virus particles date: 2010-06-09 journal: Proteome Sci DOI: 10.1186/1477-5956-8-29 sha: doc_id: 259505 cord_uid: 7hiss0j3 file: cache/cord-260667-5aurua6o.json key: cord-260667-5aurua6o authors: Falchieri, Marco; Lupini, Caterina; Cecchinato, Mattia; Catelli, Elena; Kontolaimou, Maria; Naylor, Clive J. title: Avian metapneumoviruses expressing Infectious Bronchitis virus genes are stable and induce protection date: 2013-05-24 journal: Vaccine DOI: 10.1016/j.vaccine.2013.03.055 sha: doc_id: 260667 cord_uid: 5aurua6o file: cache/cord-003334-ion97n4b.json key: cord-003334-ion97n4b authors: De Silva Senapathi, Upasama; Abdul-Cader, Mohamed Sarjoon; Amarasinghe, Aruna; van Marle, Guido; Czub, Markus; Gomis, Susantha; Abdul-Careem, Mohamed Faizal title: The In Ovo Delivery of CpG Oligonucleotides Protects against Infectious Bronchitis with the Recruitment of Immune Cells into the Respiratory Tract of Chickens date: 2018-11-15 journal: Viruses DOI: 10.3390/v10110635 sha: doc_id: 3334 cord_uid: ion97n4b file: cache/cord-265258-2rmtsyns.json key: cord-265258-2rmtsyns authors: Domanska‐Blicharz, K.; Lisowska, A.; Pikuła, A.; Sajewicz‐Krukowska, J. title: Specific detection of GII‐1 lineage of infectious bronchitis virus date: 2017-07-03 journal: Lett Appl Microbiol DOI: 10.1111/lam.12753 sha: doc_id: 265258 cord_uid: 2rmtsyns file: cache/cord-262226-7kwkla73.json key: cord-262226-7kwkla73 authors: Fang, Shouguo; 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Liu, Xiao Bo; Fang, Shou Guo; Tay, Felicia P. L.; Liu, Ding Xiang title: Acquisition of Cell–Cell Fusion Activity by Amino Acid Substitutions in Spike Protein Determines the Infectivity of a Coronavirus in Cultured Cells date: 2009-07-02 journal: PLoS One DOI: 10.1371/journal.pone.0006130 sha: doc_id: 352511 cord_uid: gkm7i62s file: cache/cord-355703-l9l4ybfn.json key: cord-355703-l9l4ybfn authors: Zhao, Fei; Han, Zongxi; Zhang, Tingting; Shao, Yuhao; Kong, Xiangang; Ma, Huijie; Liu, Shengwang title: Genomic Characteristics and Changes of Avian Infectious Bronchitis Virus Strain CK/CH/LDL/97I after Serial Passages in Chicken Embryos date: 2014-08-29 journal: Intervirology DOI: 10.1159/000365193 sha: doc_id: 355703 cord_uid: l9l4ybfn file: cache/cord-353310-19kzb6ag.json key: cord-353310-19kzb6ag authors: Quinteros, José A.; Markham, Philip F.; Lee, Sang-Won; Hewson, Kylie A.; Hartley, Carol A.; Legione, Alistair R.; Coppo, Mauricio J. C.; Vaz, Paola K.; Browning, Glenn F. title: Analysis of the complete genomic sequences of two virus subpopulations of the Australian infectious bronchitis virus vaccine VicS date: 2015-04-01 journal: Avian Pathol DOI: 10.1080/03079457.2015.1022857 sha: doc_id: 353310 cord_uid: 19kzb6ag file: cache/cord-344745-sgkq1l93.json key: cord-344745-sgkq1l93 authors: Selim, Karim; Arafa, Abdel Satar; Hussein, Hussein A.; El-Sanousi, Ahmed A. title: Molecular characterization of infectious bronchitis viruses isolated from broiler and layer chicken farms in Egypt during 2012 date: 2013-11-18 journal: Int J Vet Sci Med DOI: 10.1016/j.ijvsm.2013.10.002 sha: doc_id: 344745 cord_uid: sgkq1l93 file: cache/cord-345088-krb1eidw.json key: cord-345088-krb1eidw authors: Shen, S; Law, Y.C; Liu, D.X title: A single amino acid mutation in the spike protein of coronavirus infectious bronchitis virus hampers its maturation and incorporation into virions at the nonpermissive temperature date: 2004-09-01 journal: Virology DOI: 10.1016/j.virol.2004.06.016 sha: doc_id: 345088 cord_uid: krb1eidw file: cache/cord-343893-sophqqne.json key: cord-343893-sophqqne authors: Chu, Victor C; McElroy, Lisa J; Aronson, Jed M; Oura, Trisha J; Harbison, Carole E; Bauman, Beverley E; Whittaker, Gary R title: Feline aminopeptidase N is not a functional receptor for avian infectious bronchitis virus date: 2007-02-26 journal: Virol J DOI: 10.1186/1743-422x-4-20 sha: doc_id: 343893 cord_uid: sophqqne file: cache/cord-351564-nikcd44o.json key: cord-351564-nikcd44o authors: Zhang, Xiaozhan; Deng, Tongwei; Lu, Jianzhou; Zhao, Pandeng; Chen, Lulu; Qian, Mengwei; Guo, Yiwen; Qiao, Hongxing; Xu, Yaohui; Wang, Yan; Li, Xinzheng; Zhang, Guizhi; Wang, Zeng; Bian, Chuanzhou title: Molecular characterization of variant infectious bronchitis virus in China, 2019: Implications for control programmes date: 2020-01-24 journal: Transbound Emerg Dis DOI: 10.1111/tbed.13477 sha: doc_id: 351564 cord_uid: nikcd44o file: cache/cord-338307-vfutmwxq.json key: cord-338307-vfutmwxq authors: Sturman, Lawrence S.; Holmes, Kathryn V. title: The Molecular Biology of Coronaviruses date: 1983-12-31 journal: Advances in Virus Research DOI: 10.1016/s0065-3527(08)60721-6 sha: doc_id: 338307 cord_uid: vfutmwxq file: cache/cord-356094-sbtigcfr.json key: cord-356094-sbtigcfr authors: Chen, Huijie; Muhammad, Ishfaq; Zhang, Yue; Ren, Yudong; Zhang, Ruili; Huang, Xiaodan; Diao, Lei; Liu, Haixin; Li, Xunliang; Sun, Xiaoqi; Abbas, Ghulam; Li, Guangxing title: Antiviral Activity Against Infectious Bronchitis Virus and Bioactive Components of Hypericum perforatum L. date: 2019-10-29 journal: Front Pharmacol DOI: 10.3389/fphar.2019.01272 sha: doc_id: 356094 cord_uid: sbtigcfr Reading metadata file and updating bibliogrpahics === updating bibliographic database Building study carrel named keyword-ibv-cord === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 46628 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 46266 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 45773 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 46880 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 46001 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 47031 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 46822 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 47084 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 47026 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 46219 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 47055 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 47068 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 47120 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 47061 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 46889 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 44850 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 46745 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-009487-7xb4huyz author: GODWIN, IR title: Simple rapid method of rumen cannulation date: 2008-03-10 pages: extension: .txt txt: ./txt/cord-009487-7xb4huyz.txt cache: ./cache/cord-009487-7xb4huyz.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-009487-7xb4huyz.txt' === file2bib.sh === id: cord-007648-tm0hn0hz author: Mockett, A.P.Adrian title: Envelope proteins of avian infectious bronchitis virus: Purification and biological properties date: 2002-12-20 pages: extension: .txt txt: ./txt/cord-007648-tm0hn0hz.txt cache: ./cache/cord-007648-tm0hn0hz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-007648-tm0hn0hz.txt' === file2bib.sh === id: cord-004680-u3cnsdl8 author: Lin, Z. title: Typing of recent infectious bronchitis virus isolates causing nephritis in chicken date: 1991 pages: extension: .txt txt: ./txt/cord-004680-u3cnsdl8.txt cache: ./cache/cord-004680-u3cnsdl8.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-004680-u3cnsdl8.txt' === file2bib.sh === id: cord-017894-8iahlshj author: Loa, Chien Chang title: A Multiplex Polymerase Chain Reaction for Differential Detection of Turkey Coronavirus from Chicken Infectious Bronchitis Virus and Bovine Coronavirus date: 2015-09-10 pages: extension: .txt txt: ./txt/cord-017894-8iahlshj.txt cache: ./cache/cord-017894-8iahlshj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-017894-8iahlshj.txt' === file2bib.sh === id: cord-257064-iafm3pcc author: Kint, Joeri title: Quantification of Infectious Bronchitis Coronavirus by Titration In Vitro and In Ovo date: 2014-12-18 pages: extension: .txt txt: ./txt/cord-257064-iafm3pcc.txt cache: ./cache/cord-257064-iafm3pcc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-257064-iafm3pcc.txt' === file2bib.sh === id: cord-272437-gvzfl8c3 author: Zhao, Jing title: Replicase 1a gene plays a critical role in pathogenesis of avian coronavirus infectious bronchitis virus date: 2020-08-20 pages: extension: .txt txt: ./txt/cord-272437-gvzfl8c3.txt cache: ./cache/cord-272437-gvzfl8c3.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272437-gvzfl8c3.txt' === file2bib.sh === id: cord-263193-paeosfiu author: Zhu, Jinyan title: Infectious bronchitis virus inhibits activation of the TLR7 pathway, but not the TLR3 pathway date: 2020-06-10 pages: extension: .txt txt: ./txt/cord-263193-paeosfiu.txt cache: ./cache/cord-263193-paeosfiu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263193-paeosfiu.txt' === file2bib.sh === id: cord-269024-re0hyolh author: Bande, Faruku title: Prediction and In Silico Identification of Novel B-Cells and T-Cells Epitopes in the S1-Spike Glycoprotein of M41 and CR88 (793/B) Infectious Bronchitis Virus Serotypes for Application in Peptide Vaccines date: 2016-09-07 pages: extension: .txt txt: ./txt/cord-269024-re0hyolh.txt cache: ./cache/cord-269024-re0hyolh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269024-re0hyolh.txt' === file2bib.sh === id: cord-294679-7pklrmz5 author: Wei, Lei title: Purification, crystallization and preliminary crystallographic analysis of avian infectious bronchitis virus nsp3 ADRP domain date: 2008-08-09 pages: extension: .txt txt: ./txt/cord-294679-7pklrmz5.txt cache: ./cache/cord-294679-7pklrmz5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-294679-7pklrmz5.txt' === file2bib.sh === id: cord-285052-aql0vrzv author: Kamble, Nitin Machindra title: Evolutionary and bioinformatic analysis of the spike glycoprotein gene of H120 vaccine strain protectotype of infectious bronchitis virus from India date: 2016-02-12 pages: extension: .txt txt: ./txt/cord-285052-aql0vrzv.txt cache: ./cache/cord-285052-aql0vrzv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-285052-aql0vrzv.txt' === file2bib.sh === id: cord-258379-v3lceirh author: Liu, D. X. title: Association of the infectious bronchitis virus 3c protein with the virion envelope date: 1991-12-31 pages: extension: .txt txt: ./txt/cord-258379-v3lceirh.txt cache: ./cache/cord-258379-v3lceirh.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258379-v3lceirh.txt' === file2bib.sh === id: cord-257999-apg4uhhq author: Ababneh, Mustafa title: Presence of Infectious Bronchitis Virus Strain CK/CH/LDL/97I in the Middle East date: 2012-04-11 pages: extension: .txt txt: ./txt/cord-257999-apg4uhhq.txt cache: ./cache/cord-257999-apg4uhhq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-257999-apg4uhhq.txt' === file2bib.sh === id: cord-265681-ab8j4o1u author: Boroomand, Zahra title: Pathogenesis and Tissue Distribution of Avian Infectious Bronchitis Virus Isolate IRFIBV32 (793/B Serotype) in Experimentally Infected Broiler Chickens date: 2012-04-01 pages: extension: .txt txt: ./txt/cord-265681-ab8j4o1u.txt cache: ./cache/cord-265681-ab8j4o1u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265681-ab8j4o1u.txt' === file2bib.sh === id: cord-265508-t1nfyzf5 author: Boursnell, M.E.G. title: Sequencing of coronavirus IBV genomic RNA: a 195-base open reading frame encoded by mRNA B date: 1984-08-31 pages: extension: .txt txt: ./txt/cord-265508-t1nfyzf5.txt cache: ./cache/cord-265508-t1nfyzf5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-265508-t1nfyzf5.txt' === file2bib.sh === id: cord-293081-40pa5g89 author: Li, Jun title: Preliminary crystallographic analysis of avian infectious bronchitis virus main protease date: 2006-12-16 pages: extension: .txt txt: ./txt/cord-293081-40pa5g89.txt cache: ./cache/cord-293081-40pa5g89.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293081-40pa5g89.txt' === file2bib.sh === id: cord-259959-qzd3hf8y author: Alhatami, Abdullah O. title: Sequencing and phylogenetic analysis of infectious bronchitis virus variant strain from an outbreak in egg-layer flocks in Baghdad, Iraq date: 2020-07-16 pages: extension: .txt txt: ./txt/cord-259959-qzd3hf8y.txt cache: ./cache/cord-259959-qzd3hf8y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259959-qzd3hf8y.txt' === file2bib.sh === id: cord-273846-l0elcfe8 author: Ganapathy, Kannan title: Effects of cold storage on detection of avian infectious bronchitis virus in chicken carcasses and local antibodies in tracheal washes date: 2005-02-24 pages: extension: .txt txt: ./txt/cord-273846-l0elcfe8.txt cache: ./cache/cord-273846-l0elcfe8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273846-l0elcfe8.txt' === file2bib.sh === id: cord-022187-7c3wz6c6 author: Liu, Shengwang title: A new genotype of nephropathogenic infectious bronchitis virus circulating in vaccinated and non-vaccinated flocks in China date: 2010-10-19 pages: extension: .txt txt: ./txt/cord-022187-7c3wz6c6.txt cache: ./cache/cord-022187-7c3wz6c6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-022187-7c3wz6c6.txt' === file2bib.sh === id: cord-271359-dpa8zzc3 author: Sapats, S. I. title: Novel Variation in the N Protein of Avian Infectious Bronchitis Virus date: 1996-12-15 pages: extension: .txt txt: ./txt/cord-271359-dpa8zzc3.txt cache: ./cache/cord-271359-dpa8zzc3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-271359-dpa8zzc3.txt' === file2bib.sh === id: cord-285330-td4vr0zv author: Mohammadi, Ali title: Viral quantity and pathological changes in broilers experimentally infected by IRFIBV32 isolate of infectious bronchitis virus date: 2015-11-12 pages: extension: .txt txt: ./txt/cord-285330-td4vr0zv.txt cache: ./cache/cord-285330-td4vr0zv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-285330-td4vr0zv.txt' === file2bib.sh === id: cord-288309-6pw7t512 author: Kusters, J. G. title: Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus date: 1990-12-31 pages: extension: .txt txt: ./txt/cord-288309-6pw7t512.txt cache: ./cache/cord-288309-6pw7t512.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-288309-6pw7t512.txt' === file2bib.sh === id: cord-260667-5aurua6o author: Falchieri, Marco title: Avian metapneumoviruses expressing Infectious Bronchitis virus genes are stable and induce protection date: 2013-05-24 pages: extension: .txt txt: ./txt/cord-260667-5aurua6o.txt cache: ./cache/cord-260667-5aurua6o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260667-5aurua6o.txt' === file2bib.sh === id: cord-004810-g0y7ied0 author: Lee, S. K. title: S1 glycoprotein gene analysis of infectious bronchitis viruses isolated in Korea date: 2003-11-13 pages: extension: .txt txt: ./txt/cord-004810-g0y7ied0.txt cache: ./cache/cord-004810-g0y7ied0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-004810-g0y7ied0.txt' === file2bib.sh === id: cord-253695-tjdw2uta author: Winter, Christine title: Infection of the tracheal epithelium by infectious bronchitis virus is sialic acid dependent date: 2007-12-28 pages: extension: .txt txt: ./txt/cord-253695-tjdw2uta.txt cache: ./cache/cord-253695-tjdw2uta.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-253695-tjdw2uta.txt' === file2bib.sh === id: cord-262940-eyejnexx author: Liu, Genmei title: Assembly and immunogenicity of coronavirus-like particles carrying infectious bronchitis virus M and S proteins date: 2013-11-12 pages: extension: .txt txt: ./txt/cord-262940-eyejnexx.txt cache: ./cache/cord-262940-eyejnexx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262940-eyejnexx.txt' === file2bib.sh === id: cord-022378-ovxmy1as author: Cook, Jane K.A. title: Coronaviridae date: 2009-05-15 pages: extension: .txt txt: ./txt/cord-022378-ovxmy1as.txt cache: ./cache/cord-022378-ovxmy1as.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-022378-ovxmy1as.txt' === file2bib.sh === id: cord-276755-ctzrgqe7 author: Emmott, Edward title: Elucidation of the avian nucleolar proteome by quantitative proteomics using SILAC and changes in cells infected with the coronavirus infectious bronchitis virus date: 2010-09-08 pages: extension: .txt txt: ./txt/cord-276755-ctzrgqe7.txt cache: ./cache/cord-276755-ctzrgqe7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-276755-ctzrgqe7.txt' === file2bib.sh === id: cord-277804-ujabzic4 author: Yuk, Seong-su title: Comparison between dot-immunoblotting assay and clinical sign determination method for quantifying avian infectious bronchitis virus vaccine by titration in embryonated eggs date: 2016-01-21 pages: extension: .txt txt: ./txt/cord-277804-ujabzic4.txt cache: ./cache/cord-277804-ujabzic4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277804-ujabzic4.txt' === file2bib.sh === id: cord-273661-egpyvqrw author: Mo, Mei-Lan title: Molecular Characterization of Major Structural Protein Genes of Avian Coronavirus Infectious Bronchitis Virus Isolates in Southern China date: 2013-12-04 pages: extension: .txt txt: ./txt/cord-273661-egpyvqrw.txt cache: ./cache/cord-273661-egpyvqrw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-273661-egpyvqrw.txt' === file2bib.sh === id: cord-278324-eqqvwwh6 author: Wang, Huanan title: Development of a sensitive and specific xMAP assay for detection of antibodies against infectious laryngotracheitis and bronchitis viruses date: 2018-09-21 pages: extension: .txt txt: ./txt/cord-278324-eqqvwwh6.txt cache: ./cache/cord-278324-eqqvwwh6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-278324-eqqvwwh6.txt' === file2bib.sh === id: cord-000924-wwuqxx1r author: Yan, Fang title: Protection of chickens against infectious bronchitis virus with a multivalent DNA vaccine and boosting with an inactivated vaccine date: 2013-03-24 pages: extension: .txt txt: ./txt/cord-000924-wwuqxx1r.txt cache: ./cache/cord-000924-wwuqxx1r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000924-wwuqxx1r.txt' === file2bib.sh === id: cord-265258-2rmtsyns author: Domanska‐Blicharz, K. title: Specific detection of GII‐1 lineage of infectious bronchitis virus date: 2017-07-03 pages: extension: .txt txt: ./txt/cord-265258-2rmtsyns.txt cache: ./cache/cord-265258-2rmtsyns.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-265258-2rmtsyns.txt' === file2bib.sh === id: cord-260799-kx6hfpu0 author: Mahmood, Zana H. title: Isolation and molecular characterization of Sul/01/09 avian infectious bronchitis virus, indicates the emergence of a new genotype in the Middle East date: 2011-05-12 pages: extension: .txt txt: ./txt/cord-260799-kx6hfpu0.txt cache: ./cache/cord-260799-kx6hfpu0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-260799-kx6hfpu0.txt' === file2bib.sh === id: cord-276550-1in7m56w author: Abdel-Moneim, Ahmed S title: S1 gene sequence analysis of a nephropathogenic strain of avian infectious bronchitis virus in Egypt date: 2006-09-20 pages: extension: .txt txt: ./txt/cord-276550-1in7m56w.txt cache: ./cache/cord-276550-1in7m56w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-276550-1in7m56w.txt' === file2bib.sh === id: cord-291174-rym84kni author: Yang, Yazhi title: A label-free electrochemical assay for coronavirus IBV H120 strain quantification based on equivalent substitution effect and AuNPs-assisted signal amplification date: 2020-10-23 pages: extension: .txt txt: ./txt/cord-291174-rym84kni.txt cache: ./cache/cord-291174-rym84kni.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291174-rym84kni.txt' === file2bib.sh === id: cord-281526-7t9e4lgn author: Yin, Lijuan title: Immunogenicity and protective efficacy of recombinant fusion proteins containing spike protein of infectious bronchitis virus and hemagglutinin of H3N2 influenza virus in chickens date: 2016-09-02 pages: extension: .txt txt: ./txt/cord-281526-7t9e4lgn.txt cache: ./cache/cord-281526-7t9e4lgn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281526-7t9e4lgn.txt' === file2bib.sh === id: cord-264716-igl25jhg author: Koo, B.S. title: Molecular survey of enteric viruses in commercial chicken farms in Korea with a history of enteritis date: 2013-11-01 pages: extension: .txt txt: ./txt/cord-264716-igl25jhg.txt cache: ./cache/cord-264716-igl25jhg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-264716-igl25jhg.txt' === file2bib.sh === id: cord-006991-2q5ore6g author: Chi, X. title: Oral administration of tea saponins to relive oxidative stress and immune suppression in chickens date: 2017-06-15 pages: extension: .txt txt: ./txt/cord-006991-2q5ore6g.txt cache: ./cache/cord-006991-2q5ore6g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-006991-2q5ore6g.txt' === file2bib.sh === id: cord-001768-8vljd5cv author: Awad, Faez title: Protection conferred by live infectious bronchitis vaccine viruses against variant Middle East IS/885/00-like and IS/1494/06-like isolates in commercial broiler chicks date: 2015-09-09 pages: extension: .txt txt: ./txt/cord-001768-8vljd5cv.txt cache: ./cache/cord-001768-8vljd5cv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001768-8vljd5cv.txt' === file2bib.sh === id: cord-263785-0iift8zy author: Zhang, Xiaorong title: Evaluation of the reproductive system development and egg-laying performance of hens infected with TW I-type infectious bronchitis virus date: 2020-07-31 pages: extension: .txt txt: ./txt/cord-263785-0iift8zy.txt cache: ./cache/cord-263785-0iift8zy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263785-0iift8zy.txt' === file2bib.sh === id: cord-003208-lwirkob3 author: Yan, Liping title: Novel protein chip for the detection of antibodies against infectious bronchitis virus date: 2018-09-17 pages: extension: .txt txt: ./txt/cord-003208-lwirkob3.txt cache: ./cache/cord-003208-lwirkob3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-003208-lwirkob3.txt' === file2bib.sh === id: cord-291718-cz1bi0ym author: Yu, Liping title: The papain-like protease of avian infectious bronchitis virus has deubiquitinating activity date: 2017-03-18 pages: extension: .txt txt: ./txt/cord-291718-cz1bi0ym.txt cache: ./cache/cord-291718-cz1bi0ym.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-291718-cz1bi0ym.txt' === file2bib.sh === id: cord-290638-7ro72sv3 author: Lenstra, Johannes A. title: Antigenicity of the peplomer protein of infectious bronchitis virus date: 1989-01-31 pages: extension: .txt txt: ./txt/cord-290638-7ro72sv3.txt cache: ./cache/cord-290638-7ro72sv3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-290638-7ro72sv3.txt' === file2bib.sh === id: cord-285323-473d7zvg author: Jang, Hyesun title: Altered pro-inflammatory cytokine mRNA levels in chickens infected with infectious bronchitis virus date: 2013-09-01 pages: extension: .txt txt: ./txt/cord-285323-473d7zvg.txt cache: ./cache/cord-285323-473d7zvg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-285323-473d7zvg.txt' === file2bib.sh === id: cord-279495-zxerb7de author: Liu, Xiaoli title: Comparative analysis of four Massachusetts type infectious bronchitis coronavirus genomes reveals a novel Massachusetts type strain and evidence of natural recombination in the genome date: 2012-11-21 pages: extension: .txt txt: ./txt/cord-279495-zxerb7de.txt cache: ./cache/cord-279495-zxerb7de.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-279495-zxerb7de.txt' === file2bib.sh === id: cord-268788-jcu3pasy author: Thor, Sharmi W. title: Recombination in Avian Gamma-Coronavirus Infectious Bronchitis Virus date: 2011-09-23 pages: extension: .txt txt: ./txt/cord-268788-jcu3pasy.txt cache: ./cache/cord-268788-jcu3pasy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268788-jcu3pasy.txt' === file2bib.sh === id: cord-299428-gon6bzat author: Mondal, Shankar title: Sequence analysis of infectious bronchitis virus isolates from the 1960s in the United States date: 2012-10-11 pages: extension: .txt txt: ./txt/cord-299428-gon6bzat.txt cache: ./cache/cord-299428-gon6bzat.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299428-gon6bzat.txt' === file2bib.sh === id: cord-293651-96cmduez author: Callison, Scott A. title: Development and evaluation of a real-time Taqman RT-PCR assay for the detection of infectious bronchitis virus from infected chickens date: 2006-08-28 pages: extension: .txt txt: ./txt/cord-293651-96cmduez.txt cache: ./cache/cord-293651-96cmduez.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-293651-96cmduez.txt' === file2bib.sh === id: cord-003334-ion97n4b author: De Silva Senapathi, Upasama title: The In Ovo Delivery of CpG Oligonucleotides Protects against Infectious Bronchitis with the Recruitment of Immune Cells into the Respiratory Tract of Chickens date: 2018-11-15 pages: extension: .txt txt: ./txt/cord-003334-ion97n4b.txt cache: ./cache/cord-003334-ion97n4b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-003334-ion97n4b.txt' === file2bib.sh === id: cord-261388-d56ci0hl author: Tibbles, K.W title: Activity of a purified His-tagged 3C-like proteinase from the coronavirus infectious bronchitis virus date: 1999-05-28 pages: extension: .txt txt: ./txt/cord-261388-d56ci0hl.txt cache: ./cache/cord-261388-d56ci0hl.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261388-d56ci0hl.txt' === file2bib.sh === id: cord-265499-pbf11zy1 author: Dove, Brian K. title: Changes in nucleolar morphology and proteins during infection with the coronavirus infectious bronchitis virus date: 2006-03-03 pages: extension: .txt txt: ./txt/cord-265499-pbf11zy1.txt cache: ./cache/cord-265499-pbf11zy1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265499-pbf11zy1.txt' === file2bib.sh === id: cord-262226-7kwkla73 author: Fang, Shouguo title: Identification of two ATR-dependent phosphorylation sites on coronavirus nucleocapsid protein with nonessential functions in viral replication and infectivity in cultured cells date: 2013-07-09 pages: extension: .txt txt: ./txt/cord-262226-7kwkla73.txt cache: ./cache/cord-262226-7kwkla73.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262226-7kwkla73.txt' === file2bib.sh === id: cord-255870-gmq5zs2d author: Liu, Shengwang title: Identification of the avian infectious bronchitis coronaviruses with mutations in gene 3 date: 2008-04-15 pages: extension: .txt txt: ./txt/cord-255870-gmq5zs2d.txt cache: ./cache/cord-255870-gmq5zs2d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255870-gmq5zs2d.txt' === file2bib.sh === id: cord-259738-yuqc6dk0 author: Tang, Mengjun title: Enhancement of the immunogenicity of an infectious bronchitis virus DNA vaccine by a bicistronic plasmid encoding nucleocapsid protein and interleukin-2 date: 2008-03-07 pages: extension: .txt txt: ./txt/cord-259738-yuqc6dk0.txt cache: ./cache/cord-259738-yuqc6dk0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259738-yuqc6dk0.txt' === file2bib.sh === id: cord-256859-7ixegm72 author: Liu, S. W. title: Genetic diversity of avian infectious bronchitis coronavirus strains isolated in China between 1995 and 2004 date: 2006-01-09 pages: extension: .txt txt: ./txt/cord-256859-7ixegm72.txt cache: ./cache/cord-256859-7ixegm72.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256859-7ixegm72.txt' === file2bib.sh === id: cord-282314-9cua2jzg author: Albanese, Grace A. title: Biological and molecular characterization of ArkGA: A novel Arkansas serotype vaccine that is highly attenuated, efficacious, and protective against homologous challenge date: 2018-10-01 pages: extension: .txt txt: ./txt/cord-282314-9cua2jzg.txt cache: ./cache/cord-282314-9cua2jzg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-282314-9cua2jzg.txt' === file2bib.sh === id: cord-266585-jfjrk9gy author: Fang, Shouguo title: An arginine-to-proline mutation in a domain with undefined functions within the helicase protein (Nsp13) is lethal to the coronavirus infectious bronchitis virus in cultured cells date: 2007-02-05 pages: extension: .txt txt: ./txt/cord-266585-jfjrk9gy.txt cache: ./cache/cord-266585-jfjrk9gy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266585-jfjrk9gy.txt' === file2bib.sh === id: cord-263178-lvxxdvas author: Shan, Dan title: Effects of hypervariable regions in spike protein on pathogenicity, tropism, and serotypes of infectious bronchitis virus date: 2018-05-02 pages: extension: .txt txt: ./txt/cord-263178-lvxxdvas.txt cache: ./cache/cord-263178-lvxxdvas.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263178-lvxxdvas.txt' === file2bib.sh === id: cord-280442-jtvez46y author: Wu, Xuan title: Simultaneous and visual detection of infectious bronchitis virus and Newcastle disease virus by multiple LAMP and lateral flow dipstick date: 2019-11-01 pages: extension: .txt txt: ./txt/cord-280442-jtvez46y.txt cache: ./cache/cord-280442-jtvez46y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-280442-jtvez46y.txt' === file2bib.sh === id: cord-272305-eniovfwy author: Zhao, Ye title: Safety and efficacy of an attenuated Chinese QX-like infectious bronchitis virus strain as a candidate vaccine date: 2015-10-22 pages: extension: .txt txt: ./txt/cord-272305-eniovfwy.txt cache: ./cache/cord-272305-eniovfwy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272305-eniovfwy.txt' === file2bib.sh === id: cord-285942-mb1xwdqw author: Feng, K. Y. title: Molecular characteristic and pathogenicity analysis of a virulent recombinant avain infectious bronchitis virus isolated in China date: 2018-10-01 pages: extension: .txt txt: ./txt/cord-285942-mb1xwdqw.txt cache: ./cache/cord-285942-mb1xwdqw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-285942-mb1xwdqw.txt' === file2bib.sh === id: cord-259480-1tqfoecc author: Li, Huixin title: Recombinant duck enteritis viruses expressing major structural proteins of the infectious bronchitis virus provide protection against infectious bronchitis in chickens date: 2016-03-02 pages: extension: .txt txt: ./txt/cord-259480-1tqfoecc.txt cache: ./cache/cord-259480-1tqfoecc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259480-1tqfoecc.txt' === file2bib.sh === id: cord-263476-ju7xqwa7 author: Xia, Jing title: Phylogenetic and antigenic analysis of avian infectious bronchitis virus in southwestern China, 2012–2016 date: 2016-08-13 pages: extension: .txt txt: ./txt/cord-263476-ju7xqwa7.txt cache: ./cache/cord-263476-ju7xqwa7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263476-ju7xqwa7.txt' === file2bib.sh === id: cord-255619-5h3l6nh6 author: Kuo, Shu-Ming title: Evolution of infectious bronchitis virus in Taiwan: Positively selected sites in the nucleocapsid protein and their effects on RNA-binding activity date: 2013-03-23 pages: extension: .txt txt: ./txt/cord-255619-5h3l6nh6.txt cache: ./cache/cord-255619-5h3l6nh6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-255619-5h3l6nh6.txt' === file2bib.sh === id: cord-255141-55ho9av4 author: Abolnik, Celia title: Genomic and single nucleotide polymorphism analysis of infectious bronchitis coronavirus date: 2015-04-03 pages: extension: .txt txt: ./txt/cord-255141-55ho9av4.txt cache: ./cache/cord-255141-55ho9av4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255141-55ho9av4.txt' === file2bib.sh === id: cord-010608-eaa2znom author: Butt, Salman L. title: Real-time, MinION-based, amplicon sequencing for lineage typing of infectious bronchitis virus from upper respiratory samples date: 2020-03-05 pages: extension: .txt txt: ./txt/cord-010608-eaa2znom.txt cache: ./cache/cord-010608-eaa2znom.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-010608-eaa2znom.txt' === file2bib.sh === id: cord-260042-cs0wp99n author: Khan, Samiullah title: Genes involved in mitochondrial biogenesis and function may not show synchronised responses to mitochondria in shell gland of laying chickens under infectious bronchitis virus challenge date: 2019-04-01 pages: extension: .txt txt: ./txt/cord-260042-cs0wp99n.txt cache: ./cache/cord-260042-cs0wp99n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-260042-cs0wp99n.txt' === file2bib.sh === id: cord-300104-855iw9wi author: Hennion, Ruth M. title: The Preparation of Chicken Kidney Cell Cultures for Virus Propagation date: 2014-12-18 pages: extension: .txt txt: ./txt/cord-300104-855iw9wi.txt cache: ./cache/cord-300104-855iw9wi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-300104-855iw9wi.txt' === file2bib.sh === id: cord-284501-5i0w74q4 author: Armesto, Maria title: The Replicase Gene of Avian Coronavirus Infectious Bronchitis Virus Is a Determinant of Pathogenicity date: 2009-10-09 pages: extension: .txt txt: ./txt/cord-284501-5i0w74q4.txt cache: ./cache/cord-284501-5i0w74q4.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-284501-5i0w74q4.txt' === file2bib.sh === id: cord-259505-7hiss0j3 author: Kong, Qingming title: Proteomic analysis of purified coronavirus infectious bronchitis virus particles date: 2010-06-09 pages: extension: .txt txt: ./txt/cord-259505-7hiss0j3.txt cache: ./cache/cord-259505-7hiss0j3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-259505-7hiss0j3.txt' === file2bib.sh === id: cord-252048-ftbjsoup author: McKinley, Enid T. title: Attenuated live vaccine usage affects accurate measures of virus diversity and mutation rates in avian coronavirus infectious bronchitis virus date: 2011-04-22 pages: extension: .txt txt: ./txt/cord-252048-ftbjsoup.txt cache: ./cache/cord-252048-ftbjsoup.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-252048-ftbjsoup.txt' === file2bib.sh === id: cord-269150-d1sgnxc0 author: Tan, Yong Wah title: Binding of the 5′-untranslated region of coronavirus RNA to zinc finger CCHC-type and RNA-binding motif 1 enhances viral replication and transcription date: 2012-02-22 pages: extension: .txt txt: ./txt/cord-269150-d1sgnxc0.txt cache: ./cache/cord-269150-d1sgnxc0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-269150-d1sgnxc0.txt' === file2bib.sh === id: cord-286473-sl5zy8nj author: Gomaa, M.H. title: Complete genomic sequence of turkey coronavirus date: 2008-05-12 pages: extension: .txt txt: ./txt/cord-286473-sl5zy8nj.txt cache: ./cache/cord-286473-sl5zy8nj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-286473-sl5zy8nj.txt' === file2bib.sh === id: cord-308950-bl83r4v3 author: Miguel, B. title: The role of feline aminopeptidase N as a receptor for infectious bronchitis virus : Brief Review date: 2002 pages: extension: .txt txt: ./txt/cord-308950-bl83r4v3.txt cache: ./cache/cord-308950-bl83r4v3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-308950-bl83r4v3.txt' === file2bib.sh === id: cord-001083-vy1nxax2 author: Malagnac, Fabienne title: Rab-GDI Complex Dissociation Factor Expressed through Translational Frameshifting in Filamentous Ascomycetes date: 2013-09-19 pages: extension: .txt txt: ./txt/cord-001083-vy1nxax2.txt cache: ./cache/cord-001083-vy1nxax2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001083-vy1nxax2.txt' === file2bib.sh === id: cord-260145-grz0fe9l author: Liu, Shengwang title: Altered pathogenicity, immunogenicity, tissue tropism and 3′-7 kb region sequence of an avian infectious bronchitis coronavirus strain after serial passage in embryos date: 2009-07-23 pages: extension: .txt txt: ./txt/cord-260145-grz0fe9l.txt cache: ./cache/cord-260145-grz0fe9l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-260145-grz0fe9l.txt' === file2bib.sh === id: cord-303588-bwllypvq author: Ababneh, Mustafa title: High-resolution melting curve analysis for infectious bronchitis virus strain differentiation date: 2020-03-03 pages: extension: .txt txt: ./txt/cord-303588-bwllypvq.txt cache: ./cache/cord-303588-bwllypvq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303588-bwllypvq.txt' === file2bib.sh === id: cord-003148-o7y3wygc author: Shirvani, Edris title: A Recombinant Newcastle Disease Virus (NDV) Expressing S Protein of Infectious Bronchitis Virus (IBV) Protects Chickens against IBV and NDV date: 2018-08-10 pages: extension: .txt txt: ./txt/cord-003148-o7y3wygc.txt cache: ./cache/cord-003148-o7y3wygc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003148-o7y3wygc.txt' === file2bib.sh === id: cord-272693-432ixb7g author: Phillips, J. E. title: Changes in nonstructural protein 3 are associated with attenuation in avian coronavirus infectious bronchitis virus date: 2011-09-10 pages: extension: .txt txt: ./txt/cord-272693-432ixb7g.txt cache: ./cache/cord-272693-432ixb7g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272693-432ixb7g.txt' === file2bib.sh === id: cord-273366-xd84f8ct author: Brownsword, Matthew J. title: Infectious Bronchitis Virus Regulates Cellular Stress Granule Signaling date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-273366-xd84f8ct.txt cache: ./cache/cord-273366-xd84f8ct.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-273366-xd84f8ct.txt' === file2bib.sh === id: cord-304322-k9egxskw author: Promkuntod, N. title: Analysis of the S1 gene of the avian infectious bronchitis virus (IBV) reveals changes in the IBV genetic groups circulating in southern Thailand date: 2015-06-30 pages: extension: .txt txt: ./txt/cord-304322-k9egxskw.txt cache: ./cache/cord-304322-k9egxskw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304322-k9egxskw.txt' === file2bib.sh === id: cord-291754-1zxztadu author: Zhao, Ye title: Successful establishment of a reverse genetic system for QX-type infectious bronchitis virus and technical improvement of the rescue procedure date: 2019-10-15 pages: extension: .txt txt: ./txt/cord-291754-1zxztadu.txt cache: ./cache/cord-291754-1zxztadu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291754-1zxztadu.txt' === file2bib.sh === id: cord-306380-msk9p1yy author: Lee, C.-W. title: Evidence of genetic diversity generated by recombination among avian coronavirus IBV date: 2000 pages: extension: .txt txt: ./txt/cord-306380-msk9p1yy.txt cache: ./cache/cord-306380-msk9p1yy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-306380-msk9p1yy.txt' === file2bib.sh === id: cord-319253-8bssrn9o author: OKINO, Cintia Hiromi title: Rapid detection and differentiation of avian infectious bronchitis virus: an application of Mass genotype by melting temperature analysis in RT-qPCR using SYBR Green I date: 2018-02-27 pages: extension: .txt txt: ./txt/cord-319253-8bssrn9o.txt cache: ./cache/cord-319253-8bssrn9o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-319253-8bssrn9o.txt' === file2bib.sh === id: cord-301720-majpfxqn author: Saadat, Yousef title: Molecular characterization of infectious bronchitis viruses isolated from broiler flocks in Bushehr province, Iran: 2014 - 2015 date: 2017-09-15 pages: extension: .txt txt: ./txt/cord-301720-majpfxqn.txt cache: ./cache/cord-301720-majpfxqn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-301720-majpfxqn.txt' === file2bib.sh === id: cord-303393-9zs3qqo4 author: Alsultan, Musaed Abdulaziz title: Infectious bronchitis virus from chickens in Al-Hasa, Saudi Arabia 2015-2016 date: 2019-03-19 pages: extension: .txt txt: ./txt/cord-303393-9zs3qqo4.txt cache: ./cache/cord-303393-9zs3qqo4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-303393-9zs3qqo4.txt' === file2bib.sh === id: cord-303794-fn3jkiil author: Hassan, Kareem E. title: Experimental co-infection of infectious bronchitis and low pathogenic avian influenza H9N2 viruses in commercial broiler chickens date: 2017-06-30 pages: extension: .txt txt: ./txt/cord-303794-fn3jkiil.txt cache: ./cache/cord-303794-fn3jkiil.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-303794-fn3jkiil.txt' === file2bib.sh === id: cord-316525-uadfehr6 author: Zhang, X. W. title: Testing the hypothesis of a recombinant origin of the SARS-associated coronavirus date: 2004-10-11 pages: extension: .txt txt: ./txt/cord-316525-uadfehr6.txt cache: ./cache/cord-316525-uadfehr6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316525-uadfehr6.txt' === file2bib.sh === id: cord-309469-2naxn580 author: An, Hongliu title: Identification and formation mechanism of a novel noncoding RNA produced by avian infectious bronchitis virus date: 2019-01-05 pages: extension: .txt txt: ./txt/cord-309469-2naxn580.txt cache: ./cache/cord-309469-2naxn580.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309469-2naxn580.txt' === file2bib.sh === id: cord-310372-qc6941pm author: Ji, Jun title: Phylogenetic distribution and predominant genotype of the avian infectious bronchitis virus in China during 2008-2009 date: 2011-04-22 pages: extension: .txt txt: ./txt/cord-310372-qc6941pm.txt cache: ./cache/cord-310372-qc6941pm.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-310372-qc6941pm.txt' === file2bib.sh === id: cord-305079-foifc8ch author: Zhou, Ying Shun title: Establishment of reverse genetics system for infectious bronchitis virus attenuated vaccine strain H120 date: 2013-02-22 pages: extension: .txt txt: ./txt/cord-305079-foifc8ch.txt cache: ./cache/cord-305079-foifc8ch.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-305079-foifc8ch.txt' === file2bib.sh === id: cord-316153-wet0go35 author: Jia, W. title: A novel variant of avian infectious bronchitis virus resulting from recombination among three different strains date: 1995 pages: extension: .txt txt: ./txt/cord-316153-wet0go35.txt cache: ./cache/cord-316153-wet0go35.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316153-wet0go35.txt' === file2bib.sh === id: cord-309623-2ngr682l author: Han, Xiaoxiao title: Infectious Bronchitis Virus Infection Induces Apoptosis during Replication in Chicken Macrophage HD11 Cells date: 2017-07-26 pages: extension: .txt txt: ./txt/cord-309623-2ngr682l.txt cache: ./cache/cord-309623-2ngr682l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-309623-2ngr682l.txt' === file2bib.sh === id: cord-301810-vtgdqart author: Aston, Emily J. title: Effect of Pullet Vaccination on Development and Longevity of Immunity date: 2019-02-02 pages: extension: .txt txt: ./txt/cord-301810-vtgdqart.txt cache: ./cache/cord-301810-vtgdqart.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-301810-vtgdqart.txt' === file2bib.sh === id: cord-308591-cs8os2f5 author: Tawakol, Maram M. title: Evaluation of bacteriophage efficacy in reducing the impact of single and mixed infections with Escherichia coli and infectious bronchitis in chickens date: 2019-11-29 pages: extension: .txt txt: ./txt/cord-308591-cs8os2f5.txt cache: ./cache/cord-308591-cs8os2f5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-308591-cs8os2f5.txt' === file2bib.sh === id: cord-346516-lal35iyr author: Hughes, Laura A. title: Genetically Diverse Coronaviruses in Wild Bird Populations of Northern England date: 2009-07-17 pages: extension: .txt txt: ./txt/cord-346516-lal35iyr.txt cache: ./cache/cord-346516-lal35iyr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-346516-lal35iyr.txt' === file2bib.sh === id: cord-310536-u30cufg7 author: Finger, Paula Fonseca title: Combined use of ELISA and Western blot with recombinant N protein is a powerful tool for the immunodiagnosis of avian infectious bronchitis date: 2018-12-12 pages: extension: .txt txt: ./txt/cord-310536-u30cufg7.txt cache: ./cache/cord-310536-u30cufg7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-310536-u30cufg7.txt' === file2bib.sh === id: cord-337128-yyz7z0xj author: Abdel-Moneim, Ahmed S title: Immunohistochemistry for detection of avian infectious bronchitis virus strain M41 in the proventriculus and nervous system of experimentally infected chicken embryos date: 2009-02-05 pages: extension: .txt txt: ./txt/cord-337128-yyz7z0xj.txt cache: ./cache/cord-337128-yyz7z0xj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-337128-yyz7z0xj.txt' === file2bib.sh === id: cord-339235-8xslz4bs author: Boroomand, Zahra title: Molecular detection and phylogenetic properties of isolated infectious bronchitis viruses from broilers in Ahvaz, southwest Iran, based on partial sequences of spike gene date: 2018-09-15 pages: extension: .txt txt: ./txt/cord-339235-8xslz4bs.txt cache: ./cache/cord-339235-8xslz4bs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339235-8xslz4bs.txt' === file2bib.sh === id: cord-321545-3gzj09mr author: Pohuang, Tawatchai title: Detection and molecular characterization of infectious bronchitis virus isolated from recent outbreaks in broiler flocks in Thailand date: 2009-09-07 pages: extension: .txt txt: ./txt/cord-321545-3gzj09mr.txt cache: ./cache/cord-321545-3gzj09mr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321545-3gzj09mr.txt' === file2bib.sh === id: cord-341541-3l6tjf3t author: Hajijafari Anaraki, Mozafar title: Molecular characterization of infectious bronchitis virus based on RNA‐dependent RNA polymerase gene date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-341541-3l6tjf3t.txt cache: ./cache/cord-341541-3l6tjf3t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-341541-3l6tjf3t.txt' === file2bib.sh === id: cord-346629-770qyee8 author: Mase, M. title: Phylogenetic analysis of avian infectious bronchitis virus strains isolated in Japan date: 2004-07-15 pages: extension: .txt txt: ./txt/cord-346629-770qyee8.txt cache: ./cache/cord-346629-770qyee8.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346629-770qyee8.txt' === file2bib.sh === id: cord-337441-c5bxthwn author: You, Jae-Hwan title: Three-Dimensional Reconstruction of the Nucleolus Using Meta-Confocal Microscopy in Cells Expressing the Coronavirus Nucleoprotein date: 2006 pages: extension: .txt txt: ./txt/cord-337441-c5bxthwn.txt cache: ./cache/cord-337441-c5bxthwn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-337441-c5bxthwn.txt' === file2bib.sh === id: cord-306976-p2521bl4 author: Gao, Mengying title: Serotype, antigenicity, and pathogenicity of a naturally recombinant TW I genotype infectious bronchitis coronavirus in China date: 2016-08-15 pages: extension: .txt txt: ./txt/cord-306976-p2521bl4.txt cache: ./cache/cord-306976-p2521bl4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-306976-p2521bl4.txt' === file2bib.sh === id: cord-312489-ywep0c08 author: Andoh, Kiyohiko title: Decreased neutralizing antigenicity in IBV S1 protein expressed from mammalian cells date: 2015-10-02 pages: extension: .txt txt: ./txt/cord-312489-ywep0c08.txt cache: ./cache/cord-312489-ywep0c08.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-312489-ywep0c08.txt' === file2bib.sh === id: cord-305684-ipeup5mp author: Chen, Yuqiu title: Identification and molecular characterization of a novel serotype infectious bronchitis virus (GI-28) in China date: 2016-12-16 pages: extension: .txt txt: ./txt/cord-305684-ipeup5mp.txt cache: ./cache/cord-305684-ipeup5mp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305684-ipeup5mp.txt' === file2bib.sh === id: cord-317347-by8albr9 author: van Ginkel, Frederik W. title: Age-dependent immune responses and immune protection after avian coronavirus vaccination date: 2015-05-28 pages: extension: .txt txt: ./txt/cord-317347-by8albr9.txt cache: ./cache/cord-317347-by8albr9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-317347-by8albr9.txt' === file2bib.sh === id: cord-316234-vtjsfi2c author: Sultankulova, Kulyaisan T. title: New oligonucleotide microarray for rapid diagnosis of avian viral diseases date: 2017-04-05 pages: extension: .txt txt: ./txt/cord-316234-vtjsfi2c.txt cache: ./cache/cord-316234-vtjsfi2c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316234-vtjsfi2c.txt' === file2bib.sh === id: cord-329429-ur8g68vp author: Miłek, Justyna title: Coronaviruses in Avian Species – Review with Focus on Epidemiology and Diagnosis in Wild Birds date: 2018-12-10 pages: extension: .txt txt: ./txt/cord-329429-ur8g68vp.txt cache: ./cache/cord-329429-ur8g68vp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329429-ur8g68vp.txt' === file2bib.sh === id: cord-321602-88b2h06y author: Lv, Chenfei title: Construction of an infectious bronchitis virus vaccine strain carrying chimeric S1 gene of a virulent isolate and its pathogenicity analysis date: 2020-08-19 pages: extension: .txt txt: ./txt/cord-321602-88b2h06y.txt cache: ./cache/cord-321602-88b2h06y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-321602-88b2h06y.txt' === file2bib.sh === id: cord-307304-irji8owi author: Britton, Paul title: Generation of a recombinant avian coronavirus infectious bronchitis virus using transient dominant selection date: 2004-11-05 pages: extension: .txt txt: ./txt/cord-307304-irji8owi.txt cache: ./cache/cord-307304-irji8owi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-307304-irji8owi.txt' === file2bib.sh === id: cord-321261-3lp54mmu author: Kuo, Shu-Ming title: Evolution of infectious bronchitis virus in Taiwan: Characterisation of RNA recombination in the nucleocapsid gene date: 2010-08-26 pages: extension: .txt txt: ./txt/cord-321261-3lp54mmu.txt cache: ./cache/cord-321261-3lp54mmu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321261-3lp54mmu.txt' === file2bib.sh === id: cord-322410-k23engcx author: Naguib, Mahmoud M. title: New real time and conventional RT-PCRs for updated molecular diagnosis of infectious bronchitis virus infection (IBV) in chickens in Egypt associated with frequent co-infections with avian influenza and Newcastle Disease viruses date: 2017-03-21 pages: extension: .txt txt: ./txt/cord-322410-k23engcx.txt cache: ./cache/cord-322410-k23engcx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-322410-k23engcx.txt' === file2bib.sh === id: cord-349149-nqsohp9h author: Lounas, A. title: The first evidence of a new genotype of nephropathogenic infectious bronchitis virus circulating in vaccinated and unvaccinated broiler flocks in Algeria date: 2018-11-29 pages: extension: .txt txt: ./txt/cord-349149-nqsohp9h.txt cache: ./cache/cord-349149-nqsohp9h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-349149-nqsohp9h.txt' === file2bib.sh === id: cord-313676-6rebpe57 author: De la Torre, David I. title: Enteric Virus Diversity Examined by Molecular Methods in Brazilian Poultry Flocks date: 2018-03-29 pages: extension: .txt txt: ./txt/cord-313676-6rebpe57.txt cache: ./cache/cord-313676-6rebpe57.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313676-6rebpe57.txt' === file2bib.sh === id: cord-330260-xuw31zfn author: Chen, Hui-Wen title: Identification of Taiwan and China-like recombinant avian infectious bronchitis viruses in Taiwan date: 2009-01-20 pages: extension: .txt txt: ./txt/cord-330260-xuw31zfn.txt cache: ./cache/cord-330260-xuw31zfn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330260-xuw31zfn.txt' === file2bib.sh === id: cord-318400-l9kwxsq7 author: Chhabra, Rajesh title: Pathogenicity and tissue tropism of infectious bronchitis virus is associated with elevated apoptosis and innate immune responses date: 2016-01-15 pages: extension: .txt txt: ./txt/cord-318400-l9kwxsq7.txt cache: ./cache/cord-318400-l9kwxsq7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-318400-l9kwxsq7.txt' === file2bib.sh === id: cord-319168-i23pqiwx author: Abro, Shahid Hussain title: Emergence of novel strains of avian infectious bronchitis virus in Sweden date: 2012-03-23 pages: extension: .txt txt: ./txt/cord-319168-i23pqiwx.txt cache: ./cache/cord-319168-i23pqiwx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-319168-i23pqiwx.txt' === file2bib.sh === id: cord-351564-nikcd44o author: Zhang, Xiaozhan title: Molecular characterization of variant infectious bronchitis virus in China, 2019: Implications for control programmes date: 2020-01-24 pages: extension: .txt txt: ./txt/cord-351564-nikcd44o.txt cache: ./cache/cord-351564-nikcd44o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351564-nikcd44o.txt' === file2bib.sh === id: cord-334090-66d8c75g author: Seger, Waleed title: Genotyping of infectious bronchitis viruses from broiler farms in Iraq during 2014-2015 date: 2016-02-18 pages: extension: .txt txt: ./txt/cord-334090-66d8c75g.txt cache: ./cache/cord-334090-66d8c75g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334090-66d8c75g.txt' === file2bib.sh === id: cord-353027-bc0un6kb author: Ali, Ahmed title: Safety and efficacy of attenuated classic and variant 2 infectious bronchitis virus candidate vaccines date: 2018-08-06 pages: extension: .txt txt: ./txt/cord-353027-bc0un6kb.txt cache: ./cache/cord-353027-bc0un6kb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-353027-bc0un6kb.txt' === file2bib.sh === id: cord-344297-qqohijqi author: Smith, Jacqueline title: The early immune response to infection of chickens with Infectious Bronchitis Virus (IBV) in susceptible and resistant birds date: 2015-10-09 pages: extension: .txt txt: ./txt/cord-344297-qqohijqi.txt cache: ./cache/cord-344297-qqohijqi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344297-qqohijqi.txt' === file2bib.sh === id: cord-344745-sgkq1l93 author: Selim, Karim title: Molecular characterization of infectious bronchitis viruses isolated from broiler and layer chicken farms in Egypt during 2012 date: 2013-11-18 pages: extension: .txt txt: ./txt/cord-344745-sgkq1l93.txt cache: ./cache/cord-344745-sgkq1l93.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-344745-sgkq1l93.txt' === file2bib.sh === id: cord-328046-5us4se5o author: Xu, H. Y. title: Further Identification and Characterization of Novel Intermediate and Mature Cleavage Products Released from the ORF 1b Region of the Avian Coronavirus Infectious Bronchitis Virus 1a/1b Polyprotein date: 2001-09-30 pages: extension: .txt txt: ./txt/cord-328046-5us4se5o.txt cache: ./cache/cord-328046-5us4se5o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-328046-5us4se5o.txt' === file2bib.sh === id: cord-339259-4oi7slk9 author: Naguib, Mahmoud M. title: Full genome sequence analysis of a newly emerged QX-like infectious bronchitis virus from Sudan reveals distinct spots of recombination date: 2016-10-26 pages: extension: .txt txt: ./txt/cord-339259-4oi7slk9.txt cache: ./cache/cord-339259-4oi7slk9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339259-4oi7slk9.txt' === file2bib.sh === id: cord-322516-wekvet6f author: Maceyka, Michael title: Ceramide Accumulation Uncovers a Cycling Pathway for the cis-Golgi Network Marker, Infectious Bronchitis Virus M Protein date: 1997-12-15 pages: extension: .txt txt: ./txt/cord-322516-wekvet6f.txt cache: ./cache/cord-322516-wekvet6f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322516-wekvet6f.txt' === file2bib.sh === id: cord-335310-61wibso4 author: Chen, Hui-Wen title: Synthetic virus-like particles prepared via protein corona formation enable effective vaccination in an avian model of coronavirus infection date: 2016-08-15 pages: extension: .txt txt: ./txt/cord-335310-61wibso4.txt cache: ./cache/cord-335310-61wibso4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-335310-61wibso4.txt' === file2bib.sh === id: cord-348660-qnbgywgy author: Yilmaz, Huseyin title: Production of Recombinant N Protein of Infectious Bronchitis Virus Using the Baculovirus Expression System and Its Assessment as a Diagnostic Antigen date: 2018-07-09 pages: extension: .txt txt: ./txt/cord-348660-qnbgywgy.txt cache: ./cache/cord-348660-qnbgywgy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-348660-qnbgywgy.txt' === file2bib.sh === id: cord-331740-yjt3q9ph author: Jones, R. M. title: Development and Validation of RT‐PCR Tests for the Detection and S1 Genotyping of Infectious Bronchitis Virus and Other Closely Related Gammacoronaviruses Within Clinical Samples date: 2011-04-07 pages: extension: .txt txt: ./txt/cord-331740-yjt3q9ph.txt cache: ./cache/cord-331740-yjt3q9ph.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-331740-yjt3q9ph.txt' === file2bib.sh === id: cord-329497-3jow4xbn author: Promkuntod, Naruepol title: Dynamics of avian coronavirus circulation in commercial and non-commercial birds in Asia – a review date: 2015-12-28 pages: extension: .txt txt: ./txt/cord-329497-3jow4xbn.txt cache: ./cache/cord-329497-3jow4xbn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-329497-3jow4xbn.txt' === file2bib.sh === id: cord-343893-sophqqne author: Chu, Victor C title: Feline aminopeptidase N is not a functional receptor for avian infectious bronchitis virus date: 2007-02-26 pages: extension: .txt txt: ./txt/cord-343893-sophqqne.txt cache: ./cache/cord-343893-sophqqne.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343893-sophqqne.txt' === file2bib.sh === id: cord-354547-eomm1sl5 author: Wang, Jibin title: Interaction of the Coronavirus Infectious Bronchitis Virus Membrane Protein with β-Actin and Its Implication in Virion Assembly and Budding date: 2009-03-16 pages: extension: .txt txt: ./txt/cord-354547-eomm1sl5.txt cache: ./cache/cord-354547-eomm1sl5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-354547-eomm1sl5.txt' === file2bib.sh === id: cord-330057-3vucm0s1 author: Franzo, Giovanni title: Phylodynamic analysis and evaluation of the balance between anthropic and environmental factors affecting IBV spreading among Italian poultry farms date: 2020-04-29 pages: extension: .txt txt: ./txt/cord-330057-3vucm0s1.txt cache: ./cache/cord-330057-3vucm0s1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330057-3vucm0s1.txt' === file2bib.sh === id: cord-342354-j10m2dfh author: Chen, Huijie title: Protective effects of hypericin against infectious bronchitis virus induced apoptosis and reactive oxygen species in chicken embryo kidney cells date: 2019-12-31 pages: extension: .txt txt: ./txt/cord-342354-j10m2dfh.txt cache: ./cache/cord-342354-j10m2dfh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342354-j10m2dfh.txt' === file2bib.sh === id: cord-329468-vjsurl60 author: Okino, Cintia Hiromi title: Early immune responses and development of pathogenesis of avian infectious bronchitis viruses with different virulence profiles date: 2017-02-15 pages: extension: .txt txt: ./txt/cord-329468-vjsurl60.txt cache: ./cache/cord-329468-vjsurl60.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329468-vjsurl60.txt' === file2bib.sh === id: cord-329245-6tj2k1yn author: Corse, Emily title: The cytoplasmic tails of infectious bronchitis virus E and M proteins mediate their interaction date: 2003-07-20 pages: extension: .txt txt: ./txt/cord-329245-6tj2k1yn.txt cache: ./cache/cord-329245-6tj2k1yn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329245-6tj2k1yn.txt' === file2bib.sh === id: cord-323568-s0wmll4q author: Shang, Jian title: Cryo-EM structure of infectious bronchitis coronavirus spike protein reveals structural and functional evolution of coronavirus spike proteins date: 2018-04-23 pages: extension: .txt txt: ./txt/cord-323568-s0wmll4q.txt cache: ./cache/cord-323568-s0wmll4q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323568-s0wmll4q.txt' === file2bib.sh === id: cord-355703-l9l4ybfn author: Zhao, Fei title: Genomic Characteristics and Changes of Avian Infectious Bronchitis Virus Strain CK/CH/LDL/97I after Serial Passages in Chicken Embryos date: 2014-08-29 pages: extension: .txt txt: ./txt/cord-355703-l9l4ybfn.txt cache: ./cache/cord-355703-l9l4ybfn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-355703-l9l4ybfn.txt' === file2bib.sh === id: cord-353310-19kzb6ag author: Quinteros, José A. title: Analysis of the complete genomic sequences of two virus subpopulations of the Australian infectious bronchitis virus vaccine VicS date: 2015-04-01 pages: extension: .txt txt: ./txt/cord-353310-19kzb6ag.txt cache: ./cache/cord-353310-19kzb6ag.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353310-19kzb6ag.txt' === file2bib.sh === id: cord-331020-lyxje82u author: M. Najimudeen, Shahnas title: Infectious Bronchitis Coronavirus Infection in Chickens: Multiple System Disease with Immune Suppression date: 2020-09-24 pages: extension: .txt txt: ./txt/cord-331020-lyxje82u.txt cache: ./cache/cord-331020-lyxje82u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-331020-lyxje82u.txt' === file2bib.sh === id: cord-317587-rrx2r4n2 author: Fan, Wensheng title: Genetic Analysis of Avian Coronavirus Infectious Bronchitis Virus in Yellow Chickens in Southern China over the Past Decade: Revealing the Changes of Genetic Diversity, Dominant Genotypes, and Selection Pressure date: 2019-09-26 pages: extension: .txt txt: ./txt/cord-317587-rrx2r4n2.txt cache: ./cache/cord-317587-rrx2r4n2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-317587-rrx2r4n2.txt' === file2bib.sh === id: cord-352511-gkm7i62s author: Yamada, Yoshiyuki title: Acquisition of Cell–Cell Fusion Activity by Amino Acid Substitutions in Spike Protein Determines the Infectivity of a Coronavirus in Cultured Cells date: 2009-07-02 pages: extension: .txt txt: ./txt/cord-352511-gkm7i62s.txt cache: ./cache/cord-352511-gkm7i62s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-352511-gkm7i62s.txt' === file2bib.sh === id: cord-345630-bam3pa70 author: Lee, Han-Jung title: The complete sequence (22 kilobases) of murine coronavirus gene 1 encoding the putative proteases and RNA polymerase date: 1991-02-28 pages: extension: .txt txt: ./txt/cord-345630-bam3pa70.txt cache: ./cache/cord-345630-bam3pa70.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-345630-bam3pa70.txt' === file2bib.sh === id: cord-326319-3538jmqd author: Yuan, Yuan title: Protection against Virulent Infectious Bronchitis Virus Challenge Conferred by a Recombinant Baculovirus Co-Expressing S1 and N Proteins date: 2018-06-27 pages: extension: .txt txt: ./txt/cord-326319-3538jmqd.txt cache: ./cache/cord-326319-3538jmqd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-326319-3538jmqd.txt' === file2bib.sh === id: cord-304278-0qy1nngs author: Raj, G. Dhinakar title: Infectious bronchitis virus: immunopathogenesis of infection in the chicken date: 2007-11-12 pages: extension: .txt txt: ./txt/cord-304278-0qy1nngs.txt cache: ./cache/cord-304278-0qy1nngs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-304278-0qy1nngs.txt' === file2bib.sh === id: cord-342176-tewfm8it author: Kjærup, Rikke M. title: Adjuvant effects of mannose-binding lectin ligands on the immune response to infectious bronchitis vaccine in chickens with high or low serum mannose-binding lectin concentrations date: 2013-11-08 pages: extension: .txt txt: ./txt/cord-342176-tewfm8it.txt cache: ./cache/cord-342176-tewfm8it.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-342176-tewfm8it.txt' === file2bib.sh === id: cord-345088-krb1eidw author: Shen, S title: A single amino acid mutation in the spike protein of coronavirus infectious bronchitis virus hampers its maturation and incorporation into virions at the nonpermissive temperature date: 2004-09-01 pages: extension: .txt txt: ./txt/cord-345088-krb1eidw.txt cache: ./cache/cord-345088-krb1eidw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-345088-krb1eidw.txt' === file2bib.sh === id: cord-356094-sbtigcfr author: Chen, Huijie title: Antiviral Activity Against Infectious Bronchitis Virus and Bioactive Components of Hypericum perforatum L. date: 2019-10-29 pages: extension: .txt txt: ./txt/cord-356094-sbtigcfr.txt cache: ./cache/cord-356094-sbtigcfr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-356094-sbtigcfr.txt' === file2bib.sh === id: cord-324324-8ybfiz8f author: Decaro, Nicola title: Novel human coronavirus (SARS-CoV-2): A lesson from animal coronaviruses date: 2020-04-14 pages: extension: .txt txt: ./txt/cord-324324-8ybfiz8f.txt cache: ./cache/cord-324324-8ybfiz8f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 6 resourceName b'cord-324324-8ybfiz8f.txt' === file2bib.sh === id: cord-338307-vfutmwxq author: Sturman, Lawrence S. title: The Molecular Biology of Coronaviruses date: 1983-12-31 pages: extension: .txt txt: ./txt/cord-338307-vfutmwxq.txt cache: ./cache/cord-338307-vfutmwxq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-338307-vfutmwxq.txt' === file2bib.sh === id: cord-256444-grw5s2pf author: Lai, Michael M.C. title: The Molecular Biology of Coronaviruses date: 1997-12-31 pages: extension: .txt txt: ./txt/cord-256444-grw5s2pf.txt cache: ./cache/cord-256444-grw5s2pf.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-256444-grw5s2pf.txt' Que is empty; done keyword-ibv-cord === reduce.pl bib === id = cord-003148-o7y3wygc author = Shirvani, Edris title = A Recombinant Newcastle Disease Virus (NDV) Expressing S Protein of Infectious Bronchitis Virus (IBV) Protects Chickens against IBV and NDV date = 2018-08-10 pages = extension = .txt mime = text/plain words = 8668 sentences = 423 flesch = 55 summary = However, the results of the inoculation of the tracheal swab samples into 10-day-old embrynated chicken eggs showed that 14 out of 15 (93.3%) chickens vaccinated with rNDV expressing codon optimized S protein of IBV and 0 out of 5 (0%) of non-infected chickens were shedding virus in trachea, respectively, whereas 15 out of 15 (100%) of chickens of all other groups were shedding virus in the trachea (data not shown). To evaluate the effect of the route of inoculation of virulent IB challenge virus on the outcomes of the protective efficacy of rNDV expressing codon optimized S protein of IBV, SPF chicks were immunized at 1-day-old age. The protective efficacy of rNDV expressing codon optimized S gene of IBV was determined by challenging the immunized chickens with 10 4 EID 50 virulent IBV strain Mass-41 by the intraocular route at 3 week post-immunization. cache = ./cache/cord-003148-o7y3wygc.txt txt = ./txt/cord-003148-o7y3wygc.txt === reduce.pl bib === id = cord-263178-lvxxdvas author = Shan, Dan title = Effects of hypervariable regions in spike protein on pathogenicity, tropism, and serotypes of infectious bronchitis virus date = 2018-05-02 pages = extension = .txt mime = text/plain words = 6872 sentences = 378 flesch = 55 summary = To study the roles of hypervariable regions (HVRs) in receptor-binding subunit S1 of the spike protein, we manipulated the genome of the IBV Beaudette strain using a reverse genetics system to construct seven recombinant strains by separately or simultaneously replacing the three HVRs of the Beaudette strain with the corresponding fragments from a QX-like nephropathogenic isolate ck/CH/LDL/091022 from China. We could not detect the replication with ck/CH/ LDL/091022 in Vero cells, so the neutralization tests were performed in 9-day-old SPF embryonated eggs to confirm whether the serotypes of the recombinant IBVs belonged to ck/CH/LDL/091022. Viral antigen was observed in Vero cells infected with the Beaudette strain and the seven recombinant IBVs (Fig. 1b) . S1 gene sequencing results confirmed that the heterogenous HVRs were stably maintained in the recombinant IBVs (Sup Fig. 1) , and no additional mutations were detected in the S protein after three passages in cells or eggs. cache = ./cache/cord-263178-lvxxdvas.txt txt = ./txt/cord-263178-lvxxdvas.txt === reduce.pl bib === id = cord-017894-8iahlshj author = Loa, Chien Chang title = A Multiplex Polymerase Chain Reaction for Differential Detection of Turkey Coronavirus from Chicken Infectious Bronchitis Virus and Bovine Coronavirus date = 2015-09-10 pages = extension = .txt mime = text/plain words = 1306 sentences = 93 flesch = 55 summary = title: A Multiplex Polymerase Chain Reaction for Differential Detection of Turkey Coronavirus from Chicken Infectious Bronchitis Virus and Bovine Coronavirus A multiplex polymerase chain reaction (PCR) method for differential detection of turkey coronavirus (TCoV), infectious bronchitis virus (IBV), and bovine coronavirus (BCoV) is presented in this chapter. Primers are designed from the conserved or variable regions of nucleocapsid (N) or spike (S) protein genes of TCoV, IBV, and BCoV and used in the same PCR reaction. There is a close antigenic and genomic relationship between TCoV and infectious bronchitis virus (IBV) according to studies of immunofl uorescent antibody assay ( IFA ), enzyme-linked immunosorbent assay ( ELISA ), and sequence analysis in our and other laboratories [ 3 -8 ] . Nucleocapsid protein gene sequence analysis reveals close genomic relationship between turkey coronavirus and avian infectious bronchitis virus Differential detection of turkey coronavirus, infectious bronchitis virus, and bovine coronavirus by a multiplex polymerase chain reaction cache = ./cache/cord-017894-8iahlshj.txt txt = ./txt/cord-017894-8iahlshj.txt === reduce.pl bib === id = cord-263193-paeosfiu author = Zhu, Jinyan title = Infectious bronchitis virus inhibits activation of the TLR7 pathway, but not the TLR3 pathway date = 2020-06-10 pages = extension = .txt mime = text/plain words = 2831 sentences = 163 flesch = 55 summary = Here, primary chicken embryo kidney (CEK) cells and specific-pathogen-free (SPF) chickens were infected with three pathogenic IBV strains, and it was observed that the TLR7-MYD88 pathway was inhibited but the TLR3-TIRF pathway was activated. To investigate the effect of innate immune molecules, agonists of TLR3, TLR7, and MDA5 and inhibitors of key molecules of the TLR3 pathway were added to CEK cells that had grown to 80-90% as instructed by the reagent manufacturer (InvivoGen, CA, USA) as follows: 5 μg of imiquimod (a TLR7 agonist) per mL for 12 h, 10 μg of low-molecular-weight (LMW) polyinosinic-polycytidylic acid (poly(I:C)) (a TLR3 agonist) per mL for 12 h, 0.5 μg of poly (I:C)-LMW/LyoVec (an MDA5 agonist) per mL for 12 h, 10 μM Pepinh-TRIF (a TRIF inhibitor) for 6 h, 5 μM celastrol (an NF-κB inhibitor) for 1 h, 50 μM chloroquine (an inhibitor of endosomal acidification) for 0.5 h, and 5 μM BX795 (a TBK1 inhibitor) for 6 h. cache = ./cache/cord-263193-paeosfiu.txt txt = ./txt/cord-263193-paeosfiu.txt === reduce.pl bib === id = cord-006991-2q5ore6g author = Chi, X. title = Oral administration of tea saponins to relive oxidative stress and immune suppression in chickens date = 2017-06-15 pages = extension = .txt mime = text/plain words = 5200 sentences = 282 flesch = 47 summary = The results showed that administration of tea saponins significantly increased total antioxidant capacity, total superoxide dismutase, catalase, glutathione peroxidase, glutathione, ascorbic acid, and α-tocopherol, and decreased malondialdehyde and protein carbonyl. Enhanced immune responses, such as lymphocyte proliferation induced by concanavalin A and lipopolysaccharides, and serum Newcastle disease virusand infectious bronchitis virus-specific antibodies were also observed in chickens injected with or without cyclophosphamide. At the present study, we evaluated the effect of TS on the antioxidative activities as well as the immune responses to a live bivalent vaccine of Newcastle disease virus (NDV) and infectious bronchitis virus (IBV) vaccine in chickens in oxidative stress induced by cyclophosphamide (Cy). In this study, injection of Cy generated oxidative stress and lowered immune responses by reducing antioxidant enzymes such as T-AOC, T-SOD, GSH, and CAT, as well as inhibiting lymphocyte proliferation and antibody responses to vaccination. cache = ./cache/cord-006991-2q5ore6g.txt txt = ./txt/cord-006991-2q5ore6g.txt === reduce.pl bib === id = cord-022378-ovxmy1as author = Cook, Jane K.A. title = Coronaviridae date = 2009-05-15 pages = extension = .txt mime = text/plain words = 4034 sentences = 192 flesch = 50 summary = IBV also aff ects egg-laying performance, and renal damage associated with infectious bronchitis has become increasingly important, particularly in broilers. Economically, the most important aspects are the eff ects on egg production and quality in laying hens and production performance in broilers, where the initial respiratory infection is frequently exacerbated by secondary infections. In turkeys, coronaviruses (TCoV, also called Bluecomb disease virus and Turkey enteric coronavirus) are known to be associated with enteric disease, mortality and underperformance and to aff ect egg-laying performance in older birds. Th is is a new area of investigation and, while the coronaviruses detected in some gallinaceous and nongallinaceous birds have not so far been associated with disease, these species are potential carriers of IBV and other coronaviruses and could therefore play a role in global transmission of infection. In IBV infection of commercial layers or broiler breeders, respiratory signs may or may not be observed and the most common manifestation is the eff ect on egg production and egg quality. cache = ./cache/cord-022378-ovxmy1as.txt txt = ./txt/cord-022378-ovxmy1as.txt === reduce.pl bib === id = cord-004810-g0y7ied0 author = Lee, S. K. title = S1 glycoprotein gene analysis of infectious bronchitis viruses isolated in Korea date = 2003-11-13 pages = extension = .txt mime = text/plain words = 3750 sentences = 190 flesch = 59 summary = The S1 glycoprotein gene of IBV isolates were amplified by reverse transcriptase – polymerase chain reaction (RT-PCR) and analyzed by restriction fragment length polymorphism (RFLP) analysis. And these IBV isolates showed different patterns from each other and non-Korean IBV isolates in reverse transcriptase-polymerase chain reaction-restriction fragment length polymorphism (RT-PCR-RFLP) analysis [29] . Amplified S1 genes were first classified by RFLP analysis and then the representative strains were cloned, sequenced and compared to other non-Korean published IBV sequences. Phylogenetic trees were constructed from the nucleotide and deduced amino acid sequences of the S1 glycoprotein genes of Korean IBV isolates and non-Korean IBV strains (Fig. 3) . Korean IBV K281-01 and K210-02 isolates formed distinct clusters that were related to non-Korean IBV Ark99, Ark DPI, Gray and JMK strains although K281-01 and K210-02 isolates were classified into the Arkansas type by PCR-RFLP analysis. cache = ./cache/cord-004810-g0y7ied0.txt txt = ./txt/cord-004810-g0y7ied0.txt === reduce.pl bib === id = cord-264716-igl25jhg author = Koo, B.S. title = Molecular survey of enteric viruses in commercial chicken farms in Korea with a history of enteritis date = 2013-11-01 pages = extension = .txt mime = text/plain words = 4979 sentences = 240 flesch = 47 summary = A molecular survey was performed to determine the presence of a broad range of enteric viruses, namely chicken astrovirus (CAstV), avian nephritis virus (ANV), chicken parvovirus (ChPV), infectious bronchitis virus (IBV), avian rotavirus (AvRV), avian reovirus (ARV), and fowl adenovirus (FAdV), in intestinal samples derived from 34 commercial chicken flocks that experienced enteritis outbreaks between 2010 and 2012. Several enteric viruses have been identified in a high proportion of chickens suffering from RSS in the fields using molecular surveys, including chicken astrovirus (CAstV), avian nephritis virus (ANV), chicken parvovirus (ChPV), infectious bronchitis virus (IBV), avian rotavirus (AvRV), avian reovirus (ARV), and fowl adenovirus (FAdV; Yu et al., 2001; Otto et al., 2006; Smyth et al., 2009; Hewson et al., 2010; Palade et al., 2011; Canelli et al., 2012) . In this study, a molecular survey was performed for a broad range of enteric viruses including CAstV, ANV, ChPV, IBV, AvRV, ARV, and FAdV in intestine samples from commercial chicken flocks suffering from enteritis. cache = ./cache/cord-264716-igl25jhg.txt txt = ./txt/cord-264716-igl25jhg.txt === reduce.pl bib === id = cord-269024-re0hyolh author = Bande, Faruku title = Prediction and In Silico Identification of Novel B-Cells and T-Cells Epitopes in the S1-Spike Glycoprotein of M41 and CR88 (793/B) Infectious Bronchitis Virus Serotypes for Application in Peptide Vaccines date = 2016-09-07 pages = extension = .txt mime = text/plain words = 2566 sentences = 124 flesch = 46 summary = title: Prediction and In Silico Identification of Novel B-Cells and T-Cells Epitopes in the S1-Spike Glycoprotein of M41 and CR88 (793/B) Infectious Bronchitis Virus Serotypes for Application in Peptide Vaccines Combination of antigenic B-cells and T-cells peptides that are conserved across many strains as approach to evoke humoral and CTL immune response will potentially lead to a broad-based vaccine that could reduce the challenges in using live attenuated vaccine technology in the control of IBV infection in poultry. This study predicted novel antigenic B-cells and T-cell epitopes within the S1 glycoprotein of M41 and CR88 IBV strains. The S1 glycoprotein but not the N or M proteins of avian infectious bronchitis virus induces protection in vaccinated chickens Two novel neutralizing antigenic epitopes of the s1 subunit protein of a QX-like avian infectious bronchitis virus strain Sczy3 as revealed using a phage display peptide library cache = ./cache/cord-269024-re0hyolh.txt txt = ./txt/cord-269024-re0hyolh.txt === reduce.pl bib === id = cord-255619-5h3l6nh6 author = Kuo, Shu-Ming title = Evolution of infectious bronchitis virus in Taiwan: Positively selected sites in the nucleocapsid protein and their effects on RNA-binding activity date = 2013-03-23 pages = extension = .txt mime = text/plain words = 6329 sentences = 326 flesch = 55 summary = title: Evolution of infectious bronchitis virus in Taiwan: Positively selected sites in the nucleocapsid protein and their effects on RNA-binding activity This study illustrates that the N protein of the current TW IBV variant has been shaped by both RNA recombination and positive selection and that the latter may promote viral survival and fitness, potentially by increasing the RNA-binding capacity of the N protein. This study illustrates that the N protein of the current TW IBV variant has been shaped by both RNA recombination and positive selection and that the latter may promote viral survival and fitness, potentially by increasing the RNAbinding capacity of the N protein. In this study, we showed that substituting either of the positively selected residues with the amino acid present in most CH IBVs dramatically reduced the binding capacity of the N protein for synthetic TRS repeats (Fig. 4) . cache = ./cache/cord-255619-5h3l6nh6.txt txt = ./txt/cord-255619-5h3l6nh6.txt === reduce.pl bib === id = cord-256859-7ixegm72 author = Liu, S. W. title = Genetic diversity of avian infectious bronchitis coronavirus strains isolated in China between 1995 and 2004 date = 2006-01-09 pages = extension = .txt mime = text/plain words = 5156 sentences = 266 flesch = 56 summary = Except for isolates in genotype V, which included the Mass-type strains, none of the Chinese IBV isolates examined in this study shared more than 83% amino acid similarity in the S1 protein with the H120 vaccine strain. Furthermore, almost all of the Chinese IBV isolates contained deletions and insertions except for those of the Mass-type IBV, which were included in genotype V in this study, and had amino acid sequences similar to those of the H120 strain ( Table 4 ). The low identities (<83%) of amino acid sequences between Chinese IBV isolates and H120, except for those of the Mass-type IBV, which were included in genotype V in this study, may account for the prevalence of the viruses during the past ten years in spite of the extensive use of Mass-type vaccines in the field in China. cache = ./cache/cord-256859-7ixegm72.txt txt = ./txt/cord-256859-7ixegm72.txt === reduce.pl bib === id = cord-009487-7xb4huyz author = GODWIN, IR title = Simple rapid method of rumen cannulation date = 2008-03-10 pages = extension = .txt mime = text/plain words = 1299 sentences = 80 flesch = 63 summary = Previous methods of rumen cannulation in sheep have involved 2-stage operations in which the rumen is sutured to the skin, through dissected abdominal muscles, and then several days later an incision is made through the skin and rumen wall to form a permanent fistula, and a cannula fitted (Jarrett 1948 Hecker (1969) adapted a method previously used for cattle (Balch and Cowie 1962) . A siplple one-stage operation, requiring no suturing of the rumen'wall and an incision smaller than the neck of the Australian Veterinary Journal, Vol. 65, NO. We report the isolation of IBV from a flock of racing pigeons and assess its significance. Four 4-week-old CSIRO SPF chickens and four 8-week-old meat pigeons that were housed in the same cage were each inoculated by intranasal, intraocular and oral routes with allantoic fluid containing 10' EID,, of IBV. cache = ./cache/cord-009487-7xb4huyz.txt txt = ./txt/cord-009487-7xb4huyz.txt === reduce.pl bib === id = cord-280442-jtvez46y author = Wu, Xuan title = Simultaneous and visual detection of infectious bronchitis virus and Newcastle disease virus by multiple LAMP and lateral flow dipstick date = 2019-11-01 pages = extension = .txt mime = text/plain words = 5308 sentences = 271 flesch = 55 summary = To evaluate this novel detection method, PCR assays (including conventional RT-PCR, qRT-PCR and nRT-PCR) and reverse-transcription LAMP (RT-LAMP) monitored by electrophoresis were also conducted and the specificity and sensitivity of the assays were compared with those of the mRT-LAMP-LFD assay. A total of 13 IBV strains, 7 NDV strains, and the PCR and LAMP target sequences of 6 NDV and 1 turkey coronavirus strains (TCoV) synthesized by Sangon Biotech (Shanghai, China) Co, as well as 6 other avian virus strains, were used for the determination of the specificities of RT-PCR and RT-LAMP assays. Statistical significance difference studies showed that the mean detection rates of mRT-LAMP-LFD were significantly higher than that of conventional RT-PCR assays when detecting IBV or NDV alone (P < 0.05). The mean IBV and NDV detection rates of different samples, detected by mRT-LAMP-LFD, were both 95%, and were significantly higher than those detected by conventional RT-PCR and qRT-PCR (P < 0.05, Figure 6B) . cache = ./cache/cord-280442-jtvez46y.txt txt = ./txt/cord-280442-jtvez46y.txt === reduce.pl bib === id = cord-003208-lwirkob3 author = Yan, Liping title = Novel protein chip for the detection of antibodies against infectious bronchitis virus date = 2018-09-17 pages = extension = .txt mime = text/plain words = 3973 sentences = 220 flesch = 52 summary = RESULTS: We have developed two indirect microarray methods to detect antibodies against IBV: a chemiluminescent immunoassay test (CIT) and a rapid diagnostic test (RDT). Compared with these methods, enzyme-linked immunosorbent assay (ELISA) has been widely used for testing IBV early infection and continuous infection, and this technique can be used for both antigenic and antibody detection. The data showed that 130 serum samples were positive for antibodies against IBV, and 14 samples were negative, similar to the results of the IDEXX IBV Ab Test kit with the nsp5 concentration of 0.2 mg/mL (Table 4 ). The specific experiments of the RDT showed that no cross-reaction Fig. 4 a Distribution of the SNRs of the IDEXX-positive (n = 142) and IDEXX-negative (n = 42) serum samples of the clinical sera obtained from the IBV protein microarray. cache = ./cache/cord-003208-lwirkob3.txt txt = ./txt/cord-003208-lwirkob3.txt === reduce.pl bib === id = cord-257064-iafm3pcc author = Kint, Joeri title = Quantification of Infectious Bronchitis Coronavirus by Titration In Vitro and In Ovo date = 2014-12-18 pages = extension = .txt mime = text/plain words = 1809 sentences = 156 flesch = 63 summary = During a titration assay, tissue cultures or embryonated eggs are incubated with tenfold serial dilutions of a virus containing sample and several days later the cytopathic effect is scored. The virus titer is defined as the reciprocal of the dilution at which 50 % of the inoculated embryos or tissue cultures show CPE. Passaging of IBV in either embryonated eggs or primary cell cultures leads to attenuation of the virus in vivo [10] [11] [12] . IBV strains which have been adapted to grow in cultures of primary chicken cells can be titrated on these cells using either the TCID 50 method or plaque titration. Virus titers in the original sample, expressed as 10 log EID 50 /ml are calculated using the method described by Spearman and Kaerber [6, 7] , using the following formula: Plaque formation by infectious bronchitis virus in chicken embryo kidney cell cultures Growth kinetics of embryo-and organ-culture adapted Beaudette strain of infectious bronchitis virus in embryonated chicken eggs cache = ./cache/cord-257064-iafm3pcc.txt txt = ./txt/cord-257064-iafm3pcc.txt === reduce.pl bib === id = cord-260042-cs0wp99n author = Khan, Samiullah title = Genes involved in mitochondrial biogenesis and function may not show synchronised responses to mitochondria in shell gland of laying chickens under infectious bronchitis virus challenge date = 2019-04-01 pages = extension = .txt mime = text/plain words = 6931 sentences = 362 flesch = 47 summary = The present study aimed to: a) determine mitochondrial counts in the cells of oviduct segments in laying hens at different time-points of egg formation in relation to the requirement of energy for egg production during IBV challenge; b) to determine the expression of nuclear DNA encoded genes in the shell gland to gain insights into their responses to IBV infection and time-points of egg-shell formation. Based on the lack of significant differences in mitochondrial count in the cells between the challenged and control groups for the magnum and isthmus, we focused further on shell gland tissue and studied the expression level of genes involved in mitochondrial density, biogenesis and fission. The lack of any significant difference in the relative expression levels of all of the genes except SDHA, between the control and IBV T challenged groups, may indicate that mitochondrial function may have been enhanced and thus overall egg quality may not have been affected by fewer mitochondria in the shell gland cells of IBV T infected hens. cache = ./cache/cord-260042-cs0wp99n.txt txt = ./txt/cord-260042-cs0wp99n.txt === reduce.pl bib === id = cord-007648-tm0hn0hz author = Mockett, A.P.Adrian title = Envelope proteins of avian infectious bronchitis virus: Purification and biological properties date = 2002-12-20 pages = extension = .txt mime = text/plain words = 2217 sentences = 140 flesch = 56 summary = Immunoadsorbents, made with monoclonal antibodies, were used to purify the spike and membrane proteins of infectious bronchitis virus (IBV). A second inoculation of virus at 42 days induced an anamnestic antibody response to the spike and membrane proteins and also for the neutralizing antibodies. The objectives of this work were to produce immunoadsorbents using monoclonal antibodies which have been prepared previously (Mockett et al., 1984) and to purify the virus-coded proteins of the viral envelope in a single step in relatively large amounts. In addition the sequential humoral antibody response of chickens after IBV infection has been studied using the purified viral proteins and whole virus in ELISAs and compared to the results using the neutralization test. Thc chicken, about 10 days after an IBV infection, has antibodies to both the spike and membrane proteins in its serum but only very low concentrations of neutralizing antibodies. cache = ./cache/cord-007648-tm0hn0hz.txt txt = ./txt/cord-007648-tm0hn0hz.txt === reduce.pl bib === id = cord-265681-ab8j4o1u author = Boroomand, Zahra title = Pathogenesis and Tissue Distribution of Avian Infectious Bronchitis Virus Isolate IRFIBV32 (793/B Serotype) in Experimentally Infected Broiler Chickens date = 2012-04-01 pages = extension = .txt mime = text/plain words = 3553 sentences = 219 flesch = 53 summary = title: Pathogenesis and Tissue Distribution of Avian Infectious Bronchitis Virus Isolate IRFIBV32 (793/B Serotype) in Experimentally Infected Broiler Chickens The aim of this study was to investigate the distribution of avian infectious bronchitis virus isolate IRFIBV32 (793/B serotype) in experimentally infected chicken. Data indicated that the number of infected chickens and viral RNA detection from tissues was reduced with increasing antibody titer on day 20 PI. Gross lesions were recorded, and their trachea, lungs, kidneys, caecal tonsil, testes, and oviduct were aseptically collected for virus detection using RT-PCR assay ( Table 1) . In this study, the pathogenesis of the infectious bronchitis virus isolate IRFIBV32 which was recently isolated in Iran [12] , tissue tropism, and dissemination of the virus throughout the body were evaluated following intranasal (IN) inoculation of commercial broiler chickens by RT-PCR. Immunohistochemistry for detection of avian infectious bronchitis virus strain M41 in the proventriculus and nervous system of experimentally infected chicken embryos cache = ./cache/cord-265681-ab8j4o1u.txt txt = ./txt/cord-265681-ab8j4o1u.txt === reduce.pl bib === id = cord-256444-grw5s2pf author = Lai, Michael M.C. title = The Molecular Biology of Coronaviruses date = 1997-12-31 pages = extension = .txt mime = text/plain words = 35222 sentences = 1753 flesch = 51 summary = Publisher Summary This chapter discusses the manipulation of clones of coronavirus and of complementary DNAs (cDNAs) of defective-interfering (DI) RNAs to study coronavirus RNA replication, transcription, recombination, processing and transport of proteins, virion assembly, identification of cell receptors for coronaviruses, and processing of the polymerase. This decade has seen the manipulation of these clones, and of complementary DNAs (cDNAs) of defective-interfering (DI) RNAs, to study coronavirus RNA replication, transcription, recombination, processing and transport of proteins, virion assembly, identification of cell receptors for coronaviruses, and processing of the polymerase. The species and tissue specificity of a coronavirus infection is a t least partially dictated by the nature and distribution of cellular receptors and other related molecules that regulate virus entry, as evidenced by the viral replication that results when viral RNA is directly introduced into cell types of other animal species. cache = ./cache/cord-256444-grw5s2pf.txt txt = ./txt/cord-256444-grw5s2pf.txt === reduce.pl bib === id = cord-258379-v3lceirh author = Liu, D. X. title = Association of the infectious bronchitis virus 3c protein with the virion envelope date = 1991-12-31 pages = extension = .txt mime = text/plain words = 2868 sentences = 121 flesch = 53 summary = There was considerably less evidence of contaminating cellular proteins in this gradient, and the relative proportion of the 12K protein to the other virion proteins appeared similar to that observed at the previous stage in purification, strongly supporting the idea of a specific association between the 12K protein and virus particles. In order to establish the identity of the 12K polypeptide as the product of the 3c gene, and to examine the possibility that IBV virions might contain other new virus polypeptides in amounts too small to detect directly, we next carried out immunoprecipitation experiments using monospecific antisera directed against the predicted products of the 3a, 3b, 3c, 5a, and 5b ORFs (17, 18, 23) . Messenger RNA 4 of mouse hepatitis virus (MHV) is known to encode a 15K polypeptide, the predicted amino acid sequence of which contains a highly hydrophobic region from residues 8 to 41 (9, 22) , although the protein has not so far been found in virions. cache = ./cache/cord-258379-v3lceirh.txt txt = ./txt/cord-258379-v3lceirh.txt === reduce.pl bib === id = cord-010608-eaa2znom author = Butt, Salman L. title = Real-time, MinION-based, amplicon sequencing for lineage typing of infectious bronchitis virus from upper respiratory samples date = 2020-03-05 pages = extension = .txt mime = text/plain words = 6846 sentences = 322 flesch = 53 summary = title: Real-time, MinION-based, amplicon sequencing for lineage typing of infectious bronchitis virus from upper respiratory samples Sanger sequencing of the S1 subunit of the spike gene is currently used to genotype IBV; however, the universal S1 PCR was created to work from cultured IBV, and it is inefficient at detecting multiple viruses in a single sample. We describe herein a MinION-based, amplicon-based sequencing (AmpSeq) method that genetically categorized IBV from clinical samples, including samples with multiple IBVs. Total RNA was extracted from 15 tracheal scrapings and choanal cleft swab samples, randomly reverse transcribed, and PCR amplified using modified S1-targeted primers. Real-time data analysis, the lack of significant start-up cost investment or maintenance expenses, simultaneous and sequential multiplexing unique to MinION, and the ability to sequence long DNA molecules so that primers are in conserved regions while the product contains the variable region are the features that make the use of this technology highly feasible in disease diagnosis. cache = ./cache/cord-010608-eaa2znom.txt txt = ./txt/cord-010608-eaa2znom.txt === reduce.pl bib === id = cord-276550-1in7m56w author = Abdel-Moneim, Ahmed S title = S1 gene sequence analysis of a nephropathogenic strain of avian infectious bronchitis virus in Egypt date = 2006-09-20 pages = extension = .txt mime = text/plain words = 3957 sentences = 218 flesch = 48 summary = title: S1 gene sequence analysis of a nephropathogenic strain of avian infectious bronchitis virus in Egypt RESULTS: Infectious bronchitis virus (IBV) strain closely related to Massachusetts (Mass) serotype was isolated from broiler chickens suffering from severe renal and respiratory distresses. Protection based criteria were: virus re-isolation attempts from trachea, tracheal and renal histopathology as well as IBV antigens detection by immunofluorescent antibody technique in kidney sections. In the present study, Egypt/F/03 was isolated from 25day-old broiler chickens in Fayoum Governorate, identified by Dot-ELISA, RT-PCR and sequenced to determine its serotype. In this study, an Egyptian IBV strain; Egypt\F/03 was isolated from a tissue pool of kidney and trachea from unvaccinated broiler flock with a history of respiratory and renal disease. Challenge experiments to evaluate cross-protection induced at the trachea and kidney level by vaccine strains and Belgian nephropathogenic isolates of avian infectious bronchitis virus cache = ./cache/cord-276550-1in7m56w.txt txt = ./txt/cord-276550-1in7m56w.txt === reduce.pl bib === id = cord-278324-eqqvwwh6 author = Wang, Huanan title = Development of a sensitive and specific xMAP assay for detection of antibodies against infectious laryngotracheitis and bronchitis viruses date = 2018-09-21 pages = extension = .txt mime = text/plain words = 3512 sentences = 191 flesch = 48 summary = BACKGROUND: A serological method to simultaneously detect antibodies against infectious laryngotracheitis virus (ILTV) and infectious bronchitis virus (IBV) is imperative for the differential diagnosis and evaluation of antibodies titers after vaccination. Therefore, it is important to establish a method to simultaneously detect ILTV and IBV antibodies for the differential diagnosis and immune response evaluation after vaccination. In this study, a method employing Luminex xMAP technology to simultaneously detect ILTV and IBV antibodies in serum was established, optimized and used for the differential diagnosis of IBV and ILTV. 2 and 3 demonstrated that xMAP duplex assay for ILTV and IBV has a high specificity since there were no cross-reactions with serum positive for other avian diseases, such as avian influenza virus To compare duplex xMAP assay with ELISA for ILTV/IBV detection, 90 chicken serum samples from a chicken farm in Huizhou, China were used and the results are shown in Table 7 . cache = ./cache/cord-278324-eqqvwwh6.txt txt = ./txt/cord-278324-eqqvwwh6.txt === reduce.pl bib === id = cord-252048-ftbjsoup author = McKinley, Enid T. title = Attenuated live vaccine usage affects accurate measures of virus diversity and mutation rates in avian coronavirus infectious bronchitis virus date = 2011-04-22 pages = extension = .txt mime = text/plain words = 6380 sentences = 309 flesch = 55 summary = The full-length genomes of 11 infectious bronchitis virus (IBV) field isolates from three different types of the virus; Massachusetts (Mass), Connecticut (Conn) and California (CAL) isolated over a 41, 25 and 8 year period respectively, were sequenced and analyzed to determine the mutation rates and level of polymorphisms across the genome. The genetic data also identified a recombinant IBV isolate with 7 breakpoints distributed across the entire genome suggesting that viruses within the same serotype can have a high degree of genetic variability outside of the spike gene. The objective of this study was to determine the levels of polymorphism across the entire genome of IBV isolates with similar spike genes and to examine the mutation rates for viruses with and without vaccine selection pressure. cache = ./cache/cord-252048-ftbjsoup.txt txt = ./txt/cord-252048-ftbjsoup.txt === reduce.pl bib === id = cord-000924-wwuqxx1r author = Yan, Fang title = Protection of chickens against infectious bronchitis virus with a multivalent DNA vaccine and boosting with an inactivated vaccine date = 2013-03-24 pages = extension = .txt mime = text/plain words = 3775 sentences = 198 flesch = 51 summary = title: Protection of chickens against infectious bronchitis virus with a multivalent DNA vaccine and boosting with an inactivated vaccine The protective efficacy of DNA plasmids encoding avian infectious bronchitis virus (IBV) S1, N, or M protein was investigated in chickens. The serum antibody titers in the prime-boost birds were significantly higher than those of the multivalent DNA vaccine group (p < 0.01) but not significantly different compared to the inactivated vaccine group at 49 days of age. Additionally, the prime-boost group also showed the highest level of IBV-specific cellular proliferation compared to the monovalent groups (p < 0.01) but no significant difference was found compared to the multivalent DNA vaccine group, and the prime-boost group completely protected from followed viral challenge. These results indicate that immunization with a combination of the three-gene DNA vaccine and an inactivated vaccine not only elicited the strongest antibody response, but also induced the highest IBV-specific cellular proliferation rates in the chickens. cache = ./cache/cord-000924-wwuqxx1r.txt txt = ./txt/cord-000924-wwuqxx1r.txt === reduce.pl bib === id = cord-266585-jfjrk9gy author = Fang, Shouguo title = An arginine-to-proline mutation in a domain with undefined functions within the helicase protein (Nsp13) is lethal to the coronavirus infectious bronchitis virus in cultured cells date = 2007-02-05 pages = extension = .txt mime = text/plain words = 7152 sentences = 356 flesch = 56 summary = During construction of an infectious clone from a Vero cell-adapted coronavirus infectious bronchitis virus (IBV), we found that a G–C point mutation at nucleotide position 15526, causing Arg-to-Pro mutation at amino acid position 132 of the helicase protein, is lethal to the infectivity of IBV on Vero cells. Further characterization of the in vitro-synthesized full-length transcripts containing the G15526C mutation demonstrated that this mutation blocks the transcription of subgenomic RNAs. Substitution mutation of the Arg132 residue to a positively charged amino acid (Lys) affected neither the infectivity of the in vitro-synthesized transcripts nor the growth properties of the rescued virus. To further demonstrate that the failure to rescue infectious virus from the G15526C mutant transcripts is due to a defect in subgenomic RNA transcription, the full-length clones with and without the G15526C mutation were used to generate recombinant IBV expressing the enhanced green fluorescent protein (EGFP) by replacing the 5a gene with EGFP. cache = ./cache/cord-266585-jfjrk9gy.txt txt = ./txt/cord-266585-jfjrk9gy.txt === reduce.pl bib === id = cord-265499-pbf11zy1 author = Dove, Brian K. title = Changes in nucleolar morphology and proteins during infection with the coronavirus infectious bronchitis virus date = 2006-03-03 pages = extension = .txt mime = text/plain words = 5026 sentences = 250 flesch = 46 summary = In this study, using the avian infectious bronchitis coronavirus, we have shown that virus infection results in a number of changes to the nucleolus both in terms of gross morphology and protein content. Using IBV we tested the hypothesis that virus infection leads to perturbations in the morphology and proteins of the nucleolus which may have downstream consequences for host cell function. A change in the morphology of the nucleolus was observed in IBV-infected cells using EGFPnucleolin as a marker protein (e.g. Fig. 3B ), leading to the prediction that the levels of nucleolin might increase in virus-infected cells, which was observed in Fig. 4B . This study was undertaken with a higher resolution confocal microscope and we observed a third population of cells in which N protein was predominantly localized in the cytoplasm, but also was present in low levels in the nucleus and nucleolus (an example is shown in Fig. 7A) . cache = ./cache/cord-265499-pbf11zy1.txt txt = ./txt/cord-265499-pbf11zy1.txt === reduce.pl bib === id = cord-253695-tjdw2uta author = Winter, Christine title = Infection of the tracheal epithelium by infectious bronchitis virus is sialic acid dependent date = 2007-12-28 pages = extension = .txt mime = text/plain words = 3679 sentences = 208 flesch = 52 summary = Avian Infectious bronchitis virus (IBV) is a coronavirus that infects chickens via the respiratory epithelium as primary target cells. Here we analyze the importance of the sialic acid binding activity for the infection of tracheal organ cultures (TOCs) by different IBV strains. Desialylation induced by neuraminidase treatment of tracheal organ cultures prior to infection by IBV delayed the ciliostatic effect or resulted in partial loss of ciliary activity. After having shown recently that sialic acid serves as a receptor determinant for IBV on cultured cells, we were interested to find out whether this type of sugar is also important for an infection in vivo. From this result we conclude that a2,3-linked sialic acid serves as a receptor determinant for the infection of avian tracheal epithelial cells by the Beaudette strain of IBV. Sialic acid is a receptor determinant for infection of cells by avian Infectious bronchitis virus cache = ./cache/cord-253695-tjdw2uta.txt txt = ./txt/cord-253695-tjdw2uta.txt === reduce.pl bib === id = cord-255141-55ho9av4 author = Abolnik, Celia title = Genomic and single nucleotide polymorphism analysis of infectious bronchitis coronavirus date = 2015-04-03 pages = extension = .txt mime = text/plain words = 6284 sentences = 322 flesch = 53 summary = A QX-like strain was analysed by high-throughput Illumina sequencing and genetic variation across the entire viral genome was explored at the sub-consensus level by single nucleotide polymorphism (SNP) analysis. The E and 3b protein products play key roles in coronavirus virulence, and RNA folding demonstrated that the mutations in the 5′UTR did not alter the predicted secondary structure. Coronavirus accessory proteins are generally dispensable for virus replication, but they play vital roles in virulence and pathogenesis by affecting host innate immune responses, encoding pro-or anti-apoptotic activities, or by effecting other signalling pathways that influence disease outcomes (Susan & Julian, 2011) . Mapping of the receptor-binding domain and amino acids critical for attachment in the spike protein of avian coronavirus infectious bronchitis virus Analysis of a QX-like avian infectious bronchitis virus genome identified recombination in the region containing the ORF 5a, ORF 5b, and nucleocapsid protein gene sequences cache = ./cache/cord-255141-55ho9av4.txt txt = ./txt/cord-255141-55ho9av4.txt === reduce.pl bib === id = cord-022187-7c3wz6c6 author = Liu, Shengwang title = A new genotype of nephropathogenic infectious bronchitis virus circulating in vaccinated and non-vaccinated flocks in China date = 2010-10-19 pages = extension = .txt mime = text/plain words = 3520 sentences = 195 flesch = 60 summary = title: A new genotype of nephropathogenic infectious bronchitis virus circulating in vaccinated and non-vaccinated flocks in China Five strains of infectious bronchitis virus (IBV) were isolated from five layer flocks that had nephropathogenic infection in four provinces in China. Virulence studies indicated that the five Chinese IBV isolates caused 10 to 30% mortality in 15-day-old specific pathogen free chickens and gross lesions were mainly confined to the kidneys in all of the dead chickens. In order to investigate whether there are other genotype(s) of nephropathogenic IBV besides the Massachusetts type in flocks in China, we tested five IBV isolates from layer flocks showing clinical signs of IB by sequencing and analysis of the S1 protein genes. In the present study, we isolated three IBV strains from H120-vaccinated flocks and two from non-vaccinated flocks of layer chickens that experienced nephropathogenic infection in four provinces of north China. cache = ./cache/cord-022187-7c3wz6c6.txt txt = ./txt/cord-022187-7c3wz6c6.txt === reduce.pl bib === id = cord-285052-aql0vrzv author = Kamble, Nitin Machindra title = Evolutionary and bioinformatic analysis of the spike glycoprotein gene of H120 vaccine strain protectotype of infectious bronchitis virus from India date = 2016-02-12 pages = extension = .txt mime = text/plain words = 2820 sentences = 129 flesch = 50 summary = The complete spike gene of Indian AIB vaccine strain was amplified and sequenced using a conventional reverse transcription polymerase chain reaction and is submitted to the GenBank (accession no KF188436). Nucleotide and amino acid sequence comparisons have shown that the reported spike gene from Indian isolates have 71.8%–99% and 71.4%–96.9% genetic similarity with the sequenced H120 strain. Genotyping of IBV strains can also be done by genetic characterization of the spike glycoprotein gene by reverse transcription polymerase chain reaction (RT-PCR), restriction fragment length polymorphism, and nucleotide sequencing, which for the most part correlates with the viral serotype [10, 11] . The deduced amino acid sequences of the spike glycoprotein from the Indian IBV vaccine strain and previously reported Indian isolates exhibited 71.4%-96.9% homology. In this study, we carried out propagation, amplification, sequencing, and bioinformatic analysis of the complete spike gene from the Indian vaccine strain, routinely used for vaccination of poultry birds. cache = ./cache/cord-285052-aql0vrzv.txt txt = ./txt/cord-285052-aql0vrzv.txt === reduce.pl bib === id = cord-284501-5i0w74q4 author = Armesto, Maria title = The Replicase Gene of Avian Coronavirus Infectious Bronchitis Virus Is a Determinant of Pathogenicity date = 2009-10-09 pages = extension = .txt mime = text/plain words = 7792 sentences = 322 flesch = 54 summary = The IBV cDNA within pGPT-BeauR-Rep-M41-Struct-3UTR was introduced, by homologous recombination using the transient dominant selection (TDS) ( [25, 37] ), into the IBV Beaudette cDNA within the vaccinia virus genome in rVV-BeauR-Rep-DStruct containing Beau-R-derived sequence corresponding to the replicase gene followed by the first 376 nt of the S gene, part of the N gene and the 39-UTR (Fig. 1) . The samples were analysed for the presence of viable IBV by titration in TOCs or used for RNA extraction using the RNeasy method and analysed by RTThe M41-CK-derived cDNA, representing the M41 structural and accessory genes and the M41 39-UTR, within pGPT-BeauR-Rep-M41-Struct-3UTR was fused to the Beau-R replicase gene in the rVV by a homologous recombination event between the Beau-R replicase sequence common to both constructs. Analysis of the tracheal epithelial cells isolated from the infected chickens, for the presence of IBV by titration on TOCs, had indicated that either there was no Beau-R or rBeauR-Rep-M41-Struct-2 present or that the levels of both viruses were below detection. cache = ./cache/cord-284501-5i0w74q4.txt txt = ./txt/cord-284501-5i0w74q4.txt === reduce.pl bib === id = cord-255870-gmq5zs2d author = Liu, Shengwang title = Identification of the avian infectious bronchitis coronaviruses with mutations in gene 3 date = 2008-04-15 pages = extension = .txt mime = text/plain words = 5685 sentences = 258 flesch = 56 summary = All the IBV field and vaccine strains were propagated once in 9 to 11-day-old embryonated chicken-specific pathogen-free (SPF) eggs (Harbin Veterinary Research Institute, China) and confirmed using negative contrast electronic microscopy (JEM-1200, EX) in the allantoic fluids of inoculated eggs as described previously (Liu and Kong, 2004) , before being used in sequence analysis. Each of the nine 9-day-old SPF chicken embryos was inoculated with the isolates CK/CH/LLN/98, CK/CH/LSD/03I, CK/CH/LJL/04I, CK/CH/LDL/97I, and CK/CH/LGD/04II passage level 3 (the latter 3 virus strains, each representing different IBV serotypes in China, were used as controls) with 10 2 EID 50 per embryo in 0.1 ml inoculum into the allantoic cavity. This mutation resulted in the virus lacking ORF 3a and changed the primary structure of the 3′-encoding regions of CK/CH/LLN/98I, leading to a novel genomic organization of the avian coronavirus that had the S-3b-3c-M-5a-5b-N gene order from the 5′-end to the 3′-end, instead of the typical gene order in the 3′-encoding regions of group 3 coronaviruses isolated from chicken (IBV) (Boursnell et al., 1987) , turkey (Breslin et al., 1999; Cavanagh et al., 2001; Lin et al., 2002) , and pheasants (Cavanagh et al., 2002) . cache = ./cache/cord-255870-gmq5zs2d.txt txt = ./txt/cord-255870-gmq5zs2d.txt === reduce.pl bib === id = cord-273366-xd84f8ct author = Brownsword, Matthew J. title = Infectious Bronchitis Virus Regulates Cellular Stress Granule Signaling date = 2020-05-14 pages = extension = .txt mime = text/plain words = 8910 sentences = 520 flesch = 47 summary = Interestingly, we found that IBV is able to inhibit multiple cellular stress granule signaling pathways, whilst at the same time, IBV replication also results in the induction of seemingly canonical stress granules in a proportion of infected cells. Moreover, IBV infection uncouples translational repression and stress granule formation and both processes are independent of eIF2α phosphorylation. Vero cells were infected with IBV and at the indicated time points, cells were fixed and labelled with anti-dsRNA to detect virus infection and with anti-G3BP1 to detect SG. Following identification of SG in IBV infected cells, the requirement for active virus replication in induction of granules was assessed. At 24 hpi, cells were fixed and labelled with anti-G3BP1 (red) to detect stress granules (SG) and IBV infected cells were detected with an anti-dsRNA antibody (green). Junin virus infection impairs stress-granule formation in Vero cells treated with arsenite via inhibition of eIF2alpha phosphorylation cache = ./cache/cord-273366-xd84f8ct.txt txt = ./txt/cord-273366-xd84f8ct.txt === reduce.pl bib === id = cord-263785-0iift8zy author = Zhang, Xiaorong title = Evaluation of the reproductive system development and egg-laying performance of hens infected with TW I-type infectious bronchitis virus date = 2020-07-31 pages = extension = .txt mime = text/plain words = 3690 sentences = 171 flesch = 50 summary = title: Evaluation of the reproductive system development and egg-laying performance of hens infected with TW I-type infectious bronchitis virus Our findings suggest that TW I-type IBV is deadly to chickens and could cause permanent damage to the oviduct, resulting in the poor laying performance of female survivors and decreasing the breeding value and welfare of the infected flock. In this study, the pathogenicity of TW I-type IBV was evaluated by examining clinical symptoms, mortality rates, virus shedding, lesions, and laying performance in terms of egg quantity and quality in infected chickens. The pathogenicity of TW I-type IBV in the early stage post-infection was evaluated via the clinical symptoms, pathological lesions, and virus shedding from trachea and cloaca. Abbreviations IBV: infectious bronchitis virus; SPF: specific-pathogen-free; dpi: days post infection; RT-qPCR: reverse transcription-quantitative polymerase chain reaction. cache = ./cache/cord-263785-0iift8zy.txt txt = ./txt/cord-263785-0iift8zy.txt === reduce.pl bib === === reduce.pl bib === id = cord-277804-ujabzic4 author = Yuk, Seong-su title = Comparison between dot-immunoblotting assay and clinical sign determination method for quantifying avian infectious bronchitis virus vaccine by titration in embryonated eggs date = 2016-01-21 pages = extension = .txt mime = text/plain words = 4146 sentences = 202 flesch = 53 summary = title: Comparison between dot-immunoblotting assay and clinical sign determination method for quantifying avian infectious bronchitis virus vaccine by titration in embryonated eggs In this study, we used a dot-immunoblotting assay (DIA) to measure the titers of IBV vaccines that originated from different pathogenic strains or attenuation methods in embryonated eggs, and we compared this assay to the currently used method, clinical sign evaluation. The aim of this study was to evaluate and compare the sensitivity and specificity of the DIA to the clinical sign determination method for detecting IBV in inoculated embryonated eggs during titration of IBV vaccines. Propagation of the inoculated virus was determined using real-time RT-PCR, DIA, and the EE index method, and the 50% egg infectious dose (EID 50 ) of the five vaccines was calculated based on the method of Reed and Muench (1938) . cache = ./cache/cord-277804-ujabzic4.txt txt = ./txt/cord-277804-ujabzic4.txt === reduce.pl bib === id = cord-001768-8vljd5cv author = Awad, Faez title = Protection conferred by live infectious bronchitis vaccine viruses against variant Middle East IS/885/00-like and IS/1494/06-like isolates in commercial broiler chicks date = 2015-09-09 pages = extension = .txt mime = text/plain words = 3928 sentences = 212 flesch = 55 summary = title: Protection conferred by live infectious bronchitis vaccine viruses against variant Middle East IS/885/00-like and IS/1494/06-like isolates in commercial broiler chicks At 30 days of age (on the day of challenge), vaccinated groups showed significantly higher levels of IBV ELISA antibody titre than the unvaccinated control group. The evaluation of protection conferred by live vaccines against the virulent IS/885 and IS/1494 isolates was assessed based on ciliary activity in the tracheal explants prepared from vaccinated-challenged chicks (Darbyshire 1980 , Andrade and others 1982 , Marquardt and others 1982 , Snyder and others 1983 , Cook and others 1999 and gross lesions in the trachea and kidneys following the challenge with the respective viruses. Challenge experiments to evaluate cross-protection induced at the trachea and kidney level by vaccine strains and Belgian nephropathogenic isolates of avian infectious bronchitis virus cache = ./cache/cord-001768-8vljd5cv.txt txt = ./txt/cord-001768-8vljd5cv.txt === reduce.pl bib === id = cord-285942-mb1xwdqw author = Feng, K. Y. title = Molecular characteristic and pathogenicity analysis of a virulent recombinant avain infectious bronchitis virus isolated in China date = 2018-10-01 pages = extension = .txt mime = text/plain words = 6873 sentences = 318 flesch = 59 summary = Sequence comparison among QY16 and other IBV strains was conducted and its results demonstrate that the S1 gene of QY16 has the highest nucleotide sequence identity with that of 4/91, and the other part of its genome is highly similar to that of YX10. The results of the sequence comparison and phylogenetic analysis show that QY16 has the highest identity with 4/91 in terms of the S1 gene and is located in the 1 10/10 4/10 0/10 0/10 4/7 6/6 6/6 7/7 5/6 3/6 2 9/10 4/10 3/10 9/10 8/8 6/6 6/6 8/8 4/6 2/6 3 4/10 2/10 4/10 10/10 9/9 8/8 8/8 5/9 2/8 1/8 Control 0/10 0/10 0/10 0/10 0/10 0/10 0/10 0/10 0/10 0/10 1 Chickens in groups 2 and 3 were vaccinated with H120 and 4/91 vaccines, respectively, and challenged with QY16. Complete genome sequence analysis of a predominant infectious bronchitis virus (IBV) strain in China Complete genome sequence of a recombinant nephropathogenic infectious bronchitis virus strain in china cache = ./cache/cord-285942-mb1xwdqw.txt txt = ./txt/cord-285942-mb1xwdqw.txt === reduce.pl bib === id = cord-004680-u3cnsdl8 author = Lin, Z. title = Typing of recent infectious bronchitis virus isolates causing nephritis in chicken date = 1991 pages = extension = .txt mime = text/plain words = 860 sentences = 47 flesch = 57 summary = Four isolates of infectious bronchitis viruses (IBV) from chickens with nephritis, were characterized by polymerase chain reaction (PCR) and restriction enzyme fragment length polymorphism (RFLP), and were found to be genetically different from the other twelve strains which we previously studied. HinfI digested pUC 19 DNA was used as the molecular size markers (3//), and their sizes are indicated in base pairs (bp) on the left In this study, essentially the same procedure was used in an attempt to characterize four IBV isolates F-88, Y-4, M-l, and NI-1 from chickens with nephritis in different endemic areas of Japan between 1988 and 1989. The results of the present study, indicate that the four recently obtained IBV isolates causing nephritis are, by our genetic criteria, similar to each other but different from previous isolates, hence are classified together into a new subtype (group VI). Serological comparisons of strains of infectious bronchitis virus using plaque-purified isolants cache = ./cache/cord-004680-u3cnsdl8.txt txt = ./txt/cord-004680-u3cnsdl8.txt === reduce.pl bib === id = cord-260145-grz0fe9l author = Liu, Shengwang title = Altered pathogenicity, immunogenicity, tissue tropism and 3′-7 kb region sequence of an avian infectious bronchitis coronavirus strain after serial passage in embryos date = 2009-07-23 pages = extension = .txt mime = text/plain words = 7486 sentences = 366 flesch = 51 summary = title: Altered pathogenicity, immunogenicity, tissue tropism and 3′-7 kb region sequence of an avian infectious bronchitis coronavirus strain after serial passage in embryos In this study, we attenuated a Chinese LX4-type nephropathogenic infectious bronchitis virus (IBV) strain, CK/CH/LHLJ/04V, by serial passage in embryonated chicken eggs. At the age of 15 days, groups 1-4 were inoculated intranasally with 0.1 ml per chick containing 10 4.7 -10 4.8 median embryo infectious doses (EID 50 ) at passage level 3 of strains CH/CK/LHLJ/04V, CK/CH/LDL/04II, CK/CH/LXJ/02I and CK/CH/LSHH/03I. The CH/CK/LHLJ/04V strain was serially passaged 110 times by inoculating 9-day-old SPF chicken eggs by the allantoic cavity route as described previously [19] . Virus titrations were performed in 9-day-old embryonated chicken SPF eggs via the allantoic cavity route of inoculation, and titers were expressed as 50% (median) embryo infectious doses (EID 50 ) [9, 37] . cache = ./cache/cord-260145-grz0fe9l.txt txt = ./txt/cord-260145-grz0fe9l.txt === reduce.pl bib === id = cord-279495-zxerb7de author = Liu, Xiaoli title = Comparative analysis of four Massachusetts type infectious bronchitis coronavirus genomes reveals a novel Massachusetts type strain and evidence of natural recombination in the genome date = 2012-11-21 pages = extension = .txt mime = text/plain words = 5235 sentences = 258 flesch = 56 summary = Four Massachusetts-type (Mass-type) strains of infectious bronchitis coronavirus (IBV) were compared genetically with the pathogenic M41 and H120 vaccine strains using the complete genomic sequences. Phylogenetic analysis, and pairwise comparison of full-length genomes and the nine genes, identified the occurrence of recombination events in the genome of strain CK/VH/LHLJ/07VII, which suggests that this virus originated from recombination events between M41and H120-like strains at the switch site located at the 3′ end of the nucleocapsid (N) genes. Herein, we sequenced the complete genome of four IBV Mass-type strains that showed S1 gene diversity (Liu et al., 2009; Ma et al., 2012; Sun et al., 2011) , and we present evidence for in-field recombination between pathogenic and vaccinal strains. Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus cache = ./cache/cord-279495-zxerb7de.txt txt = ./txt/cord-279495-zxerb7de.txt === reduce.pl bib === id = cord-268788-jcu3pasy author = Thor, Sharmi W. title = Recombination in Avian Gamma-Coronavirus Infectious Bronchitis Virus date = 2011-09-23 pages = extension = .txt mime = text/plain words = 4426 sentences = 219 flesch = 49 summary = In this study, the full-length genomes of eight avian gamma-coronavirus infectious bronchitis virus (IBV) isolates were sequenced and along with other full-length IBV genomes available from GenBank were analyzed for recombination. In this study we sequenced and analyzed the entire genome of eight IBV strains that represent different serotypes that have not been previously sequenced, and we compared these sequences with other gamma-coronavirus full-length genome sequences available in GenBank for evidence of recombination [16] . A phylogenetic compatibility matrix constructed at the 70% bootstrap level for 250 bp sequence fragments at 100 bp intervals also showed that recombination breakpoints were distributed throughout the IBV genomes (data not shown). Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus Complete genome sequence and recombination analysis of infectious bronchitis virus attenuated vaccine strain H120 cache = ./cache/cord-268788-jcu3pasy.txt txt = ./txt/cord-268788-jcu3pasy.txt === reduce.pl bib === id = cord-259959-qzd3hf8y author = Alhatami, Abdullah O. title = Sequencing and phylogenetic analysis of infectious bronchitis virus variant strain from an outbreak in egg-layer flocks in Baghdad, Iraq date = 2020-07-16 pages = extension = .txt mime = text/plain words = 2358 sentences = 127 flesch = 48 summary = title: Sequencing and phylogenetic analysis of infectious bronchitis virus variant strain from an outbreak in egg-layer flocks in Baghdad, Iraq MATERIALS AND METHODS: Isolate detection, sequencing, and phylogenetic analysis were performed using a rapid IB virus antigen kit (32 tracheal swabs), flinders technology associates (FTA) card (32 tracheal swabs), and partial gene sequencing (16 positive FTA samples). Therefore, the current report describes the role of IBV during an outbreak of the respiratory disease in an egg-layer farm in the Baghdad region of Iraq, investigates the genetic characteristics of this field strain by analyzing the S1 gene and compares it with other isolates registered globally for developing significant vaccines to control this disease. FA and YIK visited the infected farm, collected the samples, run the rapid IBV antigen detection, confirmed the results using FTA card that was sent to Germany, deposited the genetic information into the NCBI database, analyzed the differences between the strains of the virus, and drafted the manuscript. cache = ./cache/cord-259959-qzd3hf8y.txt txt = ./txt/cord-259959-qzd3hf8y.txt === reduce.pl bib === id = cord-257999-apg4uhhq author = Ababneh, Mustafa title = Presence of Infectious Bronchitis Virus Strain CK/CH/LDL/97I in the Middle East date = 2012-04-11 pages = extension = .txt mime = text/plain words = 2375 sentences = 117 flesch = 60 summary = The sequenced fragment of the S1 gene of the CK/CH/LDL/97I strain had less than 80% nucleotide identity to the IBV vaccine strains commonly used in the Middle East (M41 and H120). In this study, the CK/CH/LDL/97I-like strains were isolated from three different Middle Eastern countries (Jordan, Saudi Arabia, and Iraq) in 2011. Pathogenicity of a QX strain of infectious bronchitis virus in specific pathogen free and commercial broiler chickens, and evaluation of protection induced by a vaccination programme based on the Ma5 and 4/91 serotypes Phylogenetic analysis of infectious bronchitis coronaviruses newly isolated in China, and pathogenicity and evaluation of protection induced by Massachusetts serotype H120 vaccine against QX-like strains Evaluation of the protection conferred by commercial vaccines and attenuated heterologous isolates in China against the CK/CH/LDL/97I strain of infectious bronchitis coronavirus Characterization of three infectious bronchitis virus isolates from China associated with proventriculus in vaccinated chickens cache = ./cache/cord-257999-apg4uhhq.txt txt = ./txt/cord-257999-apg4uhhq.txt === reduce.pl bib === id = cord-269150-d1sgnxc0 author = Tan, Yong Wah title = Binding of the 5′-untranslated region of coronavirus RNA to zinc finger CCHC-type and RNA-binding motif 1 enhances viral replication and transcription date = 2012-02-22 pages = extension = .txt mime = text/plain words = 6977 sentences = 346 flesch = 53 summary = In a screen based on a yeast three-hybrid system using the 5′-untranslated region (5′-UTR) of SARS coronavirus (SARS-CoV) RNA as bait against a human cDNA library derived from HeLa cells, we found a positive candidate cellular protein, zinc finger CCHC-type and RNA-binding motif 1 (MADP1), to be able to interact with this region of the SARS-CoV genome. In this study, we describe the interaction of a cellular protein, MADP1 (zinc finger CCHC-type and RNA binding motif 1) with the 5 0 -UTR of IBV and SARS-CoV, using yeast-based three hybrid screen (34) and RNA-binding assays. Using indirect immunofluorescence, we confirmed that MADP1, despite being reported as a nuclear protein (35) , was detected in the cytoplasm of virus-infected cells and partially co-localized with the RTCs. Upon silencing of MADP1 using siRNA, viral RNA synthesis on general has been affected, resulting in a lower replication efficiency and infectivity. cache = ./cache/cord-269150-d1sgnxc0.txt txt = ./txt/cord-269150-d1sgnxc0.txt === reduce.pl bib === id = cord-260799-kx6hfpu0 author = Mahmood, Zana H. title = Isolation and molecular characterization of Sul/01/09 avian infectious bronchitis virus, indicates the emergence of a new genotype in the Middle East date = 2011-05-12 pages = extension = .txt mime = text/plain words = 3504 sentences = 176 flesch = 54 summary = title: Isolation and molecular characterization of Sul/01/09 avian infectious bronchitis virus, indicates the emergence of a new genotype in the Middle East Infectious bronchitis virus (IBV) was isolated from trachea and kidney tissues of eight broiler farms in Kurdistan region of North Iraq from 2008 to 2010. Veterinary Microbiology 150 (2011) 21-27 Infectious bronchitis virus (IBV) was isolated from trachea and kidney tissues of eight broiler farms in Kurdistan region of North Iraq from 2008 to 2010. In order to investigate IBV genotypes in Iraq, where the disease is endemic and widely spread in vaccinated and unvaccinated poultry farms mainly associated with kidney damage and urolethiasis, identification and molecular characterization of IBV (Sul/01/09) isolated from eight infected broiler farms was conducted and the deduced amino acid sequence of the S1 subunit of the virus was compared with geographically related isolates. cache = ./cache/cord-260799-kx6hfpu0.txt txt = ./txt/cord-260799-kx6hfpu0.txt === reduce.pl bib === id = cord-259505-7hiss0j3 author = Kong, Qingming title = Proteomic analysis of purified coronavirus infectious bronchitis virus particles date = 2010-06-09 pages = extension = .txt mime = text/plain words = 6907 sentences = 355 flesch = 44 summary = It is an important prerequisite for the functional studies to know the protein composition of the purified viral particles, as it allows the analysis of specific proteins and their roles during the virus life cycle, resulting in better understanding of the infection process and the pathogenesis of viruses. To date, there have been no reports about TENP associated with virus, but it's an enriched and abundant protein identified in purified infectious bronchitis particles which suggests to us that it may be a requisite host protein in IBV life cycles. The present study 1) provides the first proteomic analysis of infectious bronchitis particles, 2) establishes the most comprehensive proteomic index of IBV and 3) shows that most of the virion incorporated host proteins have central roles in virus life cycle. cache = ./cache/cord-259505-7hiss0j3.txt txt = ./txt/cord-259505-7hiss0j3.txt === reduce.pl bib === id = cord-260667-5aurua6o author = Falchieri, Marco title = Avian metapneumoviruses expressing Infectious Bronchitis virus genes are stable and induce protection date = 2013-05-24 pages = extension = .txt mime = text/plain words = 3817 sentences = 216 flesch = 51 summary = The study investigates the ability of subtype A Avian metapneumovirus (AMPV) to accept foreign genes and be used as a vector for delivery of Infectious bronchitis virus (IBV) QX genes to chickens. First was a German field isolate (Virus A) passaged in Vero cells [9] and found avirulent in turkeys [12] , second was Virus AvF which contained an F gene modification found to better induce protection in turkeys [12] and third was 309/04, a virulent field isolate deriving from a subtype A vaccine and arising in field conditions [23] . When IBV MF recombinants were used to inoculate one-day-old chickens, many induced IBV protection of the trachea, yet serology and real time RT PCR virus detection indicated poor tracheal replication. Induction of protective immunity in chickens vaccinated with infectious bronchitis virus S1 glycoprotein expressed by a recombinant baculovirus cache = ./cache/cord-260667-5aurua6o.txt txt = ./txt/cord-260667-5aurua6o.txt === reduce.pl bib === id = cord-265258-2rmtsyns author = Domanska‐Blicharz, K. title = Specific detection of GII‐1 lineage of infectious bronchitis virus date = 2017-07-03 pages = extension = .txt mime = text/plain words = 3393 sentences = 170 flesch = 53 summary = The real-time RT-PCR assays seem to be effective tools for IBV-type identification and although S1 coding region is prone to mutations, methods aimed in this gene detection has been recently developed and used for GI-1 (Mass, Connecticut), GI-9 (Arkansas), GI-11 (SAI), G1-16 (ASAII) and GIV-1 (DE072/GA98) lineages (Acevedo et al. Here, we describe the development of a TaqMan probe-based real-time RT-PCR for the detection of GII-1 (D1466-like) IBV lineage. Moreover, the assay developed in the present study showed to be highly specific as no fluorescent signals were detected with other tested IBV lineages or chicken RNA viral pathogens. In conclusion, the TaqMan probe-based real-time RT-PCR assay described here is a time-saving, specific, sensitive and reliable method of detection of GII-1 lineage (D1466-like) of IBV which could successfully replace standard nested RT-PCR. Development and evaluation of a real-time Taqman RT-PCR assay for the detection of infectious bronchitis virus from infected chickens cache = ./cache/cord-265258-2rmtsyns.txt txt = ./txt/cord-265258-2rmtsyns.txt === reduce.pl bib === id = cord-003334-ion97n4b author = De Silva Senapathi, Upasama title = The In Ovo Delivery of CpG Oligonucleotides Protects against Infectious Bronchitis with the Recruitment of Immune Cells into the Respiratory Tract of Chickens date = 2018-11-15 pages = extension = .txt mime = text/plain words = 5827 sentences = 266 flesch = 54 summary = Although the delivery of CpG ODNs in ovo at embryo day (ED) 18 has been shown to reduce infectious bronchitis virus (IBV) loads in embryonic chicken lungs pre-hatch, whether in ovo delivered CpG ODNs are capable of protecting chickens against a post-hatch challenge is unknown. We found significantly higher survival rates and reduced IBV infection in the chickens following the pre-treatment of the ED 18 eggs with CpG ODNs. At 3 days post infection (dpi), we found an increased recruitment of macrophages, cluster of differentiation (CD)8α+ and CD4+ T lymphocytes, and an up-regulation of interferon (IFN)-γ mRNA in the respiratory tract of the chickens. Considering that we observed a significant reduction in the IBV induced morbidity and mortality of in ovo CpG ODN pre-treated birds correlating with varying degrees of increased macrophages, CD4+, and CD8α+ T cells in the tracheal and lung tissues, we needed to further elucidate the mechanisms by which these immune cells were efficiently recruited. cache = ./cache/cord-003334-ion97n4b.txt txt = ./txt/cord-003334-ion97n4b.txt === reduce.pl bib === id = cord-282314-9cua2jzg author = Albanese, Grace A. title = Biological and molecular characterization of ArkGA: A novel Arkansas serotype vaccine that is highly attenuated, efficacious, and protective against homologous challenge date = 2018-10-01 pages = extension = .txt mime = text/plain words = 6368 sentences = 324 flesch = 50 summary = Abbreviations: Ark99, Arkansas 99; ArkDPI, Arkansas Delmarva Poultry Industry; ArkGA, Arkansas Georgia; CAS, chorioallantoic sac; C T , cycle threshold; EID 50 , 50% embryo infective dose; IBV, infectious bronchitis virus; MHV, murine hepatitis virus; nsp2, nonstructural protein 2; nsp3, nonstructural protein 3; P, passage; PBS, phosphate-buffered saline; qRT-PCR, quantitative real-time reverse-transcriptase polymerase chain reaction; RT-PCR, reverse-transcriptase polymerase chain reaction; SARS-CoV, severe acute respiratory syndrome coronavirus; SD, standard deviation; SEM, standard error of mean; SNP, single nucleotide polymorphism; SPF, specific-pathogen free; US, United States; USDA, United States Department of Agriculture. In P60, SNPs were seen in S1 as well as S2 of the Table 2 S1 amino acid sequence comparison of ArkGA vaccine virus and viral RNA isolated from 5 choanal cleft palate swabs on days 7, 10, and 14 post-vaccination. cache = ./cache/cord-282314-9cua2jzg.txt txt = ./txt/cord-282314-9cua2jzg.txt === reduce.pl bib === id = cord-262226-7kwkla73 author = Fang, Shouguo title = Identification of two ATR-dependent phosphorylation sites on coronavirus nucleocapsid protein with nonessential functions in viral replication and infectivity in cultured cells date = 2013-07-09 pages = extension = .txt mime = text/plain words = 5629 sentences = 277 flesch = 51 summary = authors: Fang, Shouguo; Xu, Linghui; Huang, Mei; Qisheng Li, Frank; Liu, D.X. title: Identification of two ATR-dependent phosphorylation sites on coronavirus nucleocapsid protein with nonessential functions in viral replication and infectivity in cultured cells Western blot analysis with antibodies against IBN N and ATM/ATR substrates showed that significantly less phosphorylated IBV N protein was detected in the UV-irradiated, transfected cells in the presence of 10 μM of SchB (Fig. 2d ). The results showed that the ATR-dependent phosphorylation of N protein was detected only in cells infected with wild type, Nm1 and Nm2 mutant viruses (Fig. 4a) . Western blot analysis of total cell lysates with antibodies against ATM/ATR substrates showed, once again, detection of the ATR-dependent phosphorylation of IBV N protein in cells infected with the virus (Fig. 4b) . cache = ./cache/cord-262226-7kwkla73.txt txt = ./txt/cord-262226-7kwkla73.txt === reduce.pl bib === id = cord-291754-1zxztadu author = Zhao, Ye title = Successful establishment of a reverse genetic system for QX-type infectious bronchitis virus and technical improvement of the rescue procedure date = 2019-10-15 pages = extension = .txt mime = text/plain words = 6848 sentences = 344 flesch = 54 summary = In this study, a pathogenic avian infectious bronchitis virus (IBV) QX-type strain YN was successfully rescued by vaccinia virus based reverse genetic technology. To compare the in vitro replication of the rescued virus rYN and its parental strain YN on CEK cells, 200 μl PBS containing 10 3.0 TCID 50 of rYN or YN virus were inoculated onto the CEK cells in 24-well plates, and 200 μl supernatants from three wells from each group were harvested at the time points of 6, 12, 24, 36, 48, and 60 hpi for a real-time PCR detection assay for IBV N gene as described above. Collectively, these results demonstrate the successful rescue of the pathogenic IBV strain YN from cloned cDNA by using electroporation of full-length IBV in vitro transcripts into N-protein expressing cells and subsequent virus amplification in the allantoic cavities of ECE. cache = ./cache/cord-291754-1zxztadu.txt txt = ./txt/cord-291754-1zxztadu.txt === reduce.pl bib === id = cord-281526-7t9e4lgn author = Yin, Lijuan title = Immunogenicity and protective efficacy of recombinant fusion proteins containing spike protein of infectious bronchitis virus and hemagglutinin of H3N2 influenza virus in chickens date = 2016-09-02 pages = extension = .txt mime = text/plain words = 4464 sentences = 234 flesch = 47 summary = title: Immunogenicity and protective efficacy of recombinant fusion proteins containing spike protein of infectious bronchitis virus and hemagglutinin of H3N2 influenza virus in chickens To investigate whether the recombinant proteins could induce better immune response against IBV infection, we detected IBVspecific antibody in the sera of vaccinated chicken using indirect ELISA. Two weeks after booster vaccination (day 28), the levels of anti-IBV antibodies increased further in chickens immunized with inactivated M41 virus, rS1, rS1-H3(TM) and rS1-HA2. After challenged with virulent IBV M41 strain, our results demonstrated that fusion proteins performed better protection compared with inactivated M41 vaccine and recombinant rS1 protein alone, while the latter groups presented similar protection ratio. The S1 glycoprotein but not the N or M proteins of avian infectious bronchitis virus induces protection in vaccinated chickens Induction of protective immunity in chickens vaccinated with infectious bronchitis virus S1 glycoprotein expressed by a recombinant baculovirus cache = ./cache/cord-281526-7t9e4lgn.txt txt = ./txt/cord-281526-7t9e4lgn.txt === reduce.pl bib === id = cord-272437-gvzfl8c3 author = Zhao, Jing title = Replicase 1a gene plays a critical role in pathogenesis of avian coronavirus infectious bronchitis virus date = 2020-08-20 pages = extension = .txt mime = text/plain words = 565 sentences = 51 flesch = 57 summary = title: Replicase 1a gene plays a critical role in pathogenesis of avian coronavirus infectious bronchitis virus Avian coronavirus infectious bronchitis virus (IBV) is an important pathogen threatening poultry production worldwide. Our findings demonstrate that the replicase 1a gene of avian coronavirus IBV is a determinant of pathogenicity. In this study, we used an IBV reverse genetics system based on virulent strain Fig. 2. Recombinant live attenuated avian coronavirus 431 vaccines with deletions in the accessory genes 3ab and/or 5ab protect against infectious 432 bronchitis in chickens attenuated Chinese QX-like infectious bronchitis virus strain as a candidate vaccine S gene and 5a accessory gene 455 are responsible for the attenuation of virulent infectious bronchitis coronavirus cache = ./cache/cord-272437-gvzfl8c3.txt txt = ./txt/cord-272437-gvzfl8c3.txt === reduce.pl bib === id = cord-263476-ju7xqwa7 author = Xia, Jing title = Phylogenetic and antigenic analysis of avian infectious bronchitis virus in southwestern China, 2012–2016 date = 2016-08-13 pages = extension = .txt mime = text/plain words = 5699 sentences = 276 flesch = 55 summary = The aim of this study was to decipher the molecular epidemiological and antigenic characteristics of infectious bronchitis virus strains (IBVs) isolated in recent years in southwestern China. The antigenicity of ten IBVs, including seven field strains and commonly used vaccine strains, were assayed with a viral cross-neutralization assay in chicken embryonated kidney cells (CEK). To determine the antigenic relatedness between the field IBV isolates and the vaccine viral strains, double-direction viral cross-neutralization (VN) tests were performed in chicken embryo kidney (CEK) cells using constant viral titers and diluted serum. The tested strains came from six different genotypes and included seven IBV field isolates (Sczy3, cK/CH/SCDY/141030, cK/CH/SCLS/140104, cK/CH/CQKX/ 150203, cK/CH/SCYB/140913, cK/CH/SCMY/10I, cK/CH/SCYB/141102) and the three most commonly used vaccine viral strains (H120, M41, and 4/91). Ten IBVs, including seven field strains from different genotype backgrounds and three commonly used vaccine strains (H120, 4/91, and M41), were analyzed and grouped into four serotypes: Massachusetts (Mass hereafter), 793B, Sczy3, and SCYB. cache = ./cache/cord-263476-ju7xqwa7.txt txt = ./txt/cord-263476-ju7xqwa7.txt === reduce.pl bib === id = cord-291174-rym84kni author = Yang, Yazhi title = A label-free electrochemical assay for coronavirus IBV H120 strain quantification based on equivalent substitution effect and AuNPs-assisted signal amplification date = 2020-10-23 pages = extension = .txt mime = text/plain words = 3577 sentences = 234 flesch = 51 summary = title: A label-free electrochemical assay for coronavirus IBV H120 strain quantification based on equivalent substitution effect and AuNPs-assisted signal amplification According to the differences of S1 protein in various infectious bronchitis virus (IBV) strains, a target DNA sequence that can specifically recognize H120 RNA forming a DNA-RNA hybridized double-strand structure has been designed. Therefore, developing a rapid and sensitive method for identification and quantification of different IBV strains based on hypervariable region of S1 gene can effectively solve the problem, which plays important roles in IB early diagnosis and control, especially for vaccine production. Herein, a label-free electrochemical assay based on equivalent substitution effect and AuNPs-assisted signal amplification is developed for identification and quantification detection of IBV H120 strain. In this work, we designed the sequence of the target DNA based on the hypervariable region in the S1 gene between different IBV strains, then, constructed the standard plasmid containing characteristic sequence of S1 gene in H120 strain, Fig. 2 Real-time fluorescence quantitative PCR plot. cache = ./cache/cord-291174-rym84kni.txt txt = ./txt/cord-291174-rym84kni.txt === reduce.pl bib === id = cord-265508-t1nfyzf5 author = Boursnell, M.E.G. title = Sequencing of coronavirus IBV genomic RNA: a 195-base open reading frame encoded by mRNA B date = 1984-08-31 pages = extension = .txt mime = text/plain words = 2130 sentences = 125 flesch = 61 summary = authors: Boursnell, M.E.G.; Brown, T.D.K. title: Sequencing of coronavirus IBV genomic RNA: a 195-base open reading frame encoded by mRNA B Abstract DNA sequencing of genomic cDNA clones of avian infectious bronchitis virus (IBV) has been carried out. The organisation of the messenger RNAs and in vitro translation studies have led to the hypothesis that the 5'-most sequences of each mRNA, which are not present in the next smallest mRNA, contain the complete coding sequences for the major protein product produced by that messenger species (Stern and Kennedy, 1980b; Lai et al., 1981) . In this paper we report the nucleotide sequence of a cloned cDNA copy of IBV genomic RNA in the region corresponding to the 5' end of mRNA B. The region of the IBV sequence presented in this paper contains the 5' ends, on the viral genome, of mRNAs A and B. cache = ./cache/cord-265508-t1nfyzf5.txt txt = ./txt/cord-265508-t1nfyzf5.txt === reduce.pl bib === === reduce.pl bib === id = cord-001083-vy1nxax2 author = Malagnac, Fabienne title = Rab-GDI Complex Dissociation Factor Expressed through Translational Frameshifting in Filamentous Ascomycetes date = 2013-09-19 pages = extension = .txt mime = text/plain words = 6815 sentences = 339 flesch = 55 summary = In the model fungus Podospora anserina, the PaYIP3 gene encoding the orthologue of the Saccharomyces cerevisiae YIP3 Rab-GDI complex dissociation factor expresses two polypeptides, one of which, the long form, is produced through a programmed translation frameshift. To construct a C-terminal GFP fusion of the frameshifted protein, the 535 bp 39-end fragment of the 39 ORF of the PaYIP3 gene was PCR-amplified using the orf39w-bgl2 (59-GAA-GATCTGGCTCTAGTGCATCCAGGACAC-39) and orf39c-sma1 (59-TTTCCCGGGTCGCTTTCCTTCTAGCAGTACC-39) oligonucleotides, containing, respectively, the BglII and SmaI sites (underlined in the sequence). The PaYIP3 c corrected allele was created by inserting a C in codon nu168, which is just upstream of the frameshift site, and produced the 61.6 kDa polypeptide resulting from the fusion of the proteins produced by the 39 and 59 ORFs. Introduction of PaYIP3 c did not result in the restoration of a wildtype phenotype: ring and ascospore production on wood shaving medium was identical to that observed with the PaYIP3 D mutant (Fig. 5) . cache = ./cache/cord-001083-vy1nxax2.txt txt = ./txt/cord-001083-vy1nxax2.txt === reduce.pl bib === id = cord-273846-l0elcfe8 author = Ganapathy, Kannan title = Effects of cold storage on detection of avian infectious bronchitis virus in chicken carcasses and local antibodies in tracheal washes date = 2005-02-24 pages = extension = .txt mime = text/plain words = 2440 sentences = 134 flesch = 59 summary = title: Effects of cold storage on detection of avian infectious bronchitis virus in chicken carcasses and local antibodies in tracheal washes In order to test the survivability of infectious bronchitis virus (IBV) in dead chicken carcasses during 24 h of cold storage, 7 week-old specific-pathogen-free chickens were infected with virulent IBV Massachusetts strain M41, and were killed humanely 10 days later. Trachea, lung, kidney and rectum were collected for virus isolation by tracheal organ culture (TOC) or embryonated chicken eggs (ECE), and detection by nested reverse-transcriptase polymerase chain reaction (RT-PCR). Diagnosis of infectious bronchitis virus (IBV) is confirmed by isolation of the virus using either chicken embryonated eggs (ECE) or tracheal organ culture (TOC) and detection by reverse-transcriptase polymerase chain reaction (RT-PCR) (Cavanagh and Naqi, 2003; Gelb and Jackwood, 1998) . The use of chicken tracheal organ cultures for the isolation and assay of avian infectious bronchitis virus cache = ./cache/cord-273846-l0elcfe8.txt txt = ./txt/cord-273846-l0elcfe8.txt === reduce.pl bib === id = cord-259480-1tqfoecc author = Li, Huixin title = Recombinant duck enteritis viruses expressing major structural proteins of the infectious bronchitis virus provide protection against infectious bronchitis in chickens date = 2016-03-02 pages = extension = .txt mime = text/plain words = 6015 sentences = 300 flesch = 54 summary = To design an alternative vaccine for control of infectious bronchitis in chickens, three recombinant duck enteritis viruses (rDEVs) expressing the N, S, or S1 protein of infectious bronchitis virus (IBV) were constructed using conventional homologous recombination methods, and were designated as rDEV-N, rDEV-S, and rDEV-S1, respectively. After challenge with a homologous virulent IBV strain at 21 days post-immunization, vaccinated groups showed significant differences in the percentage of birds with clinical signs, as compared to the control group (p < 0.01), as the two covalent-vaccination groups and the rDEV-S group provided better protection than the rDEV-Nor rDEV-S1-vaccinated group. The N phosphoprotein is conserved among different IBV serotypes and can induce high titers of cross-reactive antibodies and cell-mediated immunity that protects chickens from acute infection, thus it is used as a target protein in designing vaccines against IB (Williams et al., 1992; Collisson et al., 2000; Seo et al., 1997) . Antibody responses of chickens vaccinated with recombinant duck enteritis viruses expressing the N, S or S1 gene of infectious bronchitis virus (IBV). cache = ./cache/cord-259480-1tqfoecc.txt txt = ./txt/cord-259480-1tqfoecc.txt === reduce.pl bib === id = cord-262940-eyejnexx author = Liu, Genmei title = Assembly and immunogenicity of coronavirus-like particles carrying infectious bronchitis virus M and S proteins date = 2013-11-12 pages = extension = .txt mime = text/plain words = 3853 sentences = 175 flesch = 49 summary = In the present study, we assembled IBV VLPs containing M and S proteins using a baculovirus expression system and we further evaluated the VLPs immune responses in mice and chickens. The results showed that, 2 weeks after the primary vaccination (day 14), both of VLPs and inactivated H120 groups could not detected serum IgG titers, and the differences between these and PBS groups were not statistically significant (P > 0.05); but following the second immunization (day 28), the IgG titers of the VLPs and inactivated H120 groups increased (Fig. 6 ) and were significantly higher (P < 0.01) than the PBS group. The results showed that VLPs and inactivated H120 groups had statistically significantly higher neutralizing antibody titers (P < 0.01) than the PBS group (Fig. 7) . Virus like particles (VLPs) and inactivated H120 groups had significantly higher neutralizing antibody titers (P < 0.01) than the PBS group. cache = ./cache/cord-262940-eyejnexx.txt txt = ./txt/cord-262940-eyejnexx.txt === reduce.pl bib === id = cord-290638-7ro72sv3 author = Lenstra, Johannes A. title = Antigenicity of the peplomer protein of infectious bronchitis virus date = 1989-01-31 pages = extension = .txt mime = text/plain words = 3960 sentences = 230 flesch = 53 summary = Abstract To study the antigenic structure of the peplomer protein of the avian coronavirus infectious bronchitis virus, fragments from the peplomer gene were generated by restriction-enzyme cleavage or by limited DNase digestion and inserted in the Escherichia coli expression plasrnid pEX (Stanley and Luzio, 1984). Recombinants expressing the IBV gene fragments were selected by immunoscreening with a rabbit antiserum or, when the expression product was not recognized antigenically, by hybridization followed by gel electrophoresis of the protein expression products. Figure 2 (C) shows a Western blot of hybrid proteins screened with this MAb. The strong binding to fragments p2, s4, psl and ps2 localizes the epitope of MAb 26.1 between residues 390 and 612, the same region that is recognized by all polyclonal sera. The localization of epitopes within stretches of 10-20 residues in several coronaviruses (Fig. 4 , unpublished results) demonstrates that the binding of antibody does not depend on particular flanking sequences, and that any nativelike folding of the epitope in the hybrid protein is confined to the same small region. cache = ./cache/cord-290638-7ro72sv3.txt txt = ./txt/cord-290638-7ro72sv3.txt === reduce.pl bib === id = cord-285330-td4vr0zv author = Mohammadi, Ali title = Viral quantity and pathological changes in broilers experimentally infected by IRFIBV32 isolate of infectious bronchitis virus date = 2015-11-12 pages = extension = .txt mime = text/plain words = 3157 sentences = 180 flesch = 56 summary = title: Viral quantity and pathological changes in broilers experimentally infected by IRFIBV32 isolate of infectious bronchitis virus An Iranian isolate of avian infectious bronchitis virus IRFIBV32 was quantified in experimentally infected broilers using real-time reverse transcriptase polymerase chain reaction and histopathological changes was investigated. In this study, we identified IBV load in different tissues of experimentally infected broilers to clarify the replication strength of IRFIBV32 Isolate at intervals post challenge. Gross lesions were recorded and their trachea, lungs, kidneys, caecal tonsils, testes and ovaries were aseptically collected separately for the virus detection, titration and histopathological evaluations. We detected the viral RNA in the caecal tonsils of infected chicken from 1 to 20 dpi and the maximal loads of the virus were on 5 dpi. Pathogenesis and tissue distribution of avian infectious bronchitis virus isolate IRFIBV32 (793/b serotype) in experimentally infected broiler chickens Development and evaluation of a real-time Taqman RT-PCR assay for the detection of infectious bronchitis virus from infected chickens cache = ./cache/cord-285330-td4vr0zv.txt txt = ./txt/cord-285330-td4vr0zv.txt === reduce.pl bib === === reduce.pl bib === id = cord-293651-96cmduez author = Callison, Scott A. title = Development and evaluation of a real-time Taqman RT-PCR assay for the detection of infectious bronchitis virus from infected chickens date = 2006-08-28 pages = extension = .txt mime = text/plain words = 4742 sentences = 216 flesch = 56 summary = We also collected a total of 120 tracheal swabs at six different time points from birds experimentally infected with different dosages of IBV and found that, independent of the dose given, the viral load in the trachea plateau at 5 days post-inoculation. Molecular assays use the reverse transcriptase-polymerase chain reaction (RT-PCR) to detect viral RNA directly from a clinical sample or from virus isolated in a laboratory host system. Clinical samples consisting of 229 tracheal swabs from commercial chickens experiencing upper-respiratory disease, submitted as routine diagnostic cases to the Delaware (Georgetown, DE) and Maryland (Salisbury, MD) State Diagnostic Laboratories were tested by the real-time RT-PCR assay, as well as, by virus isolation at those laboratories (Gelb and Jackwood, 1998) . In this report we present the development and evaluation of a real-time Taqman ® -based RT-PCR assay for the detection and quantification of IBV genomic RNA directly from tracheal swabs. cache = ./cache/cord-293651-96cmduez.txt txt = ./txt/cord-293651-96cmduez.txt === reduce.pl bib === id = cord-271359-dpa8zzc3 author = Sapats, S. I. title = Novel Variation in the N Protein of Avian Infectious Bronchitis Virus date = 1996-12-15 pages = extension = .txt mime = text/plain words = 2317 sentences = 141 flesch = 66 summary = Despite the considerable variation observed between the two virus groups, all N proteins contained a high proportion of basic residues, 80% of which were conserved in position. The N protein of all coronaviruses virus lacks a sequence of 184-196 nucleotides that has is overall very basic and in IBV contains 409 amino acids been detected in five other IBV strains. located downstream of the HVR (315 nucleotides ending The N protein of 27 strains of IBV isolated over a period at the poly(A) tail) is highly conserved in strains of IBV, of 60 years from diverse locations such as the U.S.A., the probably indicative of its role in the synthesis of negative-UK, Holland, Saudi Arabia, and Japan has been shown to strand RNA. For each virus two or more for the N proteins of IBV also contain a region of complete independent cDNA clones were sequenced using the conservation between positions 242 and 296 (4). cache = ./cache/cord-271359-dpa8zzc3.txt txt = ./txt/cord-271359-dpa8zzc3.txt === reduce.pl bib === id = cord-286473-sl5zy8nj author = Gomaa, M.H. title = Complete genomic sequence of turkey coronavirus date = 2008-05-12 pages = extension = .txt mime = text/plain words = 7980 sentences = 411 flesch = 61 summary = Turkey coronavirus (TCoV), one of the least characterized of all known coronaviruses, was isolated from an outbreak of acute enteritis in young turkeys in Ontario, Canada, and the full-length genomic sequence was determined. The RdRp motif was highly conserved among all coronaviruses, and TCoV-MG10 also showed a high degree of sequence identity for RdRp by 64%, 62%, 94% at the amino acid level to HCoV-229E, BCoV, IBV, respectively. The M gene seemed to be highly conserved within group III coronaviruses since TCoV M showed a 94% nucleotide identity to IBV M. This ORF is unique to TCoV and IBV, the only Group III coronaviruses for which sequence data in this region of the genome are available. In addition, we have identified a putatively functional gene (ORF-X) shared among all sequenced IBV and TCoV strains that may be a shared feature of all group III coronaviruses. cache = ./cache/cord-286473-sl5zy8nj.txt txt = ./txt/cord-286473-sl5zy8nj.txt === reduce.pl bib === id = cord-261388-d56ci0hl author = Tibbles, K.W title = Activity of a purified His-tagged 3C-like proteinase from the coronavirus infectious bronchitis virus date = 1999-05-28 pages = extension = .txt mime = text/plain words = 3906 sentences = 173 flesch = 51 summary = Previous studies in vitro of the processing of cloned polyprotein fragments from the coronavirus infectious bronchitis virus (IBV) large open reading frame (ORF1), confirmed the activity of a predicted 3C-like proteinase (3CLP) domain and suggested that the proteinase is released autocatalytically from the polyprotein in the form of a 35 kDa protein, 3CLpro, capable of further cleavages in trans. The bacterial expression system described utilises the minimum processing unit identified in our previous studies which established that, in addition to the 3CLP domain, MP2 protein sequence between the Q/S 4 cleavage target and a point delimited by an NcoI restriction site (ntd position 10118) was that minimally required for processing. Identification of a 24-kDa polypeptide processed from the coronavirus infectious bronchitis virus 1a polyprotein by the 3C-like proteinase and determination of its cleavage sites cache = ./cache/cord-261388-d56ci0hl.txt txt = ./txt/cord-261388-d56ci0hl.txt === reduce.pl bib === id = cord-273661-egpyvqrw author = Mo, Mei-Lan title = Molecular Characterization of Major Structural Protein Genes of Avian Coronavirus Infectious Bronchitis Virus Isolates in Southern China date = 2013-12-04 pages = extension = .txt mime = text/plain words = 4705 sentences = 215 flesch = 51 summary = To gain comprehensive genetic information of circulating avian coronavirus infectious bronchitis virus (IBV) isolates in China, analysis of the phylogenetic tree, entropy of the amino acid sequences, and the positive selection as well as computational recombinations of S1, M and N genes of 23 IBV isolates was conducted in the present study. Therefore, in the present study we performed the analysis of the phylogenetic tree, of the entropy of the amino acid sequences, of positive selection as well as of computational recombination based on the sequencing results of the viral structural protein genes S1, M and N in order to provide molecular epidemiology information of IBV and to lay a good foundation for the control of IB in the field. cache = ./cache/cord-273661-egpyvqrw.txt txt = ./txt/cord-273661-egpyvqrw.txt === reduce.pl bib === id = cord-272305-eniovfwy author = Zhao, Ye title = Safety and efficacy of an attenuated Chinese QX-like infectious bronchitis virus strain as a candidate vaccine date = 2015-10-22 pages = extension = .txt mime = text/plain words = 5918 sentences = 359 flesch = 55 summary = Strain YN-inoculated birds had clinical signs of varying severity with 30% mortality, while the attenuated group appeared healthy, with less tissue damage. The resulting attenuated YN strain was shorted as aYN and was titrated by inoculating 10-fold serial dilutions with phosphate-buffered saline (PBS) of the virus stocks into the allantoic sac of 10-day-old SPF embryonated eggs. Gross changes were noted and samples of trachea, kidney, lung, proventriculus, duodenum, and bursa of Fabricius were collected for virus detection via real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) and in 10% neutral formalin for histopathological examination. In terms of the real-time RT-qPCR examination, both strains were detected in respiratory and non-respiratory tissues, including the kidney, trachea, lungs, proventriculus, duodenum, and bursa of Fabricius, indicating viral replication in these organs; however, this was relatively limited in the birds infected with the YN attenuated strain. Efficacy and safety of an attenuated live QX-like infectious bronchitis virus strain as a vaccine for chickens cache = ./cache/cord-272305-eniovfwy.txt txt = ./txt/cord-272305-eniovfwy.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-291718-cz1bi0ym author = Yu, Liping title = The papain-like protease of avian infectious bronchitis virus has deubiquitinating activity date = 2017-03-18 pages = extension = .txt mime = text/plain words = 3426 sentences = 180 flesch = 54 summary = Furthermore, the IBV replicase-encoded PLP, including the downstream transmembrane (TM) domain, is a DUB enzyme and dramatically reduced the level of Ub-conjugated proteins, while processing both K48and K63-linked polyubiquitin chains. Overall, these results demonstrate that the IBV-encoded PLP-TM functions as a DUB enzyme and suggest that IBV may interfere with the activation of host antiviral signaling pathway by degrading polyubiquitin-associated proteins. Further experiments indicated that the proteinase PLP-TM plays an important role in IBV DUB activity and can process both K48-and K63-linked polyubiquitin chains. Overall, the results of our study show that IBV has DUB activity and confirm that PLP-TM is not only a classic papain-like protease encoded by IBV but is also a multifunctional protein that plays important roles in the regulation of interactions between IBV and host antiviral innate immune response proteins. IBV PLP-TM may prevent the activation of host antiviral signaling pathways by degrading polyubiquitin chains associated with ubiquitin proteins. cache = ./cache/cord-291718-cz1bi0ym.txt txt = ./txt/cord-291718-cz1bi0ym.txt === reduce.pl bib === id = cord-293081-40pa5g89 author = Li, Jun title = Preliminary crystallographic analysis of avian infectious bronchitis virus main protease date = 2006-12-16 pages = extension = .txt mime = text/plain words = 1510 sentences = 95 flesch = 61 summary = IBV belongs to group III (Lai & Holmes, 2001) , which only infects avian species, and leads to a highly contagious disease affecting the respiratory, reproductive, neurological and renal systems of chickens, resulting in a drop in egg production in adult birds and damaging the developing reproductive system in young birds. To date, several crystal structures of coronavirus M pro s have been reported for group I and II coronaviruses, which mostly infect mammals (Anand et al., 2002 Yang et al., 2003) . The crystals belong to space group P6 1 22, with unit-cell parameters a = b = 119.1, c = 270.7 Å , = = 90, = 120 (see Table 1 Typical crystals of IBV M pro grown by the hanging-drop method in 2.5% PEG 4000, 12% 2-propanol, 0.1 M sodium cacodylate pH 6.5. cache = ./cache/cord-293081-40pa5g89.txt txt = ./txt/cord-293081-40pa5g89.txt === reduce.pl bib === id = cord-294679-7pklrmz5 author = Wei, Lei title = Purification, crystallization and preliminary crystallographic analysis of avian infectious bronchitis virus nsp3 ADRP domain date = 2008-08-09 pages = extension = .txt mime = text/plain words = 1069 sentences = 73 flesch = 61 summary = title: Purification, crystallization and preliminary crystallographic analysis of avian infectious bronchitis virus nsp3 ADRP domain Avian infectious bronchitis virus (IBV) encodes 15 nonstructural proteins (nsps) which play crucial roles in RNA transcription and genome replication. One of them, nsp3, contains an ADRP (adenosine diphosphate-ribose-1′-phosphatase) domain which was revealed in recent studies to have ADP-ribose-1′-monophos­phatase (Appr-1′-pase) activity. The gene segment encoding the IBV nsp3 ADRP domain has been cloned and expressed in Escherichia coli. Considering that the genomes encoding the nonstructural proteins (nsps) are conserved among SARS-Cov, IBV, human-Cov 229E etc., the study of IBV will facilitate the thorough understanding of coronaviruses. Initial crystals were obtained from Index Screen condition No. 84 containing 0.2 M magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5, 25%(w/v) polyethylene glycol 3350. A typical diffraction pattern of an IBV nsp3 ADRP domain crystal collected on a Rigaku R-AXIS IV ++ image-plate detector. Avian infectious bronchitis virus nsp3 cache = ./cache/cord-294679-7pklrmz5.txt txt = ./txt/cord-294679-7pklrmz5.txt === reduce.pl bib === id = cord-285323-473d7zvg author = Jang, Hyesun title = Altered pro-inflammatory cytokine mRNA levels in chickens infected with infectious bronchitis virus date = 2013-09-01 pages = extension = .txt mime = text/plain words = 4802 sentences = 228 flesch = 49 summary = The KIIa genotype (Kr/ADL110002/2011) induced clinical signs accompanied by the excessive production of pro-inflammatory cytokines and a higher viral load. In chickens infected with this isolate, simultaneous peaks in the viral copy number and cytokine production were observed at 7 dpi in the trachea and 9 d postinoculation in the kidney. In chickens infected with this isolate, simultaneous peaks in the viral copy number and cytokine production were observed at 7 dpi in the trachea and 9 d postinoculation in the kidney. In this study, we observed changes in the transcriptional levels of 3 pro-inflammatory cytokines that are known to be involved in the innate immune response in chickens (Hong et al., 2006; Davison et al., 2008) after inoculation with 2 IB isolates. On the other hand, an active infection of the ChVI genotype isolate kr/ADL120003/2012, which resulted in an increase in serum AGP level at 9 dpi (Table 3) , evoked only a limited range of pro-inflammatory responses. cache = ./cache/cord-285323-473d7zvg.txt txt = ./txt/cord-285323-473d7zvg.txt === reduce.pl bib === id = cord-259738-yuqc6dk0 author = Tang, Mengjun title = Enhancement of the immunogenicity of an infectious bronchitis virus DNA vaccine by a bicistronic plasmid encoding nucleocapsid protein and interleukin-2 date = 2008-03-07 pages = extension = .txt mime = text/plain words = 3841 sentences = 209 flesch = 49 summary = title: Enhancement of the immunogenicity of an infectious bronchitis virus DNA vaccine by a bicistronic plasmid encoding nucleocapsid protein and interleukin-2 A DNA vaccine against infectious bronchitis virus (IBV) can induce specific humoral and cell-mediated immunity. When chickens were challenged with a virulent strain of IBV, the protective efficacy could be enhanced significantly after immunization with bicistronic DNA vaccine. In the present study, a bicistronic plasmid encoding the nucleocapsid protein and immune-stimulatory interleukin-2 has been constructed and its immunogenicity and protective effect in chickens has been evaluated. These recombinant plasmids were inoculated in chickens and tested in a protection-challenge experiment, demonstrating that vaccination with the co-expression plasmid pIRES-N/IL2 can induce stronger immune response than vaccination with pIRES-N. These results suggested that vaccination with the co-expression plasmid of N protein gene and IL-2 may have increased the protection rate against challenge. Partial protection against infectious bursal disease virus through DNA-mediated vaccination with the VP2 capsid protein and chicken IL-2 genes cache = ./cache/cord-259738-yuqc6dk0.txt txt = ./txt/cord-259738-yuqc6dk0.txt === reduce.pl bib === id = cord-272693-432ixb7g author = Phillips, J. E. title = Changes in nonstructural protein 3 are associated with attenuation in avian coronavirus infectious bronchitis virus date = 2011-09-10 pages = extension = .txt mime = text/plain words = 6255 sentences = 290 flesch = 56 summary = Full-length genome sequencing of pathogenic and attenuated (for chickens) avian coronavirus infectious bronchitis virus (IBV) strains of the same serotype was conducted to identify genetic differences between the pathotypes. Analysis of the consensus full-length genome for three different IBV serotypes (Ark, GA98, and Mass41) showed that passage in embryonated eggs, to attenuate the viruses for chickens, resulted in 34.75–43.66% of all the amino acid changes occurring in nsp 3 within a virus type, whereas changes in the spike glycoprotein, thought to be the most variable protein in IBV, ranged from 5.8 to 13.4% of all changes. In this study, we analyzed the consensus full-length genome for the pathogenic and attenuated viruses of three different IBV types and showed that within a virus type, 34.75 to 43.66% of all the amino acid changes between the pathotypes occurred in nsp 3, whereas changes in spike ranged from 5.8 to 13.4% of all changes. cache = ./cache/cord-272693-432ixb7g.txt txt = ./txt/cord-272693-432ixb7g.txt === reduce.pl bib === id = cord-276755-ctzrgqe7 author = Emmott, Edward title = Elucidation of the avian nucleolar proteome by quantitative proteomics using SILAC and changes in cells infected with the coronavirus infectious bronchitis virus date = 2010-09-08 pages = extension = .txt mime = text/plain words = 2488 sentences = 120 flesch = 35 summary = A recent quantitative analysis of the nucleolar proteome isolated from HeLa cells infected with the nuclear replicating DNA virus adenovirus identified 351 proteins, of which 24 proteins showed at least a twofold change in abundance, compared with nucleoli from mock-infected cells [14] . For example, in one such virus, avian infectious bronchitis virus (IBV), the virally encoded nucleocapsid (N) protein localized to the nucleolus in a cell cycle-dependent manner [15] and contained appropriate targeting motifs [16] [17] [18] . Several proteins were selected from the SILAC LC-MS/ MS analysis and their abundance and localization investigated in mock and IBV-infected cells using indirect immunofluorescence confocal microscopy (as described in [18, 19] ) in order to validate the quantitative proteomic approach (Supporting Information Fig. 1 ). Ingenuity Pathway Analysis was used to investigate the data sets to group together any proteins that shared similar functions in order to build an overview of the avian nucleolar proteome (Fig. 2) and potential roles of proteins in infectious and respiratory disease. cache = ./cache/cord-276755-ctzrgqe7.txt txt = ./txt/cord-276755-ctzrgqe7.txt === reduce.pl bib === === reduce.pl bib === id = cord-288309-6pw7t512 author = Kusters, J. G. title = Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus date = 1990-12-31 pages = extension = .txt mime = text/plain words = 1972 sentences = 164 flesch = 68 summary = J.; Niesters, H.G.M.; van der Zeijst, B.A.M. title: Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus Nucleotide sequences of eight IBV isolates in a region of the genome suspected to contain recombination, were aligned and compared. To address the question of the frequency of recombination in the generation of new field isolates the nucleotide sequences in five windows of homologous sequences of the genomes of eight IBV strains have been compared. With the murine coronavirus MHV a high frequency of recombination was found both in vitro and in mouse brain after infection with a ts mutant of MHV strain A59 and wild type JHM-virus 18'19 Phylogenetic trees constructed from five different windows of the genomes of eight IBV strains were used to detect crossover events. Cloning and sequencing of genes encoding structural proteins of avian infectious bronchitis virus cache = ./cache/cord-288309-6pw7t512.txt txt = ./txt/cord-288309-6pw7t512.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-299428-gon6bzat author = Mondal, Shankar title = Sequence analysis of infectious bronchitis virus isolates from the 1960s in the United States date = 2012-10-11 pages = extension = .txt mime = text/plain words = 3262 sentences = 152 flesch = 56 summary = To better understand the molecular epidemiology of infectious bronchitis virus (IBV) in the United States following the introduction of commercial IBV vaccines, we sequenced the S1 and N structural protein genes of thirteen IBV field isolates collected in the 1960s. Analysis of the S1 sequence showed that seven isolates were of the Massachusetts (Mass) genotype, five were SE17, and one was of the Connecticut (Conn) genotype, suggesting that these three IBVs were circulating in commercial poultry raised in different regions in the United States during the 1960s. In addition, the Mass-type isolates had high levels of sequence identity in the S1 gene compared with widely used modified live vaccines (Mass41, Ma5 and H120) and modern field strains from the USA and other countries, suggesting a common ancestor. cache = ./cache/cord-299428-gon6bzat.txt txt = ./txt/cord-299428-gon6bzat.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-303588-bwllypvq author = Ababneh, Mustafa title = High-resolution melting curve analysis for infectious bronchitis virus strain differentiation date = 2020-03-03 pages = extension = .txt mime = text/plain words = 3137 sentences = 159 flesch = 58 summary = MATERIALS AND METHODS: In this study, qRT-PCR was conducted on a partial fragment S1 gene followed by a high resolution melting curve analysis (qRT-PCR/HRM) on 23 IBV-positive samples in Jordan. Although the third cluster contained the highest number of samples, it displayed no similarity to any of the reference vaccine strains, and, after comparing them with the sequencing results, we found that the samples in the third cluster were similar to the variant II-like (IS-1494-06) IBV field strain. CONCLUSION: Our developed qRT-PCR/HRM curve analysis was able to detect and rapidly identify novel and vaccine-related IBV strains as confirmed by S1 gene nucleotide sequences, making it a rapid and cost-effective tool. High-resolution melting (HRM) curve analysis is a newly established PCR-based technique that has been used to differentiate related strains of the same animal or avian virus [16] [17] [18] [19] . Those 22 samples, along with the five IBV vaccine reference strains, were subjected to qRT-PCR targeting the S1 gene followed with HRM curve analysis. cache = ./cache/cord-303588-bwllypvq.txt txt = ./txt/cord-303588-bwllypvq.txt === reduce.pl bib === id = cord-301720-majpfxqn author = Saadat, Yousef title = Molecular characterization of infectious bronchitis viruses isolated from broiler flocks in Bushehr province, Iran: 2014 - 2015 date = 2017-09-15 pages = extension = .txt mime = text/plain words = 2836 sentences = 192 flesch = 53 summary = title: Molecular characterization of infectious bronchitis viruses isolated from broiler flocks in Bushehr province, Iran: 2014 2015 The aim of this study was to provide information on the molecular characteristic and the phylogenic relationship of infectious bronchitis viruses (IBV) strains in Bushehr province in comparison to other strains reported in the Middle East. [27] [28] [29] The aim of this study was to provide information on the molecular characteristic and the phylogenetic relationship of prevalent IBV genotypes circulating in chicken flocks in Bushehr province, Iran. Some Iraqi researchers studied circulating viruses in Broiler farm and showed that these strains belong to variant 2 (IS/1494-lik) that had high nucleotide sequence identity with IBV isolates from Iran, Israel, Egypt, Turkey, and Kurdistan. Detection and molecular characterization of infectious bronchitis virus isolated from recent outbreaks in broiler flocks in Thailand Molecular characterization of infectious bronchitis viruses isolated from broiler chicken farms in Iran cache = ./cache/cord-301720-majpfxqn.txt txt = ./txt/cord-301720-majpfxqn.txt === reduce.pl bib === id = cord-300104-855iw9wi author = Hennion, Ruth M. title = The Preparation of Chicken Kidney Cell Cultures for Virus Propagation date = 2014-12-18 pages = extension = .txt mime = text/plain words = 1487 sentences = 112 flesch = 76 summary = Chicken kidney (CK) cell cultures have historically proved useful for the assay of a number of viruses including coronaviruses. A technique for the preparation of such cell cultures, using a combination of manual and trypsin disaggregation of kidneys dissected from 2to 3-week-old birds is described. When all the kidneys required have been removed from the birds, agitate them in the beaker and discard the PBSa. Repeat this process until the wash PBSa looks clear ( see Note 6 ). 5. Dilute cell suspension in growth medium to the cell concentration required, seed culture fl asks and place in incubator until intact monolayer forms ( see Note 10 ). 6. Whilst some kidney cells may be lost in this process, it is an effective way of removing many of the red blood cells that are still present at this stage of the preparation. cache = ./cache/cord-300104-855iw9wi.txt txt = ./txt/cord-300104-855iw9wi.txt === reduce.pl bib === id = cord-301810-vtgdqart author = Aston, Emily J. title = Effect of Pullet Vaccination on Development and Longevity of Immunity date = 2019-02-02 pages = extension = .txt mime = text/plain words = 7115 sentences = 321 flesch = 45 summary = Because of the need to protect long-lived poultry against respiratory tract pathogens from an early age, vaccination programs for pullets typically involve serial administration of a variety of vaccines, including infectious bronchitis virus (IBV), Newcastle disease virus (NDV), and infectious laryngotracheitis virus (ILTV). At 5 days following challenge with IBV GA98, vaccinated/challenged birds had significantly lower RNA loads compared to positive controls at all collection times and in all tissue samples, with the exception of cecal tonsil at 24 WOA (Table 1 ). ILTV-specific IgG titers in serum collected 5 days post-challenge were significantly higher in vaccinated birds from both challenged and non-challenged groups, compared to the positive and negative controls ( Figure 6 ). ILTV-specific IgG titers in serum collected 5 days post-challenge were significantly higher in vaccinated birds from both challenged and non-challenged groups, compared to the positive and negative controls ( Figure 6 ). cache = ./cache/cord-301810-vtgdqart.txt txt = ./txt/cord-301810-vtgdqart.txt === reduce.pl bib === id = cord-304322-k9egxskw author = Promkuntod, N. title = Analysis of the S1 gene of the avian infectious bronchitis virus (IBV) reveals changes in the IBV genetic groups circulating in southern Thailand date = 2015-06-30 pages = extension = .txt mime = text/plain words = 2249 sentences = 132 flesch = 50 summary = title: Analysis of the S1 gene of the avian infectious bronchitis virus (IBV) reveals changes in the IBV genetic groups circulating in southern Thailand Abstract The new variants of the avian infectious bronchitis virus (IBV) produce a range of symptoms and cause global economic losses to the poultry industry. We investigated the S1 glycoprotein of 24 recent IBV isolates from chickens and demonstrated that two predominant genetic groups were circulating in southern Thailand between 2008 and 2013. In this study we investigated the situation and distribution of IBV strains in southern Thailand by collecting isolates from different bird species, with confirmed infections, from different regions between 2008 and 2013. Finally, we determined the phylogenetic relationships of the local isolates both with vaccine strains commercially used in Thailand and with the IBV sequences available in GenBank from other geographical origins. S1 glycoprotein gene analysis of avian infectious bronchitis virus strains isolated in southern Thailand cache = ./cache/cord-304322-k9egxskw.txt txt = ./txt/cord-304322-k9egxskw.txt === reduce.pl bib === id = cord-308950-bl83r4v3 author = Miguel, B. title = The role of feline aminopeptidase N as a receptor for infectious bronchitis virus : Brief Review date = 2002 pages = extension = .txt mime = text/plain words = 2543 sentences = 157 flesch = 56 summary = Our objective was to determine if fAPN can serve as a receptor for infectious bronchitis virus (IBV). Feline kidney cells that express fAPN and hamster kidney fibroblasts that do not express fAPN were inoculated with IBV and monitored for replication by indirect fluorescent assay and confocal microscopy and in chicken embryonated eggs. To evaluate the permissiveness of cells to IBV, monolayers of transfected (pBK-fAPN and pBK-CMV) BHK-21, non-transfected BHK-21 and FEK on coverslips were infected with a 10 3.2 EID 50 of Ark/IBV virus. To test the hypothesis that the feline APN had a role in permissiveness of FEK cells to Ark/IBV, BHK-21 cells were transfected with pBK-CMV plasmid or pBK-fAPN. The BHK-21 cells transfected with pBK-fAPN were shown to express the fAPN receptor on the cell surface (Fig. 3) , and were permissive to Ark/IBV (Figs. cache = ./cache/cord-308950-bl83r4v3.txt txt = ./txt/cord-308950-bl83r4v3.txt === reduce.pl bib === id = cord-309623-2ngr682l author = Han, Xiaoxiao title = Infectious Bronchitis Virus Infection Induces Apoptosis during Replication in Chicken Macrophage HD11 Cells date = 2017-07-26 pages = extension = .txt mime = text/plain words = 5618 sentences = 317 flesch = 46 summary = Previous studies have reported that infectious bronchitis virus (IBV) infection can produce cytopathic effects (CPE) and apoptosis in some mammalian cells and primary cells. The Beaudette strains were used previously to study the resistance of IBV to the antiviral state induced by type I interferon (IFN) [7] , induction of apoptosis through endoplasmic reticulum stress in Vero cells by IBV infection [8] and activate autophagy by IBV nonstructural protein (NSP) 6 [9] . The rate of apoptosis significantly increased at 12 h.p.i. in virus-infected cells when compared with the mockInfection of HD11 cells with IBV Beaudette caused cell death in a time-and dose-dependent manner, as tested by CCK-8 assay. The results also showed that activation of caspase-9 in IBV Beaudette-infected cells was regulated by decreased expression of Bcl-2 and increased expression of Bax. The caspase-3 activation and virus-induced apoptosis might be triggered through both extrinsic and intrinsic pathways. cache = ./cache/cord-309623-2ngr682l.txt txt = ./txt/cord-309623-2ngr682l.txt === reduce.pl bib === id = cord-306380-msk9p1yy author = Lee, C.-W. title = Evidence of genetic diversity generated by recombination among avian coronavirus IBV date = 2000 pages = extension = .txt mime = text/plain words = 2796 sentences = 146 flesch = 58 summary = Phylogenetic analysis of selected regions of the genome of the DE072 serotype field isolates further support those results and indicate that isolates within the same serotype may have different amounts of nucleotide sequence similarity with each other in individual genes other than the S gene. Further, we conducted sequence analysis of six isolates of the DE072 serotype in order to determine if recombination is frequently occurring in this region in field isolates of IBV. We conducted phylogenetic analysis by dividing 3.8 kb of the 3 end of the genome among five IBV strains at the IG sequences. However, these 6 isolates had a much different level of nucleotide sequence similarity with each other in gene 3 and gene 4, and clustered randomly with other serotypes of IBV (Fig. 3) . Sequence analysis of gene 3, gene 4 and gene 5 of avian infectious bronchitis virus strain CU-T2 Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus cache = ./cache/cord-306380-msk9p1yy.txt txt = ./txt/cord-306380-msk9p1yy.txt === reduce.pl bib === id = cord-310372-qc6941pm author = Ji, Jun title = Phylogenetic distribution and predominant genotype of the avian infectious bronchitis virus in China during 2008-2009 date = 2011-04-22 pages = extension = .txt mime = text/plain words = 3554 sentences = 169 flesch = 47 summary = The genetic characterization of recent IBV field isolates in China was performed by sequencing the whole S1 genes, sequence alignment and phylogenetic analysis compared with other reference strains. The results of virus recovery in chicks indicated 87.5% (70/80) isolates caused serious kidney lesions, which were presented with swollen specked kidney and distended ureters filled with uric acid were nephropathogenic type, and the other ten isolates in the study caused respiratory system signs, which were consistent with the clinical record of each strain (Table 1) . In the present study, nucleotide and derived amino acid sequences of S1 protein genes of the 80 field strains were aligned and compared to the representative strains, to determine the relationship of circulating field isolates, vaccine strains and previously described variant strains. Isolation and genetic analysis revealed no predominant new strains of avian infectious bronchitis virus circulating in South China during cache = ./cache/cord-310372-qc6941pm.txt txt = ./txt/cord-310372-qc6941pm.txt === reduce.pl bib === id = cord-305079-foifc8ch author = Zhou, Ying Shun title = Establishment of reverse genetics system for infectious bronchitis virus attenuated vaccine strain H120 date = 2013-02-22 pages = extension = .txt mime = text/plain words = 4842 sentences = 229 flesch = 54 summary = The remaining one third of the genome encodes the structural proteins and group-specific ORFs, including spike glycoprotein (S), envelope protein (E), membrane Veterinary Microbiology 162 (2013) Infectious bronchitis virus (IBV) strain H120 was successfully rescued as infectious clone by reverse genetics. In this study, we describe the in vitro assembly and recovery of an infectious clone of IBV-H120, the biological and immune characteristics of the rescued H120 virus (R-H120), and the potential to use R120 as a candidate of vaccine vector in the future vaccine development. The IBV strains, H120 and Mass41, obtained from China Institute of Veterinary Drug Control (IVDC), were propagated in the allantoic cavities of the 10-day-old specific pathogen-free (SPF) embryonated chicken eggs (ECE), and the allantoic fluid was harvested 36 h post inoculation. Three groups of chickens were challenged with the virulent strain Mass41 to test if the rescued virus could protect the immunized animals from IBV infection. cache = ./cache/cord-305079-foifc8ch.txt txt = ./txt/cord-305079-foifc8ch.txt === reduce.pl bib === id = cord-316525-uadfehr6 author = Zhang, X. W. title = Testing the hypothesis of a recombinant origin of the SARS-associated coronavirus date = 2004-10-11 pages = extension = .txt mime = text/plain words = 3023 sentences = 152 flesch = 52 summary = Surprisingly, we found that 7 putative recombination regions, located in Replicase 1ab and Spike protein, exist between SARS-CoV and other 6 coronaviruses: porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), bovine coronavirus (BCoV), human coronavirus 229E (HCoV), murine hepatitis virus (MHV), and avian infectious bronchitis virus (IBV). After potential recombination events were identified by at least 3 methods above, separate neighbor joining trees were constructed for each putative recombination region to better evaluate the evidence for conflicting evolutionary histories of different sequence regions. Two regions (13151-13299 and 16051-16449, position in alignment) are identified as putative recombination regions and all 6 coronaviruses are potential parents with SARS-CoV as potential daughter. In this study, seven recombination detection methods and phylogenetic analyses were performed on SARS-CoV and the six coronaviruses identified by BLAST (IBV, BCoV, HCoV, MHV, PEDV and TGEV). cache = ./cache/cord-316525-uadfehr6.txt txt = ./txt/cord-316525-uadfehr6.txt === reduce.pl bib === id = cord-303393-9zs3qqo4 author = Alsultan, Musaed Abdulaziz title = Infectious bronchitis virus from chickens in Al-Hasa, Saudi Arabia 2015-2016 date = 2019-03-19 pages = extension = .txt mime = text/plain words = 4139 sentences = 265 flesch = 56 summary = AIM: This study aimed to isolate some of the currently circulating infectious bronchitis virus (IBV) strains from some broiler chicken farms in Al-Hasa and to do some molecular characteristics of these strains. MATERIALS AND METHODS: We collected 300 tissue specimens, including the trachea, bronchi, lungs, and kidneys from some four commercial chicken farms showing respiratory manifestations. We used three tissue suspensions (trachea, lungs, and kidneys) from three specimens representing three different IBV outbreaks in some chicken farms from Al-Hasa region. Some of these farms were reporting IBV outbreaks based on Figure-4: Phylogenetic analysis based on the partial S1 gene for the circulating infectious bronchitis virus (IBV) strains from some chicken farms in Al-Hasa region 2015-2016. Table-5: Pairwise distance analysis of partial S1 gene for the circulating IBV strains in some chicken farms in Al-Hasa region cache = ./cache/cord-303393-9zs3qqo4.txt txt = ./txt/cord-303393-9zs3qqo4.txt === reduce.pl bib === id = cord-303794-fn3jkiil author = Hassan, Kareem E. title = Experimental co-infection of infectious bronchitis and low pathogenic avian influenza H9N2 viruses in commercial broiler chickens date = 2017-06-30 pages = extension = .txt mime = text/plain words = 3787 sentences = 202 flesch = 52 summary = title: Experimental co-infection of infectious bronchitis and low pathogenic avian influenza H9N2 viruses in commercial broiler chickens Avian influenza H9N2 and H5N1 subtypes, Infectious bronchitis virus (IBV), and virulent Newcastle disease virus (vNDV) have been frequently isolated from different broiler chicken flocks (Hassan et al., 2016) . Experimentally infected commercial broilers with classical and variant IBV and vaccine IBV strains in presence or absence of AIV-H9N2N2 infection were monitored for clinical outcomes, virus shedding, postmortem and histopathological lesions. Histopathologically, trachea in all mixed infection groups including the AIV-H9N2 with vaccine IBV strain showed severe changes comparable to the milder changes in single classical or variant IBV challenged groups (Purcell et al., 1976) . Similarly, in this study, significant increases of AIV-H9N2 virus shedding with classical IBV infection especially at 2 and 5 DPI and with the variant and vaccine IBV strains co-infections up to 7 DPI were observed. cache = ./cache/cord-303794-fn3jkiil.txt txt = ./txt/cord-303794-fn3jkiil.txt === reduce.pl bib === id = cord-319253-8bssrn9o author = OKINO, Cintia Hiromi title = Rapid detection and differentiation of avian infectious bronchitis virus: an application of Mass genotype by melting temperature analysis in RT-qPCR using SYBR Green I date = 2018-02-27 pages = extension = .txt mime = text/plain words = 2502 sentences = 114 flesch = 42 summary = title: Rapid detection and differentiation of avian infectious bronchitis virus: an application of Mass genotype by melting temperature analysis in RT-qPCR using SYBR Green I A method based on Melting Temperature analysis of Hypervariable regions (HVR) of S1 gene within a RT-qPCR was developed to detect different genotypes of avian infectious bronchitis virus (IBV) and identify the Mass genotype. Finally, considering that HVR I and HVR II of S1 gene were thought to be closely associated with major neutralization epitopes and consequently a reliable target for genotyping method, we developed a diagnostic method using Melting Temperature analysis based on these regions aiming to rapid detect and differentiate Mass and non-Mass IBV strains in samples previously isolated and directly in clinical samples. A Real-Time Reverse-Transcription Polymerase Chain Reaction for Differentiation of Massachusetts Vaccine and Brazilian Field Genotypes of Avian Infectious Bronchitis Virus cache = ./cache/cord-319253-8bssrn9o.txt txt = ./txt/cord-319253-8bssrn9o.txt === reduce.pl bib === id = cord-304278-0qy1nngs author = Raj, G. Dhinakar title = Infectious bronchitis virus: immunopathogenesis of infection in the chicken date = 2007-11-12 pages = extension = .txt mime = text/plain words = 12530 sentences = 665 flesch = 45 summary = While infectious bronchitis (IB) is considered primarily a disease of the respiratory system, different IBV strains may show variable tissue tropisms and also affect the oviduct and the kidneys, with serious consequences. Nevertheless, the lack of correlation between antibodies and resistance, discrepancies between in vitro strain differentiation by VN tests and in vivo cross-protection results (Darbyshire, 1985) and re-excretion of virus in the presence of high titres of circulating antibodies (Jones & Ambali, 1987) all suggest that while humoral antibodies play a role in recovery from IBV infection, other immunological mechanisms are involved. Comparison of the susceptibility of chicks of different ages to infection with nephrosis-nephritis causing strain of infectious bronchitis virus Challenge experiments to evaluate cross-protection induced at the trachea and kidney level by vaccine strains and Belgian nephropathogenic isolates of avian infectious bronchitis virus Effects of avian infectious bronchitis virus (Arkansas strain) on vaccinated laying chickens cache = ./cache/cord-304278-0qy1nngs.txt txt = ./txt/cord-304278-0qy1nngs.txt === reduce.pl bib === id = cord-316153-wet0go35 author = Jia, W. title = A novel variant of avian infectious bronchitis virus resulting from recombination among three different strains date = 1995 pages = extension = .txt mime = text/plain words = 3917 sentences = 232 flesch = 61 summary = An antigenic variant of avian infectious bronchitis virus (IBV), a coronavirus, was isolated and characterized. Therefore, several recently reported diagnostic and serotyping methods of IBV which are based on dot-blot hybridization, restriction fragment length polymorphism (RFLP), and polymerase chain reaction (PCR), may not reveal the true antigenic and/or genetic nature of IBV isolates, and may in fact yield misleading information. More recently, two American field isolates were found to contain fragments of Mass-like sequences in the S1 gene, which were 94% to 95% homologous to IBV strain Mass41 [38] . Sequence data were obtained from cDNA clones, except for the first 1100 bases of the S gene, the last 200 bases of the N gene, the 3' end non-coding region of CU-T2, and the partial Gene3 of Ark99 and Ho1152, which were obtained from direct sequencing of IBV genomic RNA. Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus cache = ./cache/cord-316153-wet0go35.txt txt = ./txt/cord-316153-wet0go35.txt === reduce.pl bib === id = cord-309469-2naxn580 author = An, Hongliu title = Identification and formation mechanism of a novel noncoding RNA produced by avian infectious bronchitis virus date = 2019-01-05 pages = extension = .txt mime = text/plain words = 3600 sentences = 234 flesch = 54 summary = For example, polyadenylated nuclear (PAN) RNA encoded by Kaposi's sarcoma-associated herpesvirus (Sun et al., 1996; Zhong and Ganem, 1997) , the~2-kb latency-associated transcript (LAT) expressed by Herpes simplex virus (Bloom, 2004 ), a con-served~5-kb intron expressed by Human cytomegalovirus (hCMV) (Kulesza and Shenk, 2004) , and a 7.2-kb RNA expressed by mouse CMV (Kulesza and Shenk, 2006) , U-rich RNAs (HSURs) produced by Herpesvirus saimiri (HVS), (Albrecht and Fleckenstein, 1992; Ensser and Fleckenstein, 2005) ; (3) Subgenomic ncRNAs from single-stranded RNA viruses by incomplete degradation of genomic RNA by the cellular 5-3′ exonuclease XRN1. The results confirmed previous report that IBV can synthesize sgRNA via template switch mediated by a noncanonical core sequence (Bentley et al., 2013) Notably, the mutant virus carrying four mutations (A27100U/A27111U/G27113C/G27114C) was also unable to produce ncRNA (Fig. 4) , suggesting these nucleotides are required for ncRNA production. cache = ./cache/cord-309469-2naxn580.txt txt = ./txt/cord-309469-2naxn580.txt === reduce.pl bib === id = cord-305684-ipeup5mp author = Chen, Yuqiu title = Identification and molecular characterization of a novel serotype infectious bronchitis virus (GI-28) in China date = 2016-12-16 pages = extension = .txt mime = text/plain words = 5146 sentences = 311 flesch = 58 summary = In this study, based on the results of S1 sequence analysis and virus cross-neutralization tests, IBV strain ck/CH/LGX/111119 was found to be genetically and antigenically different from other known IBV types, representing not only a novel genotype, but also a novel serotype (designated as GI-28). Further studies by complete genomic analysis showed that strain ck/CH/LGX/111119 may have originated from recombination events involving LX4 genotype IBVs and an as-yet-unidentified IBV donating a S1 gene, or from the result of accumulation of mutations and selections, especially in the S1 gene, from a LX4 genotype virus. In addition, the S1 gene sequences of 93 IBV reference strains with different genotypes were also selected for comparison in this study ( Fig. 1 ) (Valastro et al., 2016) . Genotyping based on the phylogenetic analysis of the S1 gene from our ck/CH/LGX/111119 and 99 reference IBV strains assigned the viruses into different clusters (Fig. 1) . cache = ./cache/cord-305684-ipeup5mp.txt txt = ./txt/cord-305684-ipeup5mp.txt === reduce.pl bib === id = cord-307304-irji8owi author = Britton, Paul title = Generation of a recombinant avian coronavirus infectious bronchitis virus using transient dominant selection date = 2004-11-05 pages = extension = .txt mime = text/plain words = 4856 sentences = 219 flesch = 52 summary = To demonstrate the feasibility of the method we exchanged the ectodomain of the Beaudette spike gene for the corresponding region from IBV M41 and generated two recombinant infectious bronchitis viruses (rIBVs) expressing the chimaeric S protein, validating the method as an alternative way for generating rIBVs. Avian infectious bronchitis virus (IBV), a group three member of the genus Coronavirus (order Nidovirales, family Coronaviridae), is a highly infectious pathogen of domestic fowl that replicates primarily in the respiratory tract but also in epithelial cells of the gut, kidney and oviduct (Cavanagh, 2001; Cavanagh and Naqi, 2003; Cook et al., 2001) . In an alternative strategy infectious IBV was recovered following transfection of restricted vaccinia virus DNA, containing the IBV full-length cDNA, into cells infected with recombinant fowlpox virus expressing T7 RNA polymerase (Casais et al., 2001) . cache = ./cache/cord-307304-irji8owi.txt txt = ./txt/cord-307304-irji8owi.txt === reduce.pl bib === id = cord-310536-u30cufg7 author = Finger, Paula Fonseca title = Combined use of ELISA and Western blot with recombinant N protein is a powerful tool for the immunodiagnosis of avian infectious bronchitis date = 2018-12-12 pages = extension = .txt mime = text/plain words = 4663 sentences = 242 flesch = 52 summary = title: Combined use of ELISA and Western blot with recombinant N protein is a powerful tool for the immunodiagnosis of avian infectious bronchitis This study examined the combined use of an ELISA and Western blot (WB) to detect antibodies against the nucleocapsid protein (N) of IBV. Serum samples scored as negative with the commercial kit but as positive with the ELISA-rN were further analysed by Western blot analyses using the rN protein as an antigen. The aim of the current study was to evaluate the combined use of an ELISA and Western blot (WB) to detect antibodies against the nucleocapsid protein of IBV. Recombinant nucleocapsid protein based single serum dilution ELISA for the detection of antibodies to infectious bronchitis virus in poultry Development of a multiepitope antigen of S protein-based ELISA for antibodies detection against infectious bronchitis virus cache = ./cache/cord-310536-u30cufg7.txt txt = ./txt/cord-310536-u30cufg7.txt === reduce.pl bib === id = cord-308591-cs8os2f5 author = Tawakol, Maram M. title = Evaluation of bacteriophage efficacy in reducing the impact of single and mixed infections with Escherichia coli and infectious bronchitis in chickens date = 2019-11-29 pages = extension = .txt mime = text/plain words = 4183 sentences = 223 flesch = 45 summary = title: Evaluation of bacteriophage efficacy in reducing the impact of single and mixed infections with Escherichia coli and infectious bronchitis in chickens Bacteriophage treatment delayed the onset and reduced the severity of clinical signs, and prevented the mortality associated with single and mixed infection with IBV and E. In vivo study was conducted to evaluate the efficacy of bacteriophages in reducing the pathogenicity of single and mixed infections with APEC and IBV. In the present study samples were collected from birds with respiratory manifestations from a total of forty farms, and subjected to characterization based on currently circulating IBV and APEC strains. In addition, the efficacy of bacteriophage treatment in reducing APEC replication in the avian respiratory tract was studied in vivo, as well as their effect in reducing IBV pathogenicity after mixed APEC and IBV infections. cache = ./cache/cord-308591-cs8os2f5.txt txt = ./txt/cord-308591-cs8os2f5.txt === reduce.pl bib === id = cord-313676-6rebpe57 author = De la Torre, David I. title = Enteric Virus Diversity Examined by Molecular Methods in Brazilian Poultry Flocks date = 2018-03-29 pages = extension = .txt mime = text/plain words = 5867 sentences = 295 flesch = 55 summary = The most common enteric viruses affecting commercial flocks in Brazil include Fowl Adenovirus of group I (FAdV-I), Chicken Parvovirus (ChPV), Chicken Astrovirus (CAstV), Avian Nephritis Virus (ANV), Infectious Bronchitis Virus (IBV), Avian Reovirus (AReo), and Avian Rotavirus (ARtV). The main enteric viruses reported to cause enteric diseases are found in single and multiple infections and include the Fowl Adenovirus of group I (FAdV-I); Chicken Parvovirus (ChPV); two viruses from the Astroviridae family: Chicken Astrovirus (CAstV) and Avian Nephritis Virus (ANV); two viruses from the Reoviridae family: Avian Reovirus (AReo) and Avian Rotavirus (ARtV); and a member of the Coronaviridae family, Infectious Bronchitis Virus (IBV) [4, [6] [7] [8] [9] . The association of enteric virus with the age of broilers, breeders, and layers (Tables 4 and 5) showed that molecular diagnosis of these viruses can be performed at different stages of production, which can be useful in the control of vertical infections. cache = ./cache/cord-313676-6rebpe57.txt txt = ./txt/cord-313676-6rebpe57.txt === reduce.pl bib === id = cord-306976-p2521bl4 author = Gao, Mengying title = Serotype, antigenicity, and pathogenicity of a naturally recombinant TW I genotype infectious bronchitis coronavirus in China date = 2016-08-15 pages = extension = .txt mime = text/plain words = 5087 sentences = 232 flesch = 57 summary = Furthermore, neither the vaccine strains nor the attenuated viruses could provide complete respiratory protection of chickens against a challenge with the ck/CH/LDL/140520 strain, indicating that it is necessary to develop new live vaccines or to evaluate the use of established vaccines in combination to control naturally recombinant TW I-type IBV strains in the future. Our results showed that strain ck/CH/LDL/140520 is very pathogenic, and that it is able to cause cystic oviducts in a high percentage of birds, as well as mortality due to nephritis and respiratory distress with complete tracheal ciliostasis, especially in chickens infected at 1 day of age. In contrast, respiratory signs (sneezing, nasal discharge, and tracheal rales) developed at 3-4 dpc and lasted until 10 dpc in some of the chickens in the groups that were vaccinated with the H120, 4/91, and Conn vaccines, and the attenuated LSD/120720 and LGX/ 100508 viruses when challenged with the nrTW I IBV strain at 20 days of age. cache = ./cache/cord-306976-p2521bl4.txt txt = ./txt/cord-306976-p2521bl4.txt === reduce.pl bib === id = cord-318400-l9kwxsq7 author = Chhabra, Rajesh title = Pathogenicity and tissue tropism of infectious bronchitis virus is associated with elevated apoptosis and innate immune responses date = 2016-01-15 pages = extension = .txt mime = text/plain words = 5153 sentences = 287 flesch = 53 summary = To establish a characteristic host response to predict the pathogenicity and tissue tropism of infectious bronchitis viruses (IBV), we investigated innate immune responses (IIR) and apoptosis in chicken embryo kidney cells (CEKC) and tracheal organ cultures (TOC) infected with three IBV strains. In contrast, M41 infection caused greater expression of these genes than 885 or QX in TOCs. In summary, greater levels of apoptosis and elevated levels of TLR3, MDA5 and IFN-β expression are associated with increased pathogenicity of IBV strains in renal and tracheal tissues. In order to establish the characteristic host response to predict the tissue tropism and pathogenicity of IBVs, we investigated apoptosis and innate immune responses in chicken embryo kidney (CEK) cells and tracheal organ cultures (TOCs) following infection with IS/885/00-like, QX-like and M41 IBV strains. Nephropathogenic IBV strains 885 and QX resulted in significantly greater up-regulation of innate immune sensing genes namely TLR3 and MDA5 along with greater IFN-β mRNA levels in CEK cells at 9 h of infection when compared to M41 infection. cache = ./cache/cord-318400-l9kwxsq7.txt txt = ./txt/cord-318400-l9kwxsq7.txt === reduce.pl bib === id = cord-312489-ywep0c08 author = Andoh, Kiyohiko title = Decreased neutralizing antigenicity in IBV S1 protein expressed from mammalian cells date = 2015-10-02 pages = extension = .txt mime = text/plain words = 5039 sentences = 246 flesch = 43 summary = We evaluated the antigenicity of recombinant infectious bronchitis virus (IBV) S1 protein expressed in mammalian cells. Native S1 ELISA detected similar titers in the sera of animals immunized with recombinant S1 protein compared to those in sera of chickens immunized with inactivated virus (Fig. 6b ) (Control experiments (data not shown) demonstrated that mock and unvaccinated control groups did not differ from each other in VN and ELISA tests of anti-S1 activity.) These results indicated that while recombinant S1 protein retained antigenicity (the ability to induce antibodies against S1 protein), the resulting antibodies was decreased its neutralizing activity, in contrast to those induced by inactivated virus. The S1 glycoprotein but not the N or M proteins of avian infectious bronchitis virus induces protection in vaccinated chickens Induction of protective immunity in chickens vaccinated with infectious bronchitis virus S1 glycoprotein expressed by a recombinant baculovirus cache = ./cache/cord-312489-ywep0c08.txt txt = ./txt/cord-312489-ywep0c08.txt === reduce.pl bib === id = cord-316234-vtjsfi2c author = Sultankulova, Kulyaisan T. title = New oligonucleotide microarray for rapid diagnosis of avian viral diseases date = 2017-04-05 pages = extension = .txt mime = text/plain words = 4693 sentences = 228 flesch = 45 summary = BACKGROUND: We developed a new oligonucleotide microarray comprising 16 identical subarrays for simultaneous rapid detection of avian viruses: avian influenza virus (AIV), Newcastle disease virus (NDV), infection bronchitis virus (IBV), and infectious bursal disease virus (IBDV) in singleand mixed-virus infections. METHODS AND RESULTS: The paper describes the technique for rapid and simultaneous diagnosis of avian diseases such as avian influenza, Newcastle disease, infectious bronchitis and infectious bursal disease with use of oligonucleotide microarray, conditions for hybridization of fluorescent-labelled viral cDNA on the microarray and its specificity tested with use of AIV, NDV, IBV, IBDV strains as well as biomaterials from poultry. The paper describes the technique for rapid and simultaneous diagnosis of avian diseases such as avian influenza, Newcastle disease, infectious bronchitis and infectious bursal disease with use of oligonucleotide microarray, conditions for hybridization of fluorescentlabelled viral cDNA on the microarray and its specificity tested with use of AIV, NDV, IBV, IBDV strains as well as biomaterials from poultry. cache = ./cache/cord-316234-vtjsfi2c.txt txt = ./txt/cord-316234-vtjsfi2c.txt === reduce.pl bib === id = cord-329497-3jow4xbn author = Promkuntod, Naruepol title = Dynamics of avian coronavirus circulation in commercial and non-commercial birds in Asia – a review date = 2015-12-28 pages = extension = .txt mime = text/plain words = 8003 sentences = 432 flesch = 52 summary = It is essential to understand the latest situation regarding avian coronaviruses (ACoVs), commonly referred to as the well-known avian infectious bronchitis virus (IBV), given that new and diverse types of IBV are continually being identified worldwide, particularly ones that are isolated from commercial poultry and associated with a wide range of disease conditions. Vaccines against IBVs are generally effective, but new strains continue to emerge causing clinical diseases and production problems in vaccinated flocks, eventually having an economic impact on the global poultry industry Liu et al. In addition, the production of a new generation of vaccines, genetically related to the circulating IBV local strains, is economically beneficial for control of infectious bronchitis (IB) in global geographic regions. Isolation and genetic analysis revealed no predominant new strains of avian infectious bronchitis virus circulating in south China during cache = ./cache/cord-329497-3jow4xbn.txt txt = ./txt/cord-329497-3jow4xbn.txt === reduce.pl bib === id = cord-329245-6tj2k1yn author = Corse, Emily title = The cytoplasmic tails of infectious bronchitis virus E and M proteins mediate their interaction date = 2003-07-20 pages = extension = .txt mime = text/plain words = 7414 sentences = 327 flesch = 56 summary = Indeed, it has been shown that both the MHV E and the infectious bronchitis virus (IBV) E proteins are sufficient for formation of the virus-like particles (VLPs) described above (Corse and Machamer, 2000; Maeda et al., 1999) , although the efficiency probably varies with cell type and protein expression system. (B) IBV-infected Vero cells were labeled with [ 35 S]methionine-cysteine at 45 h postinfection, treated with DSP as indicated, lysed, and immunoprecipitated with anti-E or anti-M antibodies as described under Materials and methods. The E and M proteins of several coronaviruses are released from cotransfected cells in membrane-bound particles that are morphologically similar to virions (VLPs), suggesting that interactions between these proteins are an integral part of coronavirus assembly (Baudoux et al., 1998; Corse and Machamer, 2000; Godeke et al., 2000; Vennema et al., 1996) . cache = ./cache/cord-329245-6tj2k1yn.txt txt = ./txt/cord-329245-6tj2k1yn.txt === reduce.pl bib === id = cord-317347-by8albr9 author = van Ginkel, Frederik W. title = Age-dependent immune responses and immune protection after avian coronavirus vaccination date = 2015-05-28 pages = extension = .txt mime = text/plain words = 5792 sentences = 288 flesch = 53 summary = The delayed and/or lower antibody response combined with lower IgG avidity indices coincided with increased tracheal inflammation and depletion of tracheal epithelia cells and goblet cells upon IBV field strain challenge. Therefore, the ability of SPF chickens of different age to induce an IBV-specific antibody response and protect against challenge with an IBV field strain was measured. In order to measure IgG (IgY), IgA and IgM antibody levels in plasma and tears of chicken, an IBV-specific enzyme-linked immunosorbent assay (ELISA) was developed as previously described [20] . These data are consistent with a delay in the IgA plasma response to IBV in birds vaccinated at a younger age and a non-significant decline in mean IgA titers in the 1-day-old group. This would be consistent with a drop of presumably natural maternal IBV-specific IgM antibodies in these SPF chickens in the day 7 control age group. cache = ./cache/cord-317347-by8albr9.txt txt = ./txt/cord-317347-by8albr9.txt === reduce.pl bib === id = cord-337128-yyz7z0xj author = Abdel-Moneim, Ahmed S title = Immunohistochemistry for detection of avian infectious bronchitis virus strain M41 in the proventriculus and nervous system of experimentally infected chicken embryos date = 2009-02-05 pages = extension = .txt mime = text/plain words = 3308 sentences = 172 flesch = 44 summary = title: Immunohistochemistry for detection of avian infectious bronchitis virus strain M41 in the proventriculus and nervous system of experimentally infected chicken embryos Aim of this study was to investigate by immunohistochemistry (IHC) the tissue tropism of avian infectious bronchitis virus (IBV) strain M41 in experimentally infected chicken embryos. Using IHC, antigens of IBV were detected in nasal epithelium, trachea, lung, spleen, myocardial vasculature, liver, gastrointestinal tract, kidney, skin, sclera of the eye, spinal cord, as well as in brain neurons of the inoculated embryos. IBV antigens were detected in the nasal epithelium, trachea, lung, spleen, myocardium, liver, gizzard, proventriculus, kidney, skin, sclera of the eye, spinal cord, as well as in neurons of the central nervous system in infected embryos (Table 1, Figure 1 ). cache = ./cache/cord-337128-yyz7z0xj.txt txt = ./txt/cord-337128-yyz7z0xj.txt === reduce.pl bib === id = cord-321602-88b2h06y author = Lv, Chenfei title = Construction of an infectious bronchitis virus vaccine strain carrying chimeric S1 gene of a virulent isolate and its pathogenicity analysis date = 2020-08-19 pages = extension = .txt mime = text/plain words = 4902 sentences = 266 flesch = 58 summary = The full-length genomic cDNA of IBV vaccine strain H120 was constructed in pBAC vector from four IBV fragment subcloning vectors by homologous recombination, which contained the CMV promoter at the 5′ end and the hepatitis D virus ribozyme (HDVR) sequence and bovine growth hormone polyadenylation (BGH) sequence after the polyA tail at the 3′ end of the full-length cDNA. To construct the full-length cDNA of IBV H120 strain, total RNA was extracted from the allantoic fluid of SPF chicken embryonated eggs infected with H120 and transcribed to cDNA by reverse transcriptase using the Thermo Scientific RevertAid First-Strand cDNA Synthesis Kit (Thermo Fisher, USA). The SC021202 S1 gene containing same homology arms to those of the H120F4 was amplified from total RNA of allantoic fluid of SPF chicken embryonated eggs infected with IBV SC021202 by RT-PCR with the primers SCS1-F and SCS1-R listed in Table 1 and was then inserted into pBAC-F4-△S1 by the same homologous recombination process using the ClonExpress one-step cloning kit (Vazyme Biotechnology, China). cache = ./cache/cord-321602-88b2h06y.txt txt = ./txt/cord-321602-88b2h06y.txt === reduce.pl bib === id = cord-317587-rrx2r4n2 author = Fan, Wensheng title = Genetic Analysis of Avian Coronavirus Infectious Bronchitis Virus in Yellow Chickens in Southern China over the Past Decade: Revealing the Changes of Genetic Diversity, Dominant Genotypes, and Selection Pressure date = 2019-09-26 pages = extension = .txt mime = text/plain words = 9210 sentences = 479 flesch = 58 summary = title: Genetic Analysis of Avian Coronavirus Infectious Bronchitis Virus in Yellow Chickens in Southern China over the Past Decade: Revealing the Changes of Genetic Diversity, Dominant Genotypes, and Selection Pressure In conclusion, the IBVs circulating in southern China over the past decade have experienced a remarkable change in genetic diversity, dominant genotypes, and selection pressure, indicating the importance of permanent monitoring of circulating strains and the urgency for developing new vaccines to counteract the emerging LX4-type and New-type IBVs. Infectious bronchitis (IB) is one of the major viral diseases affecting the poultry industry globally. Our results indicated that there was a remarkable change in genetic diversity, dominant genotypes, and selection pressure of IBV strains in southern China over the past decade compared with the previous period of 1985-2007. Molecular characterization of major structural protein genes of avian coronavirus infectious bronchitis virus isolates in southern China cache = ./cache/cord-317587-rrx2r4n2.txt txt = ./txt/cord-317587-rrx2r4n2.txt === reduce.pl bib === id = cord-322516-wekvet6f author = Maceyka, Michael title = Ceramide Accumulation Uncovers a Cycling Pathway for the cis-Golgi Network Marker, Infectious Bronchitis Virus M Protein date = 1997-12-15 pages = extension = .txt mime = text/plain words = 6173 sentences = 326 flesch = 53 summary = Short-term treatment with two inhibitors of sphingolipid synthesis had no effect on localization of IBV M or other Golgi markers. Treatment of cells with 100 M PDMP for 1 h had no effect on the localization of either protein (Fig. 4) , suggesting that the morphology of the Golgi was not greatly altered. Pretreatment with the earlier inhibitors reduced the PDMP-induced slowing of anterograde traffic by about half, suggesting that accumulation of newly synthesized ceramide at least partially mediates this effect. The pretreatment experiments suggested that increased levels of ceramide mediate the PDMP-induced effects on IBV M localization. However, neither ␤CA nor FB1 had an effect on the rate of anterograde traffic of VSV G or the localization of IC, CGN, or Golgi stack proteins. However, the glucosylceramide analogue PDMP, at a concentration that inhibits both GlcCer and SM synthases, causes a redistribution of IBV M to the ER and a slowing of anterograde traffic in BHK-21 cells. cache = ./cache/cord-322516-wekvet6f.txt txt = ./txt/cord-322516-wekvet6f.txt === reduce.pl bib === id = cord-321261-3lp54mmu author = Kuo, Shu-Ming title = Evolution of infectious bronchitis virus in Taiwan: Characterisation of RNA recombination in the nucleocapsid gene date = 2010-08-26 pages = extension = .txt mime = text/plain words = 3884 sentences = 208 flesch = 57 summary = Putative IBV genetic recombination in the S gene has been documented in different field isolates, including a Japanese strain (KB8523), European Avian infectious bronchitis virus (IBV) belongs to the Coronaviridae family and causes significant economic loss in Taiwan (TW), even in flocks that have been extensively immunised with Massachusetts (Mass)-serotype vaccines. No major difference was observed between the results from the BI and those from the ML test (Fig. 4B , D and F), confirming that RNA recombination probably occurred between TW and US IBVs in the 5 0terminal region of the N gene and that the phylogenetic incongruence was not caused by point mutation or variation in local evolutionary rates. We here show that the recombinant N gene was detected in all the isolated TW IBVs, supporting the participation of recombination in viral evolution and showing that a recombinant RNA virion can emerge as a local dominant strain. Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus cache = ./cache/cord-321261-3lp54mmu.txt txt = ./txt/cord-321261-3lp54mmu.txt === reduce.pl bib === id = cord-322410-k23engcx author = Naguib, Mahmoud M. title = New real time and conventional RT-PCRs for updated molecular diagnosis of infectious bronchitis virus infection (IBV) in chickens in Egypt associated with frequent co-infections with avian influenza and Newcastle Disease viruses date = 2017-03-21 pages = extension = .txt mime = text/plain words = 5012 sentences = 259 flesch = 52 summary = title: New real time and conventional RT-PCRs for updated molecular diagnosis of infectious bronchitis virus infection (IBV) in chickens in Egypt associated with frequent co-infections with avian influenza and Newcastle Disease viruses Conventional RT-PCRs amplifying hypervariable regions (HVRs 1–2 and 3) of the IBV S1 gene were developed and amplificates used for nucleotide sequence-based typing of IBV field strains in Egyptian chickens directly from clinical samples. The specificity of RT-qPCR primer set was evaluated by examining different avian respiratory viruses circulating in poultry in Egypt including AIV H5N1, H9N2 and NDV as well as different coronaviruses including a panel of IBV reference strains as listed in the materials section. Within HVR 1, 2 sequences, however, the existence of two distinct Table 3 RT-qPCRs reveal frequent co-infections in Egyptian poultry samples with avian influenza (AIV), Newcastle Disease (NDV) and infectious bronchitis viruses (IBV). cache = ./cache/cord-322410-k23engcx.txt txt = ./txt/cord-322410-k23engcx.txt === reduce.pl bib === id = cord-328046-5us4se5o author = Xu, H. Y. title = Further Identification and Characterization of Novel Intermediate and Mature Cleavage Products Released from the ORF 1b Region of the Avian Coronavirus Infectious Bronchitis Virus 1a/1b Polyprotein date = 2001-09-30 pages = extension = .txt mime = text/plain words = 5643 sentences = 279 flesch = 51 summary = In cells infected with avian coronavirus infectious bronchitis virus (IBV), three proteins of 100, 39, and 35 kDa, respectively, were previously identified as mature cleavage products released from the 1b region of the 1a/1b polyprotein by the 3C-like proteinase. Immunofluorescent staining of IBV-infected cells and cells expressing individual cleavage products showed that the 100-, 68-, and 58-kDa proteins were associated with the membranes of the endoplasmic reticulum, and the 39and 35-kDa proteins displayed diffuse distribution patterns. Taken together with the Q 3928 -S 2929 dipeptide bond (encoded by nucleotides 12310-12315) identified as the N-terminal cleavage site of the 100-kDa protein, cleavage at these positions would result in the release of five mature products with molecular masses of approximately 100, 68, 58, 39, and 35 kDa. Among them, the 100-, 39-, and 35-kDa proteins were specifically identified in IBV-infected cells (Liu et al., 1994 . cache = ./cache/cord-328046-5us4se5o.txt txt = ./txt/cord-328046-5us4se5o.txt === reduce.pl bib === id = cord-319168-i23pqiwx author = Abro, Shahid Hussain title = Emergence of novel strains of avian infectious bronchitis virus in Sweden date = 2012-03-23 pages = extension = .txt mime = text/plain words = 4934 sentences = 288 flesch = 58 summary = Nucleotide and amino acid sequence comparisons have shown that the recent isolates bear 98.97% genetic similarity with strains of the QX-like genotype. Twenty Swedish IBV isolates from different outbreaks were selected for comprehensive study of the complete spike gene of the virus. Analysis of the nucleotide sequences of spike glycoprotein of Swedish isolates from 1995 to 2010 showed that they comprise distinct sets of IBV variants; differing among themselves along that timeline (Table 3 ). The phylogenetic studies, based on the partial S1 gene regions, showed that Swedish IBV isolates from 1995 to 1999 were related to the Massachusetts genotype. Taken together, the complete spike sequence data revealed different isolates of IBV of the Massachusetts type and European D388/QX-like strains circulating over a time-line in Sweden. Complete genome sequence analysis of a predominant infectious bronchitis virus (IBV) strain in China cache = ./cache/cord-319168-i23pqiwx.txt txt = ./txt/cord-319168-i23pqiwx.txt === reduce.pl bib === id = cord-329429-ur8g68vp author = Miłek, Justyna title = Coronaviruses in Avian Species – Review with Focus on Epidemiology and Diagnosis in Wild Birds date = 2018-12-10 pages = extension = .txt mime = text/plain words = 3809 sentences = 187 flesch = 50 summary = Within the gamma-CoVs the main representative is avian coronavirus, a taxonomic name which includes the highly contagious infectious bronchitis viruses (IBVs) in chickens and similar viruses infecting other domestic birds such as turkeys, guinea fowls, or quails. The methods adopted in monitoring studies of CoVs in different avian species are mainly based on detection of conservative regions within the viral replicase, nucleocapsid genes, and 3'UTR or 5'UTR. The purpose of this review is to summarise recent discoveries in the areas of epidemiology and diagnosis of CoVs in avian species and to understand the role of wild birds in the virus distribution. This taxonomic name includes IBV which causes a highly contagious disease of chickens, and genetically similar viruses isolated from other domestic galliformes: turkey coronavirus (TCoV), responsible for turkey enteritis, and the more recently detected guinea fowl coronavirus (GfCoV), the aetiological factor of fulminating disease in this species (2, 6, 27) . cache = ./cache/cord-329429-ur8g68vp.txt txt = ./txt/cord-329429-ur8g68vp.txt === reduce.pl bib === id = cord-324324-8ybfiz8f author = Decaro, Nicola title = Novel human coronavirus (SARS-CoV-2): A lesson from animal coronaviruses date = 2020-04-14 pages = extension = .txt mime = text/plain words = 14927 sentences = 720 flesch = 49 summary = In addition, the close contact between human beings and different animal species sold at the wet markets of East Asia represents the optimal situation for the host species jump and adaptation to humans of potentially zoonotic agents like CoVs. It is not a coincidence that two of the most severe zoonoses of the last two decades (highly pathogenic H5N1 avian influenza and SARS) have emerged in the same Chinese province of Guangdong where the contact between humans and animals is closer (Lorusso et al., 2020) . All these viruses as well as analogous IBV-like CoVs detected in other birds including penguins, pigeons, peafowl, parrots, waterfowl, teal, quail, duck and whooper swan (Cavanagh et al., 2002; Circella et al., 2007; Domanska-Blicharz et al., 2014; Torres et al., 2013; Hughes et al., 2009; Liu et al., 2005; Wille et al., 2016; Jordan et al., 2015; Bande et al., 2016; Suryaman et al., 2019) have been assigned to the same viral species known as Avian coronavirus (ACoV) within the subgenus Igacovirus of genus Gammacoronavirus. cache = ./cache/cord-324324-8ybfiz8f.txt txt = ./txt/cord-324324-8ybfiz8f.txt === reduce.pl bib === id = cord-330260-xuw31zfn author = Chen, Hui-Wen title = Identification of Taiwan and China-like recombinant avian infectious bronchitis viruses in Taiwan date = 2009-01-20 pages = extension = .txt mime = text/plain words = 3698 sentences = 238 flesch = 58 summary = All of the recombinants showed chimeric IBV genome arrangements originated from Taiwan and China-like parental strains. Phylogenetic analyses were performed based on the nucleotide sequence alignment using each ORF from the S to N genes among eight Taiwan and reference strains (Fig. 1) . Phylogenetic analysis of partial S1 and N gene sequences of infectious bronchitis virus isolates from Italy revealed genetic diversity and recombination Recombinant avian infectious bronchitis virus expressing a heterologous spike gene demonstrates that the spike protein is a determinant of cell tropism A novel variant of avian infectious bronchitis virus resulting from recombination among three different strains Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus Genetic diversity of avian infectious bronchitis coronavirus strains isolated in China between Genetic grouping for the isolates of avian infectious bronchitis virus in Taiwan cache = ./cache/cord-330260-xuw31zfn.txt txt = ./txt/cord-330260-xuw31zfn.txt === reduce.pl bib === id = cord-346516-lal35iyr author = Hughes, Laura A. title = Genetically Diverse Coronaviruses in Wild Bird Populations of Northern England date = 2009-07-17 pages = extension = .txt mime = text/plain words = 1490 sentences = 91 flesch = 51 summary = Coronavirus RNA was detected in 7 fecal sample pools (Table 2) , giving an individual animal-level prevalence estimate of 1.6% (95% confidence interval 0.7-3.1). Phylogenetic analysis showed that coronavirus sequences detected by this study were genetically diverse. Virus sequences from 3 pools of fecal samples from ducks and whooper swans shared high nucleotide sequence identity with sequence from the IBV H120 vaccine strain, which is commonly used for the vaccination of commercial chickens worldwide. These viIt would be useful to determine the number and genome position of accessory genes of the coronaviruses detected in wild birds and to compare them with those of IBV. Minimum-evolution tree (11) of coronaviruses based on a 146-bp fragment of the 3′ untranslated region of infectious bronchitis virus (IBV). Detection of a coronavirus from turkey poults in Europe genetically related to infectious bronchitis virus of chickens cache = ./cache/cord-346516-lal35iyr.txt txt = ./txt/cord-346516-lal35iyr.txt === reduce.pl bib === id = cord-323568-s0wmll4q author = Shang, Jian title = Cryo-EM structure of infectious bronchitis coronavirus spike protein reveals structural and functional evolution of coronavirus spike proteins date = 2018-04-23 pages = extension = .txt mime = text/plain words = 7464 sentences = 452 flesch = 60 summary = Specifically, among different genera, the two domains of S1, the N-terminal domain (S1-NTD) and C-terminal domain (S1-CTD), diverge from simpler tertiary structures and quaternary packing to more complex ones, leading to different functions of the spikes in receptor usage and membrane fusion. The initial model of IBV spike ectodomain was obtained by fitting the seven parts (S1-NTD, S1-CTD, two parts of SD1, two parts of SD2, and S2) of the porcine delta coronavirus spike structure (PDB ID: 6B7N) individually into the cryo-EM density map of IBV spike using UCSF Chimera [41] and Coot [42] . Based on the structural similarity between the S1-NTDs from different coronavirus genera, the sugar-binding site in IBV S1-NTD might also be located in the pocket formed between the core structure and the partial ceiling (Figs 2B and 3C) . The putative RBMs of IBV S1-CTD and the partial ceiling Structure, function, and evolution of IBV spike protein of IBV S1-NTD are both involved in the cross-subunit packing. cache = ./cache/cord-323568-s0wmll4q.txt txt = ./txt/cord-323568-s0wmll4q.txt === reduce.pl bib === id = cord-321545-3gzj09mr author = Pohuang, Tawatchai title = Detection and molecular characterization of infectious bronchitis virus isolated from recent outbreaks in broiler flocks in Thailand date = 2009-09-07 pages = extension = .txt mime = text/plain words = 2537 sentences = 138 flesch = 55 summary = title: Detection and molecular characterization of infectious bronchitis virus isolated from recent outbreaks in broiler flocks in Thailand The isolates in group II showed a close relationship with Chinese IBVs. They had nucleotide sequence identities of 97-98% and amino acid sequence identities 96-98% in common with Chinese IBVs (strain A2, SH and QXIBV). Viral RNA was extracted by using Viral Nucleic Acid Extraction Kit (Real Biotech, Taiwan) following the manufacturer's instructions directly from the supernatants of 10% w/v sample suspensions and from the allantoic fluid of embryonated chicken eggs used for virus isolation. For virus isolation, the supernatants of IBV-positive samples determined by RT-PCR were inoculated into 10-day-old embryonated chicken eggs. The results from both S1 gene comparison and phylogenetic analysis showed that IBV isolates in group I had a distant relation to vaccine strains used in Thailand including Ma5, H120, M41, and Connecticut. Typing of field isolates of infectious bronchitis virus based on the sequence of the hypervariable region in the S1 gene cache = ./cache/cord-321545-3gzj09mr.txt txt = ./txt/cord-321545-3gzj09mr.txt === reduce.pl bib === id = cord-331740-yjt3q9ph author = Jones, R. M. title = Development and Validation of RT‐PCR Tests for the Detection and S1 Genotyping of Infectious Bronchitis Virus and Other Closely Related Gammacoronaviruses Within Clinical Samples date = 2011-04-07 pages = extension = .txt mime = text/plain words = 5863 sentences = 257 flesch = 49 summary = This real-time RT-PCR test was used to examine a panel of field samples and its performance compared to virus isolation in embryonated fowls' eggs. Design and calibration of IBV real-time RT-PCR To confirm that the modified test was suitable for detecting contemporary UK field strains of IBV, a panel of laboratory isolates of IBV representing the major genotypes currently circulating in the UK was tested . The validity of the result obtained for 38 of the 173 real-time RT-PCR positive, virus isolation negative samples could be confirmed by sequencing of the amplicon generated by the diagnostic RT-PCR. Infectious bronchitis virus RNA has been detected in tracheal swab samples by other real-time RT-PCRs for at least 21 days post-vaccination (Callison et al., 2006) and has been isolated from faecal samples in some infected birds as long as 227 days post-infection Gough, 1977, 1978) , making it essential to be able to differentiate between vaccine and field strains for diagnostic purposes. cache = ./cache/cord-331740-yjt3q9ph.txt txt = ./txt/cord-331740-yjt3q9ph.txt === reduce.pl bib === id = cord-346629-770qyee8 author = Mase, M. title = Phylogenetic analysis of avian infectious bronchitis virus strains isolated in Japan date = 2004-07-15 pages = extension = .txt mime = text/plain words = 2367 sentences = 137 flesch = 50 summary = title: Phylogenetic analysis of avian infectious bronchitis virus strains isolated in Japan To define the origin and evolution of recent avian infectious bronchitis virus (IBV) in Japan, a genetic analysis was performed. By phylogenetic analysis based on the S1 gene including the sequence of the hypervariable regions, IBV isolates in Japan were classified into five genetic groups, which included two already-known groups (Mass and Gray). In this study, to define the origin and evolution of recent IBV in Japan, we determined the nucleotide sequences of IBV isolated in Japan using the reverse transcriptase-polymerase chain reaction (RT-PCR) method coupled with direct sequencing, and analyzed the sequences phylogenetically with viruses isolated in other countries. By phylogenetic analysis, the IBV isolates in Japan used in this study were divided into five genetic groups (Fig. 1 ). Typing of field isolates of infectious bronchitis virus based on the sequence of the hypervariable region in the S1 gene cache = ./cache/cord-346629-770qyee8.txt txt = ./txt/cord-346629-770qyee8.txt === reduce.pl bib === id = cord-339235-8xslz4bs author = Boroomand, Zahra title = Molecular detection and phylogenetic properties of isolated infectious bronchitis viruses from broilers in Ahvaz, southwest Iran, based on partial sequences of spike gene date = 2018-09-15 pages = extension = .txt mime = text/plain words = 1978 sentences = 127 flesch = 53 summary = title: Molecular detection and phylogenetic properties of isolated infectious bronchitis viruses from broilers in Ahvaz, southwest Iran, based on partial sequences of spike gene A phylogenetic tree (Fig. 2) , based on the hypervariable region of S1 gene sequences of four IBV isolates from the present study and other strains of IBV retrieved from GenBank, was generated. Infectious bronchitis virus is one of the main pathogens of commercial and backyard chickens with several serotypes and genotypes circulating in the world. Genotyping of Avian infectious bronchitis viruses in Iran (2015-2017) reveals domination of IS-1494 like virus Molecular characterization of infectious bronchitis viruses isolated from broiler chicken farms in Iran The pathogenesis of a new variant genotype and QX-like infectious bronchitis virus isolated from chickens in Thailand Isolation and molecular characterization of Sul/01/09 avian infectious bronchitis virus, indicates the emergence of a new genotype in the Middle East cache = ./cache/cord-339235-8xslz4bs.txt txt = ./txt/cord-339235-8xslz4bs.txt === reduce.pl bib === id = cord-344297-qqohijqi author = Smith, Jacqueline title = The early immune response to infection of chickens with Infectious Bronchitis Virus (IBV) in susceptible and resistant birds date = 2015-10-09 pages = extension = .txt mime = text/plain words = 5076 sentences = 284 flesch = 52 summary = title: The early immune response to infection of chickens with Infectious Bronchitis Virus (IBV) in susceptible and resistant birds RESULTS: Genes and biological pathways involved in the early host response to IBV infection were determined andgene expression differences between susceptible and resistant birds were identified. [18] we used Affymetrix wholegenome chicken microarrays to examine the tracheal gene expression profiles of a line of birds known to be susceptible to IBV infection (line 15I) and a line known to show resistance (line N). Gene expression differences found in the susceptible 15I line between infected and control birds over days 2, 3 and 4 post infection were analysed, with a view to examining the innate host response to infection by IBV. Gene expression seen during the host response to IBV infection in the trachea of susceptible birds. Genes found to be differentially expressed between susceptible and resistant lines in response to IBV infection in the trachea. cache = ./cache/cord-344297-qqohijqi.txt txt = ./txt/cord-344297-qqohijqi.txt === reduce.pl bib === id = cord-342354-j10m2dfh author = Chen, Huijie title = Protective effects of hypericin against infectious bronchitis virus induced apoptosis and reactive oxygen species in chicken embryo kidney cells date = 2019-12-31 pages = extension = .txt mime = text/plain words = 5865 sentences = 291 flesch = 50 summary = title: Protective effects of hypericin against infectious bronchitis virus induced apoptosis and reactive oxygen species in chicken embryo kidney cells These results suggested that HY showed potential antiviral activities against IBV infection involving the inhibition of apoptosis and ROS generation in CEK cells. The aim of this study is to elucidate the antiviral activity and related mechanism of HY inhibiting IBV replication in chicken embryo kidney (CEK) cells, and provide alternative approach to prevent and treat IBV infection. The impact of HY on relative mRNA expression levels of IBV, apoptosis-related genes (including Fas, FasL, JNK, Bax, Bcl-2, Caspase 3, and Caspase 8), and ROS production in IBV-infected CEK cells were studied. Our results clearly demonstrated HY had potential antiviral activities against IBV infection involving the inhibition of apoptosis and ROS generation in CEK cells. The antiviral effect of HY was analyzed by the relative mRNA expression levels of IBV-N gene (Figure 2A ) and the virus titer ( Figure 2B ) in CEK cells. cache = ./cache/cord-342354-j10m2dfh.txt txt = ./txt/cord-342354-j10m2dfh.txt === reduce.pl bib === id = cord-335310-61wibso4 author = Chen, Hui-Wen title = Synthetic virus-like particles prepared via protein corona formation enable effective vaccination in an avian model of coronavirus infection date = 2016-08-15 pages = extension = .txt mime = text/plain words = 5482 sentences = 264 flesch = 40 summary = Herein, a facile approach to formulate synthetic virus-like particles (sVLPs) is demonstrated by exploiting the phenomenon of protein corona formation induced by the high-energy surfaces of synthetic nanoparticles. As compared to inoculation with free proteins, vaccination with the sVLPs showed enhanced lymphatic antigen delivery, stronger antibody titers, increased splenic T-cell response, and reduced infection-associated symptoms in an avian model of coronavirus infection. Comparison to a commercial whole inactivated virus vaccine also showed evidence of superior antiviral protection by the sVLPs. The study demonstrates a simple yet robust method in bridging viral antigens with synthetic nanoparticles for improved vaccine application; it has practical implications in the management of human viral infections as well as in animal agriculture. In the present study, vaccination with the sVLPs resulted in enhanced humoral and cellular immune responses, improving protection against an avian model of coronavirus infection as compared to free protein antigens and a commercial WIV vaccine. cache = ./cache/cord-335310-61wibso4.txt txt = ./txt/cord-335310-61wibso4.txt === reduce.pl bib === id = cord-331020-lyxje82u author = M. Najimudeen, Shahnas title = Infectious Bronchitis Coronavirus Infection in Chickens: Multiple System Disease with Immune Suppression date = 2020-09-24 pages = extension = .txt mime = text/plain words = 6966 sentences = 349 flesch = 37 summary = The evolution of new strains of IBV during the last nine decades against vaccine-induced immune response and changing clinical and pathological manifestations emphasize the necessity of the rational development of intervention strategies based on a thorough understanding of IBV interaction with the host. For example, chickens infected with certain strains of IBV such as Mass, QX-like strain or Aust T at ages of 1-14 days develop cystic oviducts without impaired ovarian functions, which leads to false layer syndrome with no egg production [15, [63] [64] [65] . One of the immune cell types that bridges innate and adaptive host responses is the macrophages, and the available data show that certain IBV serotypes (i.e., Mass and Conn) target respiratory tract macrophages and replicate within them, thus leading to a productive infection [59, 88] . cache = ./cache/cord-331020-lyxje82u.txt txt = ./txt/cord-331020-lyxje82u.txt === reduce.pl bib === id = cord-329468-vjsurl60 author = Okino, Cintia Hiromi title = Early immune responses and development of pathogenesis of avian infectious bronchitis viruses with different virulence profiles date = 2017-02-15 pages = extension = .txt mime = text/plain words = 5853 sentences = 261 flesch = 48 summary = This study compared the expression profile of genes related to immune responses in tracheal samples after challenge with two Brazilian field isolates (A and B) of IBV from the same genotype, associating these responses with viral replication and with pathological changes in trachea and kidney. Cell-mediated immune (CMI) related genes presented also lower levels of expression in tracheal samples from birds challenged with B isolate at 1dpi. This differential pattern of early immune responses developed after challenge with IBV B isolate, related to the downregulation of TLR7, leading to insufficient pro-inflammatory response and lower CMI responses, seem to have an association with a most severe renal lesion and an enhanced capability of replication of this isolate in chicken. In this study, we found a suppressive effect on expression of some early innate and adaptive cell-mediated immune genes in the primary site of virus replication (trachea) from chickens infected with one of the tested IBV isolates (B). cache = ./cache/cord-329468-vjsurl60.txt txt = ./txt/cord-329468-vjsurl60.txt === reduce.pl bib === id = cord-349149-nqsohp9h author = Lounas, A. title = The first evidence of a new genotype of nephropathogenic infectious bronchitis virus circulating in vaccinated and unvaccinated broiler flocks in Algeria date = 2018-11-29 pages = extension = .txt mime = text/plain words = 3700 sentences = 191 flesch = 52 summary = title: The first evidence of a new genotype of nephropathogenic infectious bronchitis virus circulating in vaccinated and unvaccinated broiler flocks in Algeria BACKGROUND AND AIM: Avian infectious bronchitis virus (IBV) frequently infects broilers and is responsible for severe economic losses to the poultry industry worldwide. MATERIALS AND METHODS: 14 clinically diseased broiler flocks from Western and Central Algeria were sampled and analyzed by hemagglutination inhibition (HI) test and reverse transcriptase-polymerase chain reaction (RT-PCR) followed by phylogenic analysis. Clinically diseased broiler flocks were sampled and analyzed by the hemagglutination inhibition (HI) test and reverse transcriptase-polymerase chain reaction (RT-PCR) followed by phylogenic analysis. Phylogenetic analysis of avian infectious bronchitis virus S1 glycoprotein regions reveals emergence of a new genotype in Moroccan broiler chicken flocks S1 gene sequence analysis of a nephropathogenic strain of avian infectious bronchitis virus in Egypt Isolation and genetic analysis revealed no predominant new strains of avian infectious bronchitis virus circulating in South China during cache = ./cache/cord-349149-nqsohp9h.txt txt = ./txt/cord-349149-nqsohp9h.txt === reduce.pl bib === id = cord-337441-c5bxthwn author = You, Jae-Hwan title = Three-Dimensional Reconstruction of the Nucleolus Using Meta-Confocal Microscopy in Cells Expressing the Coronavirus Nucleoprotein date = 2006 pages = extension = .txt mime = text/plain words = 1752 sentences = 100 flesch = 52 summary = We investigated the three-dimensional structure of the nucleolus and sub-nuclear bodies within cells expressing IBV and severe acute respiratory syndrome coronavirus (SARS-CoV) N protein. Live cell imaging data indicated that both EGFP and ECFP, when expressed as individual proteins, had no distinct distribution pattern and were present in both the cytoplasm and nucleus but not nucleolus (Fig. 1A) . In contrast to EGFP-tagged IBV N protein, ECFP-tagged SARS-CoV N protein localized to the cytoplasm and, in a minority of cells, to what appeared to be a nuclear body (arrowed). To investigate whether IBV N protein localized to a specific part of the nucleolus, Cos-7 cells were transfected with pEGFP-IBV-N, fixed 24 hr post-transfection, stained with PI to visualize the nucleus and nucleolus, then sectioned by confocal microscopy (Fig. 2) . META-confocal analysis and three-dimensional reconstructions of cells expressing IBV N protein revealed that N protein does not localize throughout the nucleolus and may be confined to the DFC. cache = ./cache/cord-337441-c5bxthwn.txt txt = ./txt/cord-337441-c5bxthwn.txt === reduce.pl bib === id = cord-330057-3vucm0s1 author = Franzo, Giovanni title = Phylodynamic analysis and evaluation of the balance between anthropic and environmental factors affecting IBV spreading among Italian poultry farms date = 2020-04-29 pages = extension = .txt mime = text/plain words = 5537 sentences = 280 flesch = 40 summary = In the present study, 361 IBV QX (the most relevant field genotype in Italy) sequences were obtained between 2012 and 2016 from the two main Italian integrated poultry companies. Finally, the different viral population pattern observed in the two companies over the same time period supports the pivotal role of management and control strategies on IBV epidemiology. Almost identical results were obtained including a third "ghost" deme (i.e. an estimated deme for which no sequences were available, representative of other unsampled companies and farms) in the analysis or using the "traditional" coalescent approach. In the particular Italian QX scenario, the serially sampled (i.e. with known collection date) strains were used to infer the migration rate and history between the two integrated poultry companies (i.e. considered as different demes) over time. cache = ./cache/cord-330057-3vucm0s1.txt txt = ./txt/cord-330057-3vucm0s1.txt === reduce.pl bib === id = cord-341541-3l6tjf3t author = Hajijafari Anaraki, Mozafar title = Molecular characterization of infectious bronchitis virus based on RNA‐dependent RNA polymerase gene date = 2020-05-26 pages = extension = .txt mime = text/plain words = 1276 sentences = 87 flesch = 49 summary = title: Molecular characterization of infectious bronchitis virus based on RNA‐dependent RNA polymerase gene Extensive rate of variations in in spike glycoprotein subunit gene of infectious bronchitis virus (IBV) caused challenges for counting variants for differentiation of infected from vaccinated birds and addressing the variants of unknown significance. The study aimed at investigating the possibility use of RNA‐dependent RNA polymerase gene (RdRp) as a target for molecular characterization of IBV strains in Iran. Phylogenetic analysis of RdRp gene sequences resulted in clustering the IBV strains related to each area. Using RdRp, as a genetic marker eliminates the challenges arise from the enormous variations that making difficult the discrimination between field and vaccine strains as well as affiliation of certain variants to various geographical areas. Based on the RT-PCR detection and sequence analysis of IBV RdRp gene, an overall prevalence of field strains estimated as 44.2%. cache = ./cache/cord-341541-3l6tjf3t.txt txt = ./txt/cord-341541-3l6tjf3t.txt === reduce.pl bib === id = cord-345630-bam3pa70 author = Lee, Han-Jung title = The complete sequence (22 kilobases) of murine coronavirus gene 1 encoding the putative proteases and RNA polymerase date = 1991-02-28 pages = extension = .txt mime = text/plain words = 5973 sentences = 418 flesch = 65 summary = authors: Lee, Han-Jung; Shieh, Chien-Kou; Gorbalenya, Alexander E.; Koonin, Eugene V.; La Monica, Nicola; Tuler, Jeremy; Bagdzhadzhyan, Anush; Lai, Michael M.C. title: The complete sequence (22 kilobases) of murine coronavirus gene 1 encoding the putative proteases and RNA polymerase Third, the 3'-half of the gene 1 sequences of IBV and MHV-A59 contains the sequence motifs for RNA polymerase and helicase, which are the activities expected to be involved in RNA synthesis Gorbalenya et a/., 198913; Bredenbeek et a/., 1990) . The alignment of amino acids in ORF la of MHV-JHM and IBV showed that there are four possible stretches of moderate homology which are separated by highly diverged sequences (Fig. 8) . Although ORF la is highly diverged between MHV-JHM and IBV, common functional domains could be identified in this ORF of both viruses by detailed amino acid sequence analysis (see Materials and Methods) (Fig. 9 ). cache = ./cache/cord-345630-bam3pa70.txt txt = ./txt/cord-345630-bam3pa70.txt === reduce.pl bib === id = cord-326319-3538jmqd author = Yuan, Yuan title = Protection against Virulent Infectious Bronchitis Virus Challenge Conferred by a Recombinant Baculovirus Co-Expressing S1 and N Proteins date = 2018-06-27 pages = extension = .txt mime = text/plain words = 7470 sentences = 370 flesch = 54 summary = title: Protection against Virulent Infectious Bronchitis Virus Challenge Conferred by a Recombinant Baculovirus Co-Expressing S1 and N Proteins The levels of immune protection of these subunit vaccines were evaluated by inoculating specific pathogen-free (SPF) chickens at 14 days of age, giving them a booster with the same dose 14 days later and challenging them with a virulent GX-YL5 strain of IBV 14 days post-booster (dpb). At 14 dpv, IBV-specific antibody levels in birds immunized with subunit vaccines rHBM-S1-N, rHBM-S1, rHBM-N and inactivated vaccine strain H120 started to rise (p > 0.05). At 14 dpv, IBV-specific antibody levels in birds immunized with subunit vaccines rHBM-S1-N, rHBM-S1, rHBM-N and inactivated vaccine strain H120 started to rise (p > 0.05). Induction of protective immunity in chickens vaccinated with infectious bronchitis virus S1 glycoprotein expressed by a recombinant baculovirus The S1 glycoprotein but not the N or M proteins of avian infectious bronchitis virus induces protection in vaccinated chickens cache = ./cache/cord-326319-3538jmqd.txt txt = ./txt/cord-326319-3538jmqd.txt === reduce.pl bib === id = cord-339259-4oi7slk9 author = Naguib, Mahmoud M. title = Full genome sequence analysis of a newly emerged QX-like infectious bronchitis virus from Sudan reveals distinct spots of recombination date = 2016-10-26 pages = extension = .txt mime = text/plain words = 4017 sentences = 238 flesch = 52 summary = title: Full genome sequence analysis of a newly emerged QX-like infectious bronchitis virus from Sudan reveals distinct spots of recombination By phylogenetic analysis based on the whole S1-gene according to (Valastro et al., 2016) it appeared that the IBV/Ck/Sudan/AR251-15/2014 is closely related to ITA/90254/ 2005 and the previously reported recombinant strains detected in South Africa (Ck/ZA/3665/11) and Sweden (Ck/SWE/0658946/10) which are clustered together within GI-19 lineage (Fig. 3) . The results showed that the Sudanese isolate was a recombinant virus which probably emerged from at least three different genotypes, including the 4/91 genotype as a major parent and the H120 vaccine strain as well as Italy/90254/2005-like viruses as minor parents (Fig. 4) . Characterization and analysis of the full-length genome of a strain of the european qx-like genotype of infectious bronchitis virus Complete genomic sequence analysis of infectious bronchitis virus ark dpi strain and its evolution by recombination cache = ./cache/cord-339259-4oi7slk9.txt txt = ./txt/cord-339259-4oi7slk9.txt === reduce.pl bib === id = cord-353027-bc0un6kb author = Ali, Ahmed title = Safety and efficacy of attenuated classic and variant 2 infectious bronchitis virus candidate vaccines date = 2018-08-06 pages = extension = .txt mime = text/plain words = 4144 sentences = 231 flesch = 54 summary = Virulence of the attenuated viruses was then tested via the ocular route inoculation and the in vivo back passage in day-old SPF chickens. In conclusion, the attenuated strains IBM41, IB2, and IBvar2 are efficient vaccine candidates against currently circulating classic and variant IB viruses, respectively. The first 3 groups were vaccinated via the ocular route with 10 3.5 EID 50 /bird of att-IBM41 virus, att-IB2, and att-IBvar2 viruses, respectively. The 3 viruses (IBV-EG/11539F-2011, IBV-EG/M41-ME01/2011, and Eg/1212B/2012) were successfully adapted to embryonated chicken eggs and showed the typical embryonic changes including dwarfing, stunting, and curling of embryos by the 10th or 14th passages for the classic (IB2 and IBM41) and the variant virus (IBvar2) (data not shown). Recent studies also indicated that the IBV strains circulating in Egypt represent a distinct a Day-old SPF chicks received 10 4 EID 50 /bird of the attenuated viruses separately via the ocular route. cache = ./cache/cord-353027-bc0un6kb.txt txt = ./txt/cord-353027-bc0un6kb.txt === reduce.pl bib === id = cord-348660-qnbgywgy author = Yilmaz, Huseyin title = Production of Recombinant N Protein of Infectious Bronchitis Virus Using the Baculovirus Expression System and Its Assessment as a Diagnostic Antigen date = 2018-07-09 pages = extension = .txt mime = text/plain words = 3921 sentences = 183 flesch = 43 summary = Following optimization of the ELISA protocol, 18 test sera were obtained from broiler chickens exposed to natural wild-type IBV infection, 18 test sera from broiler chickens vaccinated with a live-attenuated commercial IBV vaccine, and sera obtained at different time-points from chicks immunized with recombinant IBV N protein (described above) were analyzed to detect IBV N-specific antibodies. To assess the reliability of the performance of our in-house indirect IBV N ELISA, a panel of sera was obtained from chickens naturally infected with local wild-type IBV strains, chickens vaccinated with live-attenuated commercial IBV vaccine, and chickens immunized with recombinant IBV N protein (expressed in a baculovirus expression system). This represents the first study in Turkey that expressed recombinant IBV N protein in baculovirus and examined its reactivity against antisera obtained from Turkish chickens for potential use as antigen Fig. 5 Detection of IBV N specific antibodies in sera obtained from naturally infected chicken (a) and vaccinated chickens (b) using an in-house IBV-N ELISA and a commercial ELISA. cache = ./cache/cord-348660-qnbgywgy.txt txt = ./txt/cord-348660-qnbgywgy.txt === reduce.pl bib === id = cord-342176-tewfm8it author = Kjærup, Rikke M. title = Adjuvant effects of mannose-binding lectin ligands on the immune response to infectious bronchitis vaccine in chickens with high or low serum mannose-binding lectin concentrations date = 2013-11-08 pages = extension = .txt mime = text/plain words = 8381 sentences = 479 flesch = 62 summary = title: Adjuvant effects of mannose-binding lectin ligands on the immune response to infectious bronchitis vaccine in chickens with high or low serum mannose-binding lectin concentrations Chickens from two inbred lines (L10H and L10L) selected for high or low MBL serum concentrations, respectively, were vaccinated against IBV with or without the addition of the MBL ligands mannan, chitosan and fructooligosaccharide (FOS). Studies using these chicken sublines as well as outbred chickens have shown an inverse relationship between the MBL concentrations and the pathogen-specific antibody response (Juul-Madsen et al. However, MBL has an influence as the difference was more pronounced for the L10H chickens than L10L chickens for both the IBV-specific IgG antibody titres and the numbers of CD4−CD8␣+ and CD4−CD8␣− cells. Mannan-binding lectin (MBL) serum concentration in relation to propagation of infectious bronchitis virus (IBV) in chickens Crosstalk between innate and adaptive immune responses to infectious bronchitis virus after vaccination and challenge of chickens varying in serum mannose-binding lectin concentrations cache = ./cache/cord-342176-tewfm8it.txt txt = ./txt/cord-342176-tewfm8it.txt === reduce.pl bib === id = cord-334090-66d8c75g author = Seger, Waleed title = Genotyping of infectious bronchitis viruses from broiler farms in Iraq during 2014-2015 date = 2016-02-18 pages = extension = .txt mime = text/plain words = 3613 sentences = 178 flesch = 54 summary = Thus, the spread of viral respiratory diseases has become the most commonly reported condition in commercial broiler flocks in Iraq; however, there have been no studies on the detection and genotyping of these viruses using molecular techniques and sequencing. Phylogenetic analysis of the 32 strains (Fig. 2) revealed that Iraqi IBV strains could be classified into four genetic groups or genotypes: group I, variant 2 IS/1494-like viruses, including 15 field isolates (46.87 %); group II, 793/Blike viruses, including 13 field strains (40.62 %); group III, QX-like viruses, including three field strains (9.37); and caused by bacteria and mycoplasmas have already been detected on broiler farms located in the central and southern parts of Iraq. Our result were in line with those of Mahmood et al., who conducted the first study of identification and genotyping of IBV isolates and indicated that the 4/91-like virus is circulating on vaccinated broiler farms of the Kurdistan region of Iraq [21] . cache = ./cache/cord-334090-66d8c75g.txt txt = ./txt/cord-334090-66d8c75g.txt === reduce.pl bib === id = cord-352511-gkm7i62s author = Yamada, Yoshiyuki title = Acquisition of Cell–Cell Fusion Activity by Amino Acid Substitutions in Spike Protein Determines the Infectivity of a Coronavirus in Cultured Cells date = 2009-07-02 pages = extension = .txt mime = text/plain words = 5731 sentences = 317 flesch = 55 summary = title: Acquisition of Cell–Cell Fusion Activity by Amino Acid Substitutions in Spike Protein Determines the Infectivity of a Coronavirus in Cultured Cells Here we report that acquisition of the cell–cell fusion activity by amino acid mutations in the S protein determines the infectivity of IBV in cultured cells. This study demonstrates that acquisition of the cell–cell fusion activity in S protein determines the selection and/or adaptation of a coronavirus from chicken embryo to cultured cells of human and animal origins. In this study, we report that acquisition of the cell-cell fusion activity by point mutations in the spike (S) protein of avian coronavirus infectious bronchitis virus (IBV) plays a critical role in adaptation and/or selection of a variant that infects cultured cells. Sequence comparison of two S protein constructs, S(EP3) and S(CK), cloned from EP3 and CK-adapted IBV strains, respectively, showed amino acid substitutions at 31 positions (Fig. 1a) . cache = ./cache/cord-352511-gkm7i62s.txt txt = ./txt/cord-352511-gkm7i62s.txt === reduce.pl bib === id = cord-354547-eomm1sl5 author = Wang, Jibin title = Interaction of the Coronavirus Infectious Bronchitis Virus Membrane Protein with β-Actin and Its Implication in Virion Assembly and Budding date = 2009-03-16 pages = extension = .txt mime = text/plain words = 6319 sentences = 295 flesch = 51 summary = title: Interaction of the Coronavirus Infectious Bronchitis Virus Membrane Protein with β-Actin and Its Implication in Virion Assembly and Budding In this study, we report that interaction between coronavirus membrane protein (M) and actin with functional implication in facilitating virion assembly and budding. Similarly, analysis of cells expressing the M protein either on its own or together with the Myc-tagged actin by Western blot with anti-M polyclonal antibodies showed the detection of the full-length glycosylated (two upper bands) and unglycosylated (25 kDa) forms of the M protein (Fig. 2, lanes 5 and 6) . In cells transfected with both wild type and MD5 constructs with or without IBV infection, detection of similar amounts of M protein was observed (Fig. 5b, top two panels, lanes 1 and 2) , suggesting that both constructs were expressed at similar efficiencies. cache = ./cache/cord-354547-eomm1sl5.txt txt = ./txt/cord-354547-eomm1sl5.txt === reduce.pl bib === id = cord-355703-l9l4ybfn author = Zhao, Fei title = Genomic Characteristics and Changes of Avian Infectious Bronchitis Virus Strain CK/CH/LDL/97I after Serial Passages in Chicken Embryos date = 2014-08-29 pages = extension = .txt mime = text/plain words = 5859 sentences = 300 flesch = 49 summary = title: Genomic Characteristics and Changes of Avian Infectious Bronchitis Virus Strain CK/CH/LDL/97I after Serial Passages in Chicken Embryos To identify specific sequence changes responsible for adaptation of the field IBV isolate to chicken embryonic tissue and subsequent attenuation, the whole viral genome of the IBV P5 pathogenic parental CK/CH/LDL/97I strain was sequenced and compared with the attenuated, P115 level virus, to provide a better understanding of the relationship between the genomic differences and related characteristics of the pathogenic and attenuated viruses. Limited information is currently available regarding the pathogenicity of CK/CH/ LDL/97I-type IBV strains and embryo-passaged, attenuated P115 in the chicken oviduct. Altered pathogenicity, immunogenicity, tissue tropism and 3 ′ -7 kb region sequence of an avian infectious bronchitis coronavirus strain after serial passage in embryos Sequence changes of infectious bronchitis virus isolates in the 3 ′ -7.3 kb of the genome after attenuating passage in embryonated eggs cache = ./cache/cord-355703-l9l4ybfn.txt txt = ./txt/cord-355703-l9l4ybfn.txt === reduce.pl bib === id = cord-353310-19kzb6ag author = Quinteros, José A. title = Analysis of the complete genomic sequences of two virus subpopulations of the Australian infectious bronchitis virus vaccine VicS date = 2015-04-01 pages = extension = .txt mime = text/plain words = 5201 sentences = 250 flesch = 56 summary = Compared with VicS-v, the more attenuated VicS-del strain had two non-synonymous changes in the non-structural protein 6 (nsp6), a transmembrane (TM) domain that may participate in autocatalytic release of the 3-chymotrypsin-like protease, a polymorphic difference at the end of the S2 gene, which coincided with the body transcription-regulating sequence (B-TRS) of mRNA 3 and a truncated open reading frame for a peptide encoded by gene 4 (4b). Phylogenetic analysis of the whole genome showed that VicS-v and VicS-del did not cluster with strains from other countries, supporting the hypothesis that Australian IBV strains have been evolving independently for some time, and analyses of individual polymerase peptide and S glycoprotein genes suggested a distant common ancestor with no recent recombination. For VicSdel, the readings were mapped to the genome of VicS-v and the previously determined sequence of the structural protein gene region of VicS-del (GAN JN983807). cache = ./cache/cord-353310-19kzb6ag.txt txt = ./txt/cord-353310-19kzb6ag.txt === reduce.pl bib === id = cord-344745-sgkq1l93 author = Selim, Karim title = Molecular characterization of infectious bronchitis viruses isolated from broiler and layer chicken farms in Egypt during 2012 date = 2013-11-18 pages = extension = .txt mime = text/plain words = 2757 sentences = 172 flesch = 56 summary = title: Molecular characterization of infectious bronchitis viruses isolated from broiler and layer chicken farms in Egypt during 2012 The aim of this study aimed to survey the Egyptian chicken field for infectious bronchitis virus and study the genomic differentiation between isolated field samples seeking the new variant strain emerged in the Egyptian field. For virus isolation, the supernatants of IBV-positive selected 13 samples determined by RT-PCR were inoculated into five specific pathogen free embryonated chicken eggs (KoumOshiem SPF chicken farm, Fayoum, Egypt) 10-day-old for each sample. The genetic analysis of 100 amino acids sequence from position 263-362 of SP1 gene for the selected 13 Egyptian viruses was done and the hypervariable region of SP1 gene showed multiple mutations as shown in Table 4 in comparison with variant-2 strain. S1 gene sequence analysis of a nephro-pathogenic strain of avian infectious bronchitis virus in Egypt cache = ./cache/cord-344745-sgkq1l93.txt txt = ./txt/cord-344745-sgkq1l93.txt === reduce.pl bib === id = cord-345088-krb1eidw author = Shen, S title = A single amino acid mutation in the spike protein of coronavirus infectious bronchitis virus hampers its maturation and incorporation into virions at the nonpermissive temperature date = 2004-09-01 pages = extension = .txt mime = text/plain words = 6949 sentences = 316 flesch = 56 summary = title: A single amino acid mutation in the spike protein of coronavirus infectious bronchitis virus hampers its maturation and incorporation into virions at the nonpermissive temperature Here, we report the emergence and isolation of two temperature sensitive (ts) mutants and a revertant in the process of cold-adaptation of coronavirus infectious bronchitis virus (IBV) to a monkey kidney cell line. Evidence presented demonstrated that the Q(294)-to-L(294) mutation, located at a highly conserved domain of the S1 subunit, might hamper processing of the S protein to a matured 180-kDa, endo-glycosidase H-resistant glycoprotein and the translocation of the protein to the cell surface. In virus-infected cells, the Endo-H sensitive, 155-kDa form of ts291602 was abundant at the nonpermissive temperature, clearly indicating that the mutant S protein was trimmed in the ER and cis-Golgi but was not transported to the trans-Golgi. cache = ./cache/cord-345088-krb1eidw.txt txt = ./txt/cord-345088-krb1eidw.txt === reduce.pl bib === id = cord-343893-sophqqne author = Chu, Victor C title = Feline aminopeptidase N is not a functional receptor for avian infectious bronchitis virus date = 2007-02-26 pages = extension = .txt mime = text/plain words = 3972 sentences = 232 flesch = 54 summary = Feline aminopeptidase N (fAPN) serves as a functional receptor for most group 1 coronaviruses including feline infectious peritonitis virus (FIPV), canine coronavirus, transmissible gastroenteritis virus (TGEV), and human coronavirus 229E (HCoV-229E). Group 1 CoVs -including human coronavirus-229E (HCoV-229E), feline infectious peritonitis virus (FIPV), transmissible gastroenteritis virus (TGEV) and canine coronavirus (CCV) -utilize human, feline, porcine, and canine aminopeptidase N (APN) as functional receptors during virus entry [10] [11] [12] [13] . We also cultured seven strains of IBV, including Arkansas 99, Arkansas_DPI, California 99, Connecticut 46, Holland 52, Iowa 97, and Massachusetts 41 (designated as Ark99, Ark_DPI, CA99, Conn46, H52, Iowa97, and Mass41) as candidates to test for fAPN utilization by group 3 avian CoVs. Surprisingly, expression of fAPN did not increase viral infection in any of the strains tested. To verify the functionality of fAPN as a coronavirus receptor, we first tested its ability to rescue FIPV-1146 and TGEV infection of non-permissive cells, as reported in previous studies [11] . cache = ./cache/cord-343893-sophqqne.txt txt = ./txt/cord-343893-sophqqne.txt === reduce.pl bib === id = cord-351564-nikcd44o author = Zhang, Xiaozhan title = Molecular characterization of variant infectious bronchitis virus in China, 2019: Implications for control programmes date = 2020-01-24 pages = extension = .txt mime = text/plain words = 2798 sentences = 124 flesch = 45 summary = Although the gross pathologic appearance of these two IB outbreaks was different, the newly identified IBV strains were all closely related to the ck/China/I0529/17 strain and grouped into GI‐19 genotype clade based on the sequencing and phylogenetic analysis of the complete S1 genes. In conclusion, this study provided an insight of the recently emerging IBV outbreaks in IBV‐vaccinated commercial poultry farms and identified the genetic characteristics of three virulent GI‐19 IBV strains, which shows the need to carry out proper preventive measures and control strategies. Herein, we reported two IB outbreaks in IBV-vaccinated commercial broiler farms in central China, and the complete S1 genes of the newly identified IBV strains were sequenced, and its genotype, phylogeny and variations were analysed further. cache = ./cache/cord-351564-nikcd44o.txt txt = ./txt/cord-351564-nikcd44o.txt === reduce.pl bib === id = cord-338307-vfutmwxq author = Sturman, Lawrence S. title = The Molecular Biology of Coronaviruses date = 1983-12-31 pages = extension = .txt mime = text/plain words = 21959 sentences = 1287 flesch = 52 summary = The pattern of three major structural proteins and their organization in the virion as shown for MHV-A59 in Fig. 3 is generally applicable to most other species of coronaviruses (reviewed in detail by Siddell et al., 1982) . (1981b) , using a cDNA probe prepared against the mRNA of MHV-A59 which coded for the nucleocapsid protein, obtained evidence of 7 0 4 0 % homology by analysis of hybridization kinetics of viral RNA from cells infected with MHV-1, -3, -S, and -JHM. t 1980) demonstrated that different size classes of poly(A)containing intracellular MHV-JHM RNAs fractionated on sucroseformamide gradients directed the synthesis of different structural proteins in cell-free translation systems. The studies showed that, like avian coronaviruses, for the murine coronavirus MHV-A59, the oligonucleotides of each of the subgenomic RNAs were included within the next larger species, starting from the 3' end of the genome. cache = ./cache/cord-338307-vfutmwxq.txt txt = ./txt/cord-338307-vfutmwxq.txt === reduce.pl bib === id = cord-356094-sbtigcfr author = Chen, Huijie title = Antiviral Activity Against Infectious Bronchitis Virus and Bioactive Components of Hypericum perforatum L. date = 2019-10-29 pages = extension = .txt mime = text/plain words = 8921 sentences = 485 flesch = 55 summary = perforatum was ethyl acetate extraction section (HPE), and results showed that treatment with HPE significantly reduced the relative messenger ribonucleic acid (mRNA) expression and virus titer of IBV, and reduced positive green immunofluorescence signal of IBV in chicken embryo kidney (CEK) cells. The results of adaptation and replication in CEK cells, such as CPE, reverse transcription polymerase chain reaction (RT-PCR), and IBV growth curve determined by tissue culture infective dose (TCID 50 ) at different time were tested. The relative mRNA expression level of IBV-N gene was detected by qRT-PCR and the virus titer of IBV was determined by TCID 50 to analyze the antiviral effect of HPE, HPW and SEE (Figure 3) . FIgUre 8 | The effects of Hypericum perforatum ethyl acetate (HPE) on infectious bronchitis virus (IBV) messenger ribonucleic acid (mRNA) expression levels of trachea (A) and kidney (B). cache = ./cache/cord-356094-sbtigcfr.txt txt = ./txt/cord-356094-sbtigcfr.txt ===== Reducing email addresses cord-280442-jtvez46y cord-271568-qgpi2kcs cord-330260-xuw31zfn Creating transaction Updating adr table ===== Reducing keywords cord-003148-o7y3wygc cord-263178-lvxxdvas cord-017894-8iahlshj cord-263193-paeosfiu cord-006991-2q5ore6g cord-022378-ovxmy1as cord-004810-g0y7ied0 cord-264716-igl25jhg cord-269024-re0hyolh cord-255619-5h3l6nh6 cord-256859-7ixegm72 cord-009487-7xb4huyz cord-280442-jtvez46y cord-003208-lwirkob3 cord-257064-iafm3pcc cord-260042-cs0wp99n cord-007648-tm0hn0hz cord-265681-ab8j4o1u cord-256444-grw5s2pf cord-258379-v3lceirh cord-010608-eaa2znom cord-276550-1in7m56w cord-278324-eqqvwwh6 parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. cord-252048-ftbjsoup cord-000924-wwuqxx1r cord-265499-pbf11zy1 cord-266585-jfjrk9gy cord-253695-tjdw2uta cord-255141-55ho9av4 cord-022187-7c3wz6c6 cord-285052-aql0vrzv cord-284501-5i0w74q4 cord-255870-gmq5zs2d cord-273366-xd84f8ct cord-263785-0iift8zy cord-002407-25cawzi0 cord-277804-ujabzic4 cord-001768-8vljd5cv cord-285942-mb1xwdqw cord-004680-u3cnsdl8 cord-260145-grz0fe9l cord-279495-zxerb7de cord-268788-jcu3pasy cord-259959-qzd3hf8y cord-257999-apg4uhhq cord-269150-d1sgnxc0 cord-260799-kx6hfpu0 cord-259505-7hiss0j3 cord-260667-5aurua6o cord-265258-2rmtsyns cord-003334-ion97n4b cord-282314-9cua2jzg cord-262226-7kwkla73 cord-291754-1zxztadu cord-281526-7t9e4lgn cord-272437-gvzfl8c3 cord-263476-ju7xqwa7 cord-291174-rym84kni cord-265508-t1nfyzf5 cord-268454-w4qca90s cord-001083-vy1nxax2 cord-273846-l0elcfe8 cord-259480-1tqfoecc cord-262940-eyejnexx cord-290638-7ro72sv3 cord-285330-td4vr0zv cord-293651-96cmduez cord-271897-9oqzsd70 cord-271359-dpa8zzc3 cord-261388-d56ci0hl cord-286473-sl5zy8nj cord-273661-egpyvqrw cord-272305-eniovfwy cord-272666-3uidpr79 cord-286332-cdg4im5h cord-291718-cz1bi0ym cord-293081-40pa5g89 cord-294679-7pklrmz5 cord-285323-473d7zvg cord-272693-432ixb7g cord-259738-yuqc6dk0 cord-276755-ctzrgqe7 cord-295312-68b3zio6 cord-288309-6pw7t512 cord-271568-qgpi2kcs cord-286658-9kco7qad cord-292428-j3wdlpp6 cord-296831-wdpatr2z cord-291510-jh2fdks4 cord-299428-gon6bzat cord-296167-np0b9a7o cord-296364-7rp60d2m parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. cord-296611-ma32oz4o cord-298078-uqrwq5qk cord-296524-68gwusfe cord-298920-1lc2xf7u parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. cord-300104-855iw9wi cord-301720-majpfxqn cord-301810-vtgdqart cord-303588-bwllypvq cord-304322-k9egxskw cord-306380-msk9p1yy cord-308950-bl83r4v3 cord-309623-2ngr682l cord-316525-uadfehr6 cord-310372-qc6941pm cord-305079-foifc8ch cord-303393-9zs3qqo4 cord-303794-fn3jkiil cord-319253-8bssrn9o cord-304278-0qy1nngs cord-316153-wet0go35 cord-305684-ipeup5mp cord-309469-2naxn580 cord-307304-irji8owi cord-310536-u30cufg7 cord-308591-cs8os2f5 cord-313676-6rebpe57 cord-306976-p2521bl4 cord-318400-l9kwxsq7 cord-316234-vtjsfi2c cord-312489-ywep0c08 cord-329497-3jow4xbn cord-329245-6tj2k1yn cord-317347-by8albr9 cord-321602-88b2h06y cord-337128-yyz7z0xj cord-317587-rrx2r4n2 cord-328046-5us4se5o cord-321261-3lp54mmu cord-322410-k23engcx cord-322516-wekvet6f cord-324324-8ybfiz8f cord-329429-ur8g68vp cord-319168-i23pqiwx cord-330260-xuw31zfn cord-346516-lal35iyr cord-323568-s0wmll4q cord-321545-3gzj09mr cord-331740-yjt3q9ph cord-344297-qqohijqi cord-346629-770qyee8 cord-339235-8xslz4bs cord-335310-61wibso4 cord-342354-j10m2dfh cord-349149-nqsohp9h cord-329468-vjsurl60 cord-341541-3l6tjf3t parallel: Warning: No more processes: Decreasing number of running jobs to 92. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. cord-330057-3vucm0s1 cord-337441-c5bxthwn cord-326319-3538jmqd cord-348660-qnbgywgy cord-355703-l9l4ybfn cord-353027-bc0un6kb cord-339259-4oi7slk9 cord-345630-bam3pa70 cord-331020-lyxje82u cord-342176-tewfm8it cord-352511-gkm7i62s cord-354547-eomm1sl5 cord-334090-66d8c75g cord-353310-19kzb6ag cord-344745-sgkq1l93 cord-345088-krb1eidw cord-338307-vfutmwxq cord-356094-sbtigcfr cord-351564-nikcd44o cord-343893-sophqqne Creating transaction Updating wrd table ===== Reducing urls cord-003148-o7y3wygc cord-263178-lvxxdvas cord-264716-igl25jhg cord-269024-re0hyolh cord-255619-5h3l6nh6 cord-280442-jtvez46y cord-010608-eaa2znom cord-252048-ftbjsoup cord-255141-55ho9av4 cord-022187-7c3wz6c6 cord-285052-aql0vrzv cord-255870-gmq5zs2d cord-273366-xd84f8ct cord-277804-ujabzic4 cord-260145-grz0fe9l cord-279495-zxerb7de cord-259959-qzd3hf8y cord-265258-2rmtsyns cord-282314-9cua2jzg cord-291174-rym84kni cord-001083-vy1nxax2 cord-293651-96cmduez cord-271897-9oqzsd70 cord-272666-3uidpr79 cord-285323-473d7zvg cord-272693-432ixb7g cord-286658-9kco7qad cord-271568-qgpi2kcs cord-291510-jh2fdks4 cord-296611-ma32oz4o cord-298078-uqrwq5qk cord-304322-k9egxskw cord-316525-uadfehr6 cord-303393-9zs3qqo4 cord-303794-fn3jkiil cord-309469-2naxn580 cord-305684-ipeup5mp cord-308591-cs8os2f5 cord-306976-p2521bl4 cord-316234-vtjsfi2c cord-312489-ywep0c08 cord-317347-by8albr9 cord-317587-rrx2r4n2 cord-322410-k23engcx cord-319168-i23pqiwx cord-339235-8xslz4bs cord-323568-s0wmll4q cord-331020-lyxje82u cord-324324-8ybfiz8f cord-344297-qqohijqi cord-329468-vjsurl60 cord-330057-3vucm0s1 cord-341541-3l6tjf3t parallel: Warning: No more processes: Decreasing number of running jobs to 58. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. cord-339259-4oi7slk9 cord-326319-3538jmqd cord-342176-tewfm8it cord-344745-sgkq1l93 cord-355703-l9l4ybfn cord-351564-nikcd44o Creating transaction Updating url table ===== Reducing named entities cord-003148-o7y3wygc cord-263178-lvxxdvas cord-017894-8iahlshj cord-263193-paeosfiu cord-006991-2q5ore6g cord-022378-ovxmy1as cord-004810-g0y7ied0 cord-264716-igl25jhg parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. cord-269024-re0hyolh cord-255619-5h3l6nh6 cord-256859-7ixegm72 cord-009487-7xb4huyz cord-280442-jtvez46y cord-003208-lwirkob3 cord-257064-iafm3pcc cord-260042-cs0wp99n cord-007648-tm0hn0hz cord-265681-ab8j4o1u cord-258379-v3lceirh cord-256444-grw5s2pf cord-010608-eaa2znom cord-276550-1in7m56w cord-278324-eqqvwwh6 cord-252048-ftbjsoup cord-000924-wwuqxx1r cord-266585-jfjrk9gy cord-265499-pbf11zy1 cord-253695-tjdw2uta cord-255141-55ho9av4 cord-022187-7c3wz6c6 cord-285052-aql0vrzv cord-284501-5i0w74q4 cord-255870-gmq5zs2d cord-273366-xd84f8ct cord-263785-0iift8zy cord-002407-25cawzi0 cord-277804-ujabzic4 cord-001768-8vljd5cv cord-285942-mb1xwdqw cord-004680-u3cnsdl8 cord-260145-grz0fe9l cord-279495-zxerb7de parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. cord-268788-jcu3pasy cord-259959-qzd3hf8y cord-257999-apg4uhhq cord-269150-d1sgnxc0 cord-260799-kx6hfpu0 cord-259505-7hiss0j3 cord-260667-5aurua6o cord-265258-2rmtsyns cord-003334-ion97n4b cord-282314-9cua2jzg cord-262226-7kwkla73 cord-291754-1zxztadu parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. cord-281526-7t9e4lgn cord-272437-gvzfl8c3 cord-263476-ju7xqwa7 cord-291174-rym84kni cord-265508-t1nfyzf5 cord-268454-w4qca90s cord-001083-vy1nxax2 cord-273846-l0elcfe8 cord-259480-1tqfoecc cord-262940-eyejnexx cord-290638-7ro72sv3 cord-285330-td4vr0zv cord-293651-96cmduez cord-271897-9oqzsd70 cord-271359-dpa8zzc3 cord-261388-d56ci0hl parallel: Warning: No more processes: Decreasing number of running jobs to 92. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. cord-286473-sl5zy8nj cord-273661-egpyvqrw cord-272305-eniovfwy cord-272666-3uidpr79 cord-286332-cdg4im5h cord-291718-cz1bi0ym cord-293081-40pa5g89 cord-294679-7pklrmz5 cord-285323-473d7zvg cord-259738-yuqc6dk0 cord-272693-432ixb7g cord-276755-ctzrgqe7 parallel: Warning: No more processes: Decreasing number of running jobs to 91. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. cord-295312-68b3zio6 cord-286658-9kco7qad cord-288309-6pw7t512 cord-271568-qgpi2kcs cord-292428-j3wdlpp6 cord-296831-wdpatr2z cord-291510-jh2fdks4 cord-296167-np0b9a7o cord-299428-gon6bzat cord-296364-7rp60d2m cord-296611-ma32oz4o cord-298078-uqrwq5qk cord-296524-68gwusfe cord-298920-1lc2xf7u cord-300104-855iw9wi cord-301720-majpfxqn cord-303588-bwllypvq cord-301810-vtgdqart cord-304322-k9egxskw cord-306380-msk9p1yy cord-308950-bl83r4v3 cord-309623-2ngr682l cord-310372-qc6941pm cord-316525-uadfehr6 cord-305079-foifc8ch cord-303393-9zs3qqo4 cord-303794-fn3jkiil cord-319253-8bssrn9o cord-304278-0qy1nngs cord-305684-ipeup5mp cord-309469-2naxn580 cord-316153-wet0go35 cord-310536-u30cufg7 cord-307304-irji8owi cord-308591-cs8os2f5 cord-313676-6rebpe57 cord-306976-p2521bl4 cord-318400-l9kwxsq7 cord-316234-vtjsfi2c cord-312489-ywep0c08 cord-329245-6tj2k1yn cord-329497-3jow4xbn cord-317347-by8albr9 cord-337128-yyz7z0xj cord-321602-88b2h06y cord-321261-3lp54mmu cord-317587-rrx2r4n2 cord-322516-wekvet6f cord-322410-k23engcx cord-328046-5us4se5o parallel: Warning: No more processes: Decreasing number of running jobs to 90. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. cord-329429-ur8g68vp cord-330260-xuw31zfn cord-324324-8ybfiz8f cord-319168-i23pqiwx 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Raising ulimit -u or /etc/security/limits.conf parallel: Warning: or /proc/sys/kernel/pid_max may help. cord-017894-8iahlshj cord-263193-paeosfiu cord-263178-lvxxdvas cord-022378-ovxmy1as cord-006991-2q5ore6g cord-003148-o7y3wygc cord-004810-g0y7ied0 cord-264716-igl25jhg cord-269024-re0hyolh cord-255619-5h3l6nh6 cord-009487-7xb4huyz cord-280442-jtvez46y cord-256859-7ixegm72 cord-003208-lwirkob3 cord-257064-iafm3pcc cord-007648-tm0hn0hz cord-265681-ab8j4o1u cord-258379-v3lceirh cord-260042-cs0wp99n cord-010608-eaa2znom cord-276550-1in7m56w cord-278324-eqqvwwh6 cord-000924-wwuqxx1r cord-252048-ftbjsoup cord-265499-pbf11zy1 cord-266585-jfjrk9gy cord-253695-tjdw2uta cord-022187-7c3wz6c6 cord-285052-aql0vrzv cord-255870-gmq5zs2d cord-255141-55ho9av4 cord-263785-0iift8zy cord-284501-5i0w74q4 cord-277804-ujabzic4 cord-001768-8vljd5cv cord-004680-u3cnsdl8 cord-273366-xd84f8ct cord-002407-25cawzi0 cord-285942-mb1xwdqw cord-260145-grz0fe9l cord-268788-jcu3pasy cord-279495-zxerb7de 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cord-316234-vtjsfi2c cord-321602-88b2h06y cord-317587-rrx2r4n2 cord-337128-yyz7z0xj cord-329497-3jow4xbn cord-329245-6tj2k1yn cord-322516-wekvet6f cord-321261-3lp54mmu cord-322410-k23engcx cord-328046-5us4se5o cord-319168-i23pqiwx cord-329429-ur8g68vp cord-330260-xuw31zfn cord-317347-by8albr9 cord-346516-lal35iyr cord-323568-s0wmll4q cord-321545-3gzj09mr cord-331740-yjt3q9ph cord-346629-770qyee8 cord-339235-8xslz4bs cord-324324-8ybfiz8f cord-344297-qqohijqi cord-342354-j10m2dfh cord-335310-61wibso4 cord-329468-vjsurl60 cord-337441-c5bxthwn cord-341541-3l6tjf3t cord-331020-lyxje82u cord-339259-4oi7slk9 cord-330057-3vucm0s1 cord-348660-qnbgywgy cord-345630-bam3pa70 cord-334090-66d8c75g cord-326319-3538jmqd cord-353027-bc0un6kb cord-352511-gkm7i62s cord-355703-l9l4ybfn cord-344745-sgkq1l93 cord-349149-nqsohp9h cord-351564-nikcd44o cord-354547-eomm1sl5 cord-353310-19kzb6ag cord-343893-sophqqne cord-342176-tewfm8it cord-345088-krb1eidw cord-356094-sbtigcfr cord-338307-vfutmwxq Creating transaction Updating pos table Building ./etc/reader.txt cord-256444-grw5s2pf cord-338307-vfutmwxq cord-324324-8ybfiz8f cord-304278-0qy1nngs cord-331020-lyxje82u cord-329497-3jow4xbn number of items: 168 sum of words: 753,986 average size in words: 4,993 average readability score: 52 nouns: virus; protein; bronchitis; cells; strains; gene; coronavirus; chickens; strain; viruses; sequence; vaccine; infection; proteins; cell; analysis; group; study; s1; genome; sequences; birds; type; chicken; recombination; replication; spike; samples; genes; region; isolates; coronaviruses; groups; results; acid; disease; vaccines; expression; time; control; amino; detection; antibody; vaccination; challenge; protection; days; influenza; antibodies; data verbs: used; showed; isolates; infect; detect; contains; induce; indicated; observed; include; based; followed; found; compared; expressed; identify; cause; determined; describes; suggested; associated; resulted; performed; binding; reported; inoculated; demonstrated; obtained; encoding; increased; provides; collected; occurs; strain; generated; involved; confirmed; according; challenged; analyzed; related; required; incubated; revealed; purified; treated; see; tested; embryonated; vaccinated adjectives: infectious; viral; avian; different; respiratory; specific; recombinant; positive; new; like; high; molecular; genetic; immune; clinical; structural; nucleotide; similar; negative; infected; old; phylogenetic; non; anti; present; significant; commercial; attenuated; several; important; first; severe; genomic; novel; human; full; single; higher; wild; real; antigenic; cellular; multiple; reverse; complete; tracheal; major; live; pathogenic; vaccinated adverbs: also; however; respectively; previously; well; highly; significantly; therefore; recently; approximately; first; closely; nt; together; furthermore; subsequently; even; currently; directly; still; briefly; mainly; probably; interestingly; alone; moreover; especially; worldwide; genetically; later; live; commonly; relatively; newly; experimentally; frequently; widely; usually; yet; prior; likely; finally; particularly; least; generally; similarly; often; far; successfully; rather pronouns: it; we; its; their; our; they; i; them; his; he; us; itself; p110; you; her; ch/; themselves; mrnas; your; one; irfibv32; svlps; is/1494; him; rh120-s1/; imagej; ibv-200; ibv-199; egfp; a2,3-linked; β2.7; αβ; ~tcttaaaa; utr41; und; s; ribvs; ribv; r132; puc; pkt0-ibvn; nsp4; is/1201; ifit5; ifih1; ibvsx4; ibv_bdtt; ibv14931-f; ibv-281; ibv-212 proper nouns: IBV; RNA; PCR; Fig; S1; S; M; RT; N; China; CH; MHV; H120; C; IB; CK; SARS; ORF; SPF; Coronavirus; Beaudette; USA; Mass; Table; PBS; QX; E; ELISA; Vero; CoV; T; NDV; S2; Cavanagh; allantoic; M41; AIV; II; ck; Massachusetts; mRNA; Liu; TCoV; GenBank; B; Taiwan; Golgi; EID; Egypt; CEK keywords: ibv; rna; pcr; virus; china; protein; strain; orf; ndv; mass; h120; cell; vero; mhv; elisa; sars; m41; iraq; group; egypt; dna; cek; aiv; iran; infectious; iltv; h9n2; gene; egfp; bronchitis; bird; beaudette; anv; yx10; woa; western; vics; vaccine; usa; tlr3; thailand; tgf; tgev; taiwan; swedish; sweden; sudan; spf; scs1; sc021202 one topic; one dimension: ibv file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6086832/ titles(s): A Recombinant Newcastle Disease Virus (NDV) Expressing S Protein of Infectious Bronchitis Virus (IBV) Protects Chickens against IBV and NDV three topics; one dimension: ibv; ibv; coronavirus file(s): https://www.ncbi.nlm.nih.gov/pubmed/31561498/, https://www.ncbi.nlm.nih.gov/pubmed/32422883/, https://api.elsevier.com/content/article/pii/S0065352708602869 titles(s): Genetic Analysis of Avian Coronavirus Infectious Bronchitis Virus in Yellow Chickens in Southern China over the Past Decade: Revealing the Changes of Genetic Diversity, Dominant Genotypes, and Selection Pressure | Infectious Bronchitis Virus Regulates Cellular Stress Granule Signaling | The Molecular Biology of Coronaviruses five topics; three dimensions: ibv virus infectious; virus ibv rna; cells protein ibv; virus influenza coronavirus; coronavirus s1 ibv file(s): https://www.ncbi.nlm.nih.gov/pubmed/31561498/, https://api.elsevier.com/content/article/pii/S0065352708602869, https://www.ncbi.nlm.nih.gov/pubmed/32422883/, https://www.ncbi.nlm.nih.gov/pubmed/32635598/, https://doi.org/10.1371/journal.ppat.1007009 titles(s): Genetic Analysis of Avian Coronavirus Infectious Bronchitis Virus in Yellow Chickens in Southern China over the Past Decade: Revealing the Changes of Genetic Diversity, Dominant Genotypes, and Selection Pressure | The Molecular Biology of Coronaviruses | Infectious Bronchitis Virus Regulates Cellular Stress Granule Signaling | Canonical and Noncanonical Autophagy as Potential Targets for COVID-19 | Cryo-EM structure of infectious bronchitis coronavirus spike protein reveals structural and functional evolution of coronavirus spike proteins Type: cord title: keyword-ibv-cord date: 2021-05-25 time: 00:34 username: emorgan patron: Eric Morgan email: emorgan@nd.edu input: keywords:ibv ==== make-pages.sh htm files ==== make-pages.sh complex files ==== make-pages.sh named enities ==== making bibliographics id: cord-257999-apg4uhhq author: Ababneh, Mustafa title: Presence of Infectious Bronchitis Virus Strain CK/CH/LDL/97I in the Middle East date: 2012-04-11 words: 2375.0 sentences: 117.0 pages: flesch: 60.0 cache: ./cache/cord-257999-apg4uhhq.txt txt: ./txt/cord-257999-apg4uhhq.txt summary: The sequenced fragment of the S1 gene of the CK/CH/LDL/97I strain had less than 80% nucleotide identity to the IBV vaccine strains commonly used in the Middle East (M41 and H120). In this study, the CK/CH/LDL/97I-like strains were isolated from three different Middle Eastern countries (Jordan, Saudi Arabia, and Iraq) in 2011. Pathogenicity of a QX strain of infectious bronchitis virus in specific pathogen free and commercial broiler chickens, and evaluation of protection induced by a vaccination programme based on the Ma5 and 4/91 serotypes Phylogenetic analysis of infectious bronchitis coronaviruses newly isolated in China, and pathogenicity and evaluation of protection induced by Massachusetts serotype H120 vaccine against QX-like strains Evaluation of the protection conferred by commercial vaccines and attenuated heterologous isolates in China against the CK/CH/LDL/97I strain of infectious bronchitis coronavirus Characterization of three infectious bronchitis virus isolates from China associated with proventriculus in vaccinated chickens abstract: Infectious bronchitis virus (IBV) is a very dynamic and evolving virus, causing major economic losses to the global poultry industry. In early 2011, respiratory disease outbreaks were investigated in Iraq, Jordan, and Saudi Arabia. Five IBV isolates (JOA2, JOA4, Saudi-1, Saudi-2, and Iraqi IBV) were detected by diagnostic-nested nucleocapsid RT-PCR. Strain identification was characterised by sequencing and phylogenetic analysis of the amplified hypervariable region of the spike 1 (S1) gene. These five IBV isolates were found to be of the IBV strain CK/CH/LDL/97I. Nucleotide identity between these five IBV isolates ranged from 96.9% to 99.7%, and between these isolates and the CK/CH/LDL/97I strain in the range of 96.6–99.1%. The sequenced fragment of the S1 gene of the CK/CH/LDL/97I strain had less than 80% nucleotide identity to the IBV vaccine strains commonly used in the Middle East (M41 and H120). The presence of these CK/CH/LDL/97I-like strains may account for vaccination failure against IBV, since all IBV isolates were from vaccinated chickens. In this paper, we documented for the first time the presence of IBV strain CK/CH/LDL/97I in the Middle East. This strain is known to have originated in China and Taiwan. url: https://doi.org/10.5402/2012/201721 doi: 10.5402/2012/201721 id: cord-303588-bwllypvq author: Ababneh, Mustafa title: High-resolution melting curve analysis for infectious bronchitis virus strain differentiation date: 2020-03-03 words: 3137.0 sentences: 159.0 pages: flesch: 58.0 cache: ./cache/cord-303588-bwllypvq.txt txt: ./txt/cord-303588-bwllypvq.txt summary: MATERIALS AND METHODS: In this study, qRT-PCR was conducted on a partial fragment S1 gene followed by a high resolution melting curve analysis (qRT-PCR/HRM) on 23 IBV-positive samples in Jordan. Although the third cluster contained the highest number of samples, it displayed no similarity to any of the reference vaccine strains, and, after comparing them with the sequencing results, we found that the samples in the third cluster were similar to the variant II-like (IS-1494-06) IBV field strain. CONCLUSION: Our developed qRT-PCR/HRM curve analysis was able to detect and rapidly identify novel and vaccine-related IBV strains as confirmed by S1 gene nucleotide sequences, making it a rapid and cost-effective tool. High-resolution melting (HRM) curve analysis is a newly established PCR-based technique that has been used to differentiate related strains of the same animal or avian virus [16] [17] [18] [19] . Those 22 samples, along with the five IBV vaccine reference strains, were subjected to qRT-PCR targeting the S1 gene followed with HRM curve analysis. abstract: BACKGROUND AND AIM: Belonging to the Coronaviridae family, avian infectious bronchitis virus (IBV) causes respiratory, reproductive, and renal diseases in poultry. Preventative measures lie mainly in vaccination, while the gold standard for IBV classification and differentiation is based on the sequence analysis of the spike 1 (S1) gene. In this study, we tested a new assay for IBV strain classification that is less expensive and requires reduced time and effort to perform. We carried out a quantitative real-time polymerase chain reaction followed by high-resolution melting (qRT-PCR/HRM) curve analysis. MATERIALS AND METHODS: In this study, qRT-PCR was conducted on a partial fragment S1 gene followed by a high resolution melting curve analysis (qRT-PCR/HRM) on 23 IBV-positive samples in Jordan. For this assay, we utilized the most common IBV vaccine strains (Mass and 4/91) as a reference in the HRM assay. To evaluate the discrimination power of the qRT-PCR/HRM, we did the sequencing of the partial S1 gene. RESULTS: It was shown that HRM was able to classify IBV samples into four clusters based on the degree of similarity between their melting points: The first cluster exhibited the highest similarity to the 4/91 strain, while the second was similar to the Mass-related IBV strain. Although the third cluster contained the highest number of samples, it displayed no similarity to any of the reference vaccine strains, and, after comparing them with the sequencing results, we found that the samples in the third cluster were similar to the variant II-like (IS-1494-06) IBV field strain. Finally, the fourth cluster comprised one unique sample that was found to belong to the Q1 IBV strain. CONCLUSION: Our developed qRT-PCR/HRM curve analysis was able to detect and rapidly identify novel and vaccine-related IBV strains as confirmed by S1 gene nucleotide sequences, making it a rapid and cost-effective tool. url: https://doi.org/10.14202/vetworld.2020.400-406 doi: 10.14202/vetworld.2020.400-406 id: cord-276550-1in7m56w author: Abdel-Moneim, Ahmed S title: S1 gene sequence analysis of a nephropathogenic strain of avian infectious bronchitis virus in Egypt date: 2006-09-20 words: 3957.0 sentences: 218.0 pages: flesch: 48.0 cache: ./cache/cord-276550-1in7m56w.txt txt: ./txt/cord-276550-1in7m56w.txt summary: title: S1 gene sequence analysis of a nephropathogenic strain of avian infectious bronchitis virus in Egypt RESULTS: Infectious bronchitis virus (IBV) strain closely related to Massachusetts (Mass) serotype was isolated from broiler chickens suffering from severe renal and respiratory distresses. Protection based criteria were: virus re-isolation attempts from trachea, tracheal and renal histopathology as well as IBV antigens detection by immunofluorescent antibody technique in kidney sections. In the present study, Egypt/F/03 was isolated from 25day-old broiler chickens in Fayoum Governorate, identified by Dot-ELISA, RT-PCR and sequenced to determine its serotype. In this study, an Egyptian IBV strain; Egypt\F/03 was isolated from a tissue pool of kidney and trachea from unvaccinated broiler flock with a history of respiratory and renal disease. Challenge experiments to evaluate cross-protection induced at the trachea and kidney level by vaccine strains and Belgian nephropathogenic isolates of avian infectious bronchitis virus abstract: BACKGROUND: Infectious bronchitis is highly contagious and constitutes one of the most common and difficult poultry diseases to control. IBV is endemic in probably all countries that raise chickens. It exists as dozens of serotypes/genotypes. Only a few amino acid differences in the S1 protein of vaccine and challenge strains of IBV may result in poor protection. Tropism of IBV includes the respiratory tract tissues, proventriculus and caecal tonsils of the alimentary tract, the oviduct and the kidney. RESULTS: Infectious bronchitis virus (IBV) strain closely related to Massachusetts (Mass) serotype was isolated from broiler chickens suffering from severe renal and respiratory distresses. The isolate was serologically identified by Dot-ELISA and further characterized by RT-PCR then genotyped using S1 gene sequence analysis. Alignment of the S1 sequence of the isolate with 16 IBV strains revealed high homology to isolates related to Mass serotype. Inoculation with the strain reproduced the disease in experimental 1-day-old chickens and resulted in 20% mortality, severe renal and moderate respiratory distresses. Marked histopathological changes in both kidney and trachea were observed in experimentally infected chickens. A protection study using the H120 live attenuated vaccine showed low protection rate in spite of high S1 sequence homology (97%). Protection based criteria were: virus re-isolation attempts from trachea, tracheal and renal histopathology as well as IBV antigens detection by immunofluorescent antibody technique in kidney sections. CONCLUSION: Periodical evaluation of cross-protective capabilities of IBV vaccine(s) versus recently recovered field isolates should be performed to ensure optimum control of IBV. url: https://www.ncbi.nlm.nih.gov/pubmed/16987422/ doi: 10.1186/1743-422x-3-78 id: cord-337128-yyz7z0xj author: Abdel-Moneim, Ahmed S title: Immunohistochemistry for detection of avian infectious bronchitis virus strain M41 in the proventriculus and nervous system of experimentally infected chicken embryos date: 2009-02-05 words: 3308.0 sentences: 172.0 pages: flesch: 44.0 cache: ./cache/cord-337128-yyz7z0xj.txt txt: ./txt/cord-337128-yyz7z0xj.txt summary: title: Immunohistochemistry for detection of avian infectious bronchitis virus strain M41 in the proventriculus and nervous system of experimentally infected chicken embryos Aim of this study was to investigate by immunohistochemistry (IHC) the tissue tropism of avian infectious bronchitis virus (IBV) strain M41 in experimentally infected chicken embryos. Using IHC, antigens of IBV were detected in nasal epithelium, trachea, lung, spleen, myocardial vasculature, liver, gastrointestinal tract, kidney, skin, sclera of the eye, spinal cord, as well as in brain neurons of the inoculated embryos. IBV antigens were detected in the nasal epithelium, trachea, lung, spleen, myocardium, liver, gizzard, proventriculus, kidney, skin, sclera of the eye, spinal cord, as well as in neurons of the central nervous system in infected embryos (Table 1, Figure 1 ). abstract: BACKGROUND: Infectious bronchitis virus primarily induces a disease of the respiratory system, different IBV strains may show variable tissue tropisms and also affect the oviduct and the kidneys. Proventriculitis was also associated with some new IBV strains. Aim of this study was to investigate by immunohistochemistry (IHC) the tissue tropism of avian infectious bronchitis virus (IBV) strain M41 in experimentally infected chicken embryos. RESULTS: To this end chicken embryos were inoculated in the allantoic sac with 10(3 )EID(50 )of IBV M41 at 10 days of age. At 48, 72, and 120 h postinoculation (PI), embryos and chorioallantoic membranes (CAM) were sampled, fixed, and paraffin-wax embedded. Allantoic fluid was also collected and titrated in chicken embryo kidney cells (CEK). The sensitivity of IHC in detecting IBV antigens in the CAM of inoculated eggs matched the virus reisolation and detection in CEK. Using IHC, antigens of IBV were detected in nasal epithelium, trachea, lung, spleen, myocardial vasculature, liver, gastrointestinal tract, kidney, skin, sclera of the eye, spinal cord, as well as in brain neurons of the inoculated embryos. These results were consistent with virus isolation and denote the wide tissue tropism of IBV M41 in the chicken embryo. Most importantly, we found infection of vasculature and smooth muscle of the proventriculus which has not seen before with IBV strain M41. CONCLUSION: IHC can be an additional useful tool for diagnosis of IBV infection in chickens and allows further studies to foster a deeper understanding of the pathogenesis of infections with IBV strains of different virulence. Moreover, these results underline that embryonic tissues in addition to CAM could be also used as possible source to generate IBV antigens for diagnostic purposes. url: https://doi.org/10.1186/1743-422x-6-15 doi: 10.1186/1743-422x-6-15 id: cord-255141-55ho9av4 author: Abolnik, Celia title: Genomic and single nucleotide polymorphism analysis of infectious bronchitis coronavirus date: 2015-04-03 words: 6284.0 sentences: 322.0 pages: flesch: 53.0 cache: ./cache/cord-255141-55ho9av4.txt txt: ./txt/cord-255141-55ho9av4.txt summary: A QX-like strain was analysed by high-throughput Illumina sequencing and genetic variation across the entire viral genome was explored at the sub-consensus level by single nucleotide polymorphism (SNP) analysis. The E and 3b protein products play key roles in coronavirus virulence, and RNA folding demonstrated that the mutations in the 5′UTR did not alter the predicted secondary structure. Coronavirus accessory proteins are generally dispensable for virus replication, but they play vital roles in virulence and pathogenesis by affecting host innate immune responses, encoding pro-or anti-apoptotic activities, or by effecting other signalling pathways that influence disease outcomes (Susan & Julian, 2011) . Mapping of the receptor-binding domain and amino acids critical for attachment in the spike protein of avian coronavirus infectious bronchitis virus Analysis of a QX-like avian infectious bronchitis virus genome identified recombination in the region containing the ORF 5a, ORF 5b, and nucleocapsid protein gene sequences abstract: Infectious bronchitis virus (IBV) is a Gammacoronavirus that causes a highly contagious respiratory disease in chickens. A QX-like strain was analysed by high-throughput Illumina sequencing and genetic variation across the entire viral genome was explored at the sub-consensus level by single nucleotide polymorphism (SNP) analysis. Thirteen open reading frames (ORFs) in the order 5′-UTR-1a-1ab-S-3a-3b-E-M-4b-4c-5a-5b-N-6b-3′UTR were predicted. The relative frequencies of missense: silent SNPs were calculated to obtain a comparative measure of variability in specific genes. The most variable ORFs in descending order were E, 3b, 5′UTR, N, 1a, S, 1ab, M, 4c, 5a, 6b. The E and 3b protein products play key roles in coronavirus virulence, and RNA folding demonstrated that the mutations in the 5′UTR did not alter the predicted secondary structure. The frequency of SNPs in the Spike (S) protein ORF of 0.67% was below the genomic average of 0.76%. Only three SNPS were identified in the S1 subunit, none of which were located in hypervariable region (HVR) 1 or HVR2. The S2 subunit was considerably more variable containing 87% of the polymorphisms detected across the entire S protein. The S2 subunit also contained a previously unreported multi-A insertion site and a stretch of four consecutive mutated amino acids, which mapped to the stalk region of the spike protein. Template-based protein structure modelling produced the first theoretical model of the IBV spike monomer. Given the lack of diversity observed at the sub-consensus level, the tenet that the HVRs in the S1 subunit are very tolerant of amino acid changes produced by genetic drift is questioned. url: https://www.sciencedirect.com/science/article/pii/S1567134815001185 doi: 10.1016/j.meegid.2015.03.033 id: cord-319168-i23pqiwx author: Abro, Shahid Hussain title: Emergence of novel strains of avian infectious bronchitis virus in Sweden date: 2012-03-23 words: 4934.0 sentences: 288.0 pages: flesch: 58.0 cache: ./cache/cord-319168-i23pqiwx.txt txt: ./txt/cord-319168-i23pqiwx.txt summary: Nucleotide and amino acid sequence comparisons have shown that the recent isolates bear 98.97% genetic similarity with strains of the QX-like genotype. Twenty Swedish IBV isolates from different outbreaks were selected for comprehensive study of the complete spike gene of the virus. Analysis of the nucleotide sequences of spike glycoprotein of Swedish isolates from 1995 to 2010 showed that they comprise distinct sets of IBV variants; differing among themselves along that timeline (Table 3 ). The phylogenetic studies, based on the partial S1 gene regions, showed that Swedish IBV isolates from 1995 to 1999 were related to the Massachusetts genotype. Taken together, the complete spike sequence data revealed different isolates of IBV of the Massachusetts type and European D388/QX-like strains circulating over a time-line in Sweden. Complete genome sequence analysis of a predominant infectious bronchitis virus (IBV) strain in China abstract: Infectious bronchitis virus (IBV) causes avian infectious bronchitis, an important disease that produces severe economic losses in the poultry industry worldwide. Recent IBV infections in Sweden have been associated with poor growth in broilers, drop in egg production and thin egg shells in layers. The complete spike gene of selected isolates from IBV cases was amplified and sequenced using conventional RT-PCR. Nucleotide and amino acid sequence comparisons have shown that the recent isolates bear 98.97% genetic similarity with strains of the QX-like genotype. The phylogenetic analysis revealed that strains predominant in the nineties, which were of the Massachusetts type, have been replaced by D388/QX-like strains, however the evolutionary link could not be established. The homology between the two genotypes was 79 and 81%. Remarkably, a strong positive selection pressure was determined, mostly involving the S1 subunit of the S gene. This strong selective pressure resulted in recombination events, insertions and deletions in the S gene. Two new isolates generated from recombination were found with nucleotide sequence diverging 1.7–2.4% from the D388/QX-like branch, indicating the emergence of a new lineage. The study demonstrates a constant evolution of IBV that might be in relation to increased poultry farming, trade and vaccine pressure. The findings underscore the importance of continuous monitoring to control spread of infections, as well as to timely adjust diagnostic methods, molecular epidemiological studies, development and use of vaccines that are adapted to the changing disease scenario. url: https://doi.org/10.1016/j.vetmic.2011.09.022 doi: 10.1016/j.vetmic.2011.09.022 id: cord-282314-9cua2jzg author: Albanese, Grace A. title: Biological and molecular characterization of ArkGA: A novel Arkansas serotype vaccine that is highly attenuated, efficacious, and protective against homologous challenge date: 2018-10-01 words: 6368.0 sentences: 324.0 pages: flesch: 50.0 cache: ./cache/cord-282314-9cua2jzg.txt txt: ./txt/cord-282314-9cua2jzg.txt summary: Abbreviations: Ark99, Arkansas 99; ArkDPI, Arkansas Delmarva Poultry Industry; ArkGA, Arkansas Georgia; CAS, chorioallantoic sac; C T , cycle threshold; EID 50 , 50% embryo infective dose; IBV, infectious bronchitis virus; MHV, murine hepatitis virus; nsp2, nonstructural protein 2; nsp3, nonstructural protein 3; P, passage; PBS, phosphate-buffered saline; qRT-PCR, quantitative real-time reverse-transcriptase polymerase chain reaction; RT-PCR, reverse-transcriptase polymerase chain reaction; SARS-CoV, severe acute respiratory syndrome coronavirus; SD, standard deviation; SEM, standard error of mean; SNP, single nucleotide polymorphism; SPF, specific-pathogen free; US, United States; USDA, United States Department of Agriculture. In P60, SNPs were seen in S1 as well as S2 of the Table 2 S1 amino acid sequence comparison of ArkGA vaccine virus and viral RNA isolated from 5 choanal cleft palate swabs on days 7, 10, and 14 post-vaccination. abstract: Almost all commercial poultry are vaccinated against avian coronavirus infectious bronchitis virus (IBV) using live attenuated vaccines mass administered by spray at day of hatch. Although many different types of IBV vaccines are used successfully, the ArkDPI serotype vaccine, when applied by spray, does not infect and replicate sufficiently to provide protection against homologous challenge. In this study, we examined a different Ark vaccine strain (Ark99), which is no longer used commercially due to its reactivity in one day old chicks, to determine if it could be further attenuated by passage in embryonated eggs but still provide adequate protection. Further attenuation of the Ark99 vaccine was achieved by passage in embryonated eggs but ArkGA P1, P20, and P40 (designated ArkGA after P1) were still too reactive to be suitable vaccine candidates. However, ArkGA P60 when given by spray had little or no vaccine reaction in one day old broiler chicks, and it induced protection from clinical signs and ciliostasis following homologous challenge. In addition, vaccinated and challenged birds had significantly less challenge virus, an important measure of protection, compared to non-vaccinated and challenged controls. The full-length genomes of viruses from egg passages 1, 20, 40, and 60 were sequenced using the Illumina platform and the data showed single nucleotide polymorphisms (SNPs) had accumulated in regions of the genome associated with viral replication, pathogenicity, and cell tropism. ArkGA P60 accumulated the most SNPs in key genes associated with pathogenicity (polyprotein gene 1ab) and cell tropism (spike gene), compared to previous passages, which likely resulted in its more attenuated phenotype. These results indicate that the ArkGA P60 vaccine is safe for spray vaccination of broiler chicks and induces suitable protection against challenge with pathogenic Ark-type virus. url: https://www.sciencedirect.com/science/article/pii/S0264410X18312283 doi: 10.1016/j.vaccine.2018.08.078 id: cord-259959-qzd3hf8y author: Alhatami, Abdullah O. title: Sequencing and phylogenetic analysis of infectious bronchitis virus variant strain from an outbreak in egg-layer flocks in Baghdad, Iraq date: 2020-07-16 words: 2358.0 sentences: 127.0 pages: flesch: 48.0 cache: ./cache/cord-259959-qzd3hf8y.txt txt: ./txt/cord-259959-qzd3hf8y.txt summary: title: Sequencing and phylogenetic analysis of infectious bronchitis virus variant strain from an outbreak in egg-layer flocks in Baghdad, Iraq MATERIALS AND METHODS: Isolate detection, sequencing, and phylogenetic analysis were performed using a rapid IB virus antigen kit (32 tracheal swabs), flinders technology associates (FTA) card (32 tracheal swabs), and partial gene sequencing (16 positive FTA samples). Therefore, the current report describes the role of IBV during an outbreak of the respiratory disease in an egg-layer farm in the Baghdad region of Iraq, investigates the genetic characteristics of this field strain by analyzing the S1 gene and compares it with other isolates registered globally for developing significant vaccines to control this disease. FA and YIK visited the infected farm, collected the samples, run the rapid IBV antigen detection, confirmed the results using FTA card that was sent to Germany, deposited the genetic information into the NCBI database, analyzed the differences between the strains of the virus, and drafted the manuscript. abstract: BACKGROUND AND AIM: Infectious bronchitis (IB) has an influential economic impact on the poultry industry, causing huge losses each year due to the condemnation of infected chickens. Despite the use of many kinds of vaccines in Iraq, it is common to find IB problems in vaccinated chickens. Information about the strains that affect Iraqi chickens is very limited. Therefore, we aimed to detect the currently circulating strains of IB virus that cause frequent outbreaks in egg layers despite the use of vaccination against the virus. MATERIALS AND METHODS: Isolate detection, sequencing, and phylogenetic analysis were performed using a rapid IB virus antigen kit (32 tracheal swabs), flinders technology associates (FTA) card (32 tracheal swabs), and partial gene sequencing (16 positive FTA samples). RESULTS: The isolated strain was different from other strains, especially the strain isolated in the North of Iraq (Sulemania Strain) and shares 98% homology with an Israeli strain (Israel variant 2, IS 1494). CONCLUSION: Although more studies are needed to detect IB virus strains circulating in Iraq, this work lays the foundation for making a good strategy to control the disease and selecting vaccines that should be used in farms. url: https://www.ncbi.nlm.nih.gov/pubmed/32848311/ doi: 10.14202/vetworld.2020.1358-1362 id: cord-353027-bc0un6kb author: Ali, Ahmed title: Safety and efficacy of attenuated classic and variant 2 infectious bronchitis virus candidate vaccines date: 2018-08-06 words: 4144.0 sentences: 231.0 pages: flesch: 54.0 cache: ./cache/cord-353027-bc0un6kb.txt txt: ./txt/cord-353027-bc0un6kb.txt summary: Virulence of the attenuated viruses was then tested via the ocular route inoculation and the in vivo back passage in day-old SPF chickens. In conclusion, the attenuated strains IBM41, IB2, and IBvar2 are efficient vaccine candidates against currently circulating classic and variant IB viruses, respectively. The first 3 groups were vaccinated via the ocular route with 10 3.5 EID 50 /bird of att-IBM41 virus, att-IB2, and att-IBvar2 viruses, respectively. The 3 viruses (IBV-EG/11539F-2011, IBV-EG/M41-ME01/2011, and Eg/1212B/2012) were successfully adapted to embryonated chicken eggs and showed the typical embryonic changes including dwarfing, stunting, and curling of embryos by the 10th or 14th passages for the classic (IB2 and IBM41) and the variant virus (IBvar2) (data not shown). Recent studies also indicated that the IBV strains circulating in Egypt represent a distinct a Day-old SPF chicks received 10 4 EID 50 /bird of the attenuated viruses separately via the ocular route. abstract: Vaccination programs against infectious bronchitis virus (IBV) in Egypt depend on both classical and/or imported variant IBV strain vaccines. However, many IBV outbreaks associated with respiratory distress, nephropathy, and high mortalities were attributed to the circulation of both classical and new nephropathogenic IBV variant 2 strains. In the present study, we report the development of attenuated IBV candidate vaccines using the classic IBV strains (IBM41 and IB2) and a nephropathogenic strain (IBvar2). The wild-type (WT) viruses were attenuated through serial passages in embryonated specific pathogen free (SPF) chicken eggs. Virulence of the attenuated viruses was then tested via the ocular route inoculation and the in vivo back passage in day-old SPF chickens. Efficacy against homologous challenge was investigated also in day-old SPF chickens. Results showed that the viruses were successfully adapted to the embryo by the 100th (IBM41 and IB2) and 110th passages (IBvar2). The attenuated viruses were safe and showed no change of virulence in day-old SPF chickens up to the 10th back passages. The efficacy experiment showed that the attenuated vaccines showed 90 to 100% protection against the homologous challenge based on ciliostasis score and protection percent. The att-IBM41 and att-IB2 vaccines were able to reduce the shedding of the challenge at 3 days post-infection (DPI) and no virus shedding was detected in both vaccinated groups by 5 DPI. In the att-IBvar2 vaccinated birds, only 20% of vaccinated birds shed the challenge virus with low titers (10(2.10±0.3) EID(50)/mL) at 3 DPI. In conclusion, the attenuated strains IBM41, IB2, and IBvar2 are efficient vaccine candidates against currently circulating classic and variant IB viruses, respectively. Further studies to evaluate the field efficacy and combining these attenuated IBV strains to induce a wider protection against heterologous IBV challenge are suggested. url: https://doi.org/10.3382/ps/pey312 doi: 10.3382/ps/pey312 id: cord-303393-9zs3qqo4 author: Alsultan, Musaed Abdulaziz title: Infectious bronchitis virus from chickens in Al-Hasa, Saudi Arabia 2015-2016 date: 2019-03-19 words: 4139.0 sentences: 265.0 pages: flesch: 56.0 cache: ./cache/cord-303393-9zs3qqo4.txt txt: ./txt/cord-303393-9zs3qqo4.txt summary: AIM: This study aimed to isolate some of the currently circulating infectious bronchitis virus (IBV) strains from some broiler chicken farms in Al-Hasa and to do some molecular characteristics of these strains. MATERIALS AND METHODS: We collected 300 tissue specimens, including the trachea, bronchi, lungs, and kidneys from some four commercial chicken farms showing respiratory manifestations. We used three tissue suspensions (trachea, lungs, and kidneys) from three specimens representing three different IBV outbreaks in some chicken farms from Al-Hasa region. Some of these farms were reporting IBV outbreaks based on Figure-4: Phylogenetic analysis based on the partial S1 gene for the circulating infectious bronchitis virus (IBV) strains from some chicken farms in Al-Hasa region 2015-2016. Table-5: Pairwise distance analysis of partial S1 gene for the circulating IBV strains in some chicken farms in Al-Hasa region abstract: AIM: This study aimed to isolate some of the currently circulating infectious bronchitis virus (IBV) strains from some broiler chicken farms in Al-Hasa and to do some molecular characteristics of these strains. MATERIALS AND METHODS: We collected 300 tissue specimens, including the trachea, bronchi, lungs, and kidneys from some four commercial chicken farms showing respiratory manifestations. We tested these tissue specimens by the real-time polymerase chain reaction (RT-PCR) and gel-based PCR. We selected some PCR positive samples for isolation in the embryonated chicken eggs (ECE). We sequenced some PCR-positive samples and conducted phylogenetic analysis based on the obtained sequences. RESULTS: Our molecular surveillance revealed that 31.6% of the tested specimens were IBV positive by PCR. We selected some positive specimens showing low Ct values by the qRT-PCR for virus isolation by the ECE. The infected eggs showed hemorrhage, dwarfing, and death in some cases after three passages in the ECE. We sequenced some of the positive PCR specimens and used the obtained sequences to draw the phylogenetic tree based on the partial IBV-ORF-1a, N, and S1 gene sequences. The phylogenetic trees based on the IBV-N and S1 gene sequences showed that the circulating IBV strains in Al-Hasa during 2016 was showing a high degree of identity to some strains from Taiwan and Italy. Meanwhile, the grouping of these strains based on the IBV-S1 sequences revealed that the currently circulating IBV strains in Al-Hasa belonged to Gr.I.7 along with strains from Taiwan. CONCLUSION: Our results confirmed the continuous circulation of the IBV among the chicken population in Al-Hasa despite the intensive application of vaccines against this virus. url: https://www.ncbi.nlm.nih.gov/pubmed/31089313/ doi: 10.14202/vetworld.2019.424-433 id: cord-309469-2naxn580 author: An, Hongliu title: Identification and formation mechanism of a novel noncoding RNA produced by avian infectious bronchitis virus date: 2019-01-05 words: 3600.0 sentences: 234.0 pages: flesch: 54.0 cache: ./cache/cord-309469-2naxn580.txt txt: ./txt/cord-309469-2naxn580.txt summary: For example, polyadenylated nuclear (PAN) RNA encoded by Kaposi''s sarcoma-associated herpesvirus (Sun et al., 1996; Zhong and Ganem, 1997) , the~2-kb latency-associated transcript (LAT) expressed by Herpes simplex virus (Bloom, 2004 ), a con-served~5-kb intron expressed by Human cytomegalovirus (hCMV) (Kulesza and Shenk, 2004) , and a 7.2-kb RNA expressed by mouse CMV (Kulesza and Shenk, 2006) , U-rich RNAs (HSURs) produced by Herpesvirus saimiri (HVS), (Albrecht and Fleckenstein, 1992; Ensser and Fleckenstein, 2005) ; (3) Subgenomic ncRNAs from single-stranded RNA viruses by incomplete degradation of genomic RNA by the cellular 5-3′ exonuclease XRN1. The results confirmed previous report that IBV can synthesize sgRNA via template switch mediated by a noncanonical core sequence (Bentley et al., 2013) Notably, the mutant virus carrying four mutations (A27100U/A27111U/G27113C/G27114C) was also unable to produce ncRNA (Fig. 4) , suggesting these nucleotides are required for ncRNA production. abstract: Viral noncoding (nc) RNAs have been shown to play important roles in viral life cycle. Many viruses employ different mechanism to produce ncRNAs. Here, we report that coronavirus infectious bronchitis virus (IBV) produces a novel ncRNA in virus-infected cells. This ncRNA consists of 563 nucleotides excluding a poly(A) tail, is mainly derived from the 3′-untranslated region of IBV genome, and contains a 63-nt-long of terminal leader sequence derived from the 5′ end of the viral genome. Using mutagenesis and reverse genetics, we reveal that this ncRNA is a subgenomic RNA generated by discontinuous transcription mechanism. url: https://doi.org/10.1016/j.virol.2018.12.019 doi: 10.1016/j.virol.2018.12.019 id: cord-312489-ywep0c08 author: Andoh, Kiyohiko title: Decreased neutralizing antigenicity in IBV S1 protein expressed from mammalian cells date: 2015-10-02 words: 5039.0 sentences: 246.0 pages: flesch: 43.0 cache: ./cache/cord-312489-ywep0c08.txt txt: ./txt/cord-312489-ywep0c08.txt summary: We evaluated the antigenicity of recombinant infectious bronchitis virus (IBV) S1 protein expressed in mammalian cells. Native S1 ELISA detected similar titers in the sera of animals immunized with recombinant S1 protein compared to those in sera of chickens immunized with inactivated virus (Fig. 6b ) (Control experiments (data not shown) demonstrated that mock and unvaccinated control groups did not differ from each other in VN and ELISA tests of anti-S1 activity.) These results indicated that while recombinant S1 protein retained antigenicity (the ability to induce antibodies against S1 protein), the resulting antibodies was decreased its neutralizing activity, in contrast to those induced by inactivated virus. The S1 glycoprotein but not the N or M proteins of avian infectious bronchitis virus induces protection in vaccinated chickens Induction of protective immunity in chickens vaccinated with infectious bronchitis virus S1 glycoprotein expressed by a recombinant baculovirus abstract: We evaluated the antigenicity of recombinant infectious bronchitis virus (IBV) S1 protein expressed in mammalian cells. Recombinant S1 was expressed as a secreted protein fused with a trimerization motif peptide, then purified using Ni Sepharose. The purified protein was analyzed by Western blotting, mixed with oil adjuvant, and administered to 29-day-old specific-pathogen-free chickens. Six weeks after immunization, anti-IBV neutralizing titer and anti-S1 ELISA titer were determined; immunized chickens then were inoculated with IBV via the trachea and ciliary activity was observed. Results showed that the recombinant S1 protein was highly glycosylated, and the neutralizing antigenicity of recombinant S1 protein was lower than that of inactivated virus. However, anti-S1 ELISA indicated that the recombinant S1 protein induced antibodies against S1. These results suggest that the recombinant S1 may retain non-neutralizing epitopes but have unnatural glycosylation pattern and conformation, resulting in lacking neutralizing conformational epitopes. In conclusion, the neutralizing antigenicity of recombinant S1 protein expressed from mammalian cells was decreased, and was not sufficient to induce neutralizing antibodies. url: https://www.sciencedirect.com/science/article/pii/S0168170215002841 doi: 10.1016/j.virusres.2015.06.019 id: cord-284501-5i0w74q4 author: Armesto, Maria title: The Replicase Gene of Avian Coronavirus Infectious Bronchitis Virus Is a Determinant of Pathogenicity date: 2009-10-09 words: 7792.0 sentences: 322.0 pages: flesch: 54.0 cache: ./cache/cord-284501-5i0w74q4.txt txt: ./txt/cord-284501-5i0w74q4.txt summary: The IBV cDNA within pGPT-BeauR-Rep-M41-Struct-3UTR was introduced, by homologous recombination using the transient dominant selection (TDS) ( [25, 37] ), into the IBV Beaudette cDNA within the vaccinia virus genome in rVV-BeauR-Rep-DStruct containing Beau-R-derived sequence corresponding to the replicase gene followed by the first 376 nt of the S gene, part of the N gene and the 39-UTR (Fig. 1) . The samples were analysed for the presence of viable IBV by titration in TOCs or used for RNA extraction using the RNeasy method and analysed by RTThe M41-CK-derived cDNA, representing the M41 structural and accessory genes and the M41 39-UTR, within pGPT-BeauR-Rep-M41-Struct-3UTR was fused to the Beau-R replicase gene in the rVV by a homologous recombination event between the Beau-R replicase sequence common to both constructs. Analysis of the tracheal epithelial cells isolated from the infected chickens, for the presence of IBV by titration on TOCs, had indicated that either there was no Beau-R or rBeauR-Rep-M41-Struct-2 present or that the levels of both viruses were below detection. abstract: We have previously demonstrated that the replacement of the S gene from an avirulent strain (Beaudette) of infectious bronchitis virus (IBV) with an S gene from a virulent strain (M41) resulted in a recombinant virus (BeauR-M41(S)) with the in vitro cell tropism of the virulent virus but that was still avirulent. In order to investigate whether any of the other structural or accessory genes played a role in pathogenicity we have now replaced these from the Beaudette strain with those from M41. The recombinant IBV was in effect a chimaeric virus with the replicase gene derived from Beaudette and the rest of the genome from M41. This demonstrated that it is possible to exchange a large region of the IBV genome, approximately 8.4 kb, using our transient dominant selection method. Recovery of a viable recombinant IBV also demonstrated that it is possible to interchange a complete replicase gene as we had in effect replaced the M41 replicase gene with the Beaudette derived gene. Analysis of the chimaeric virus showed that it was avirulent indicating that none of the structural or accessory genes derived from a virulent isolate of IBV were able to restore virulence and that therefore, the loss of virulence associated with the Beaudette strain resides in the replicase gene. url: https://doi.org/10.1371/journal.pone.0007384 doi: 10.1371/journal.pone.0007384 id: cord-301810-vtgdqart author: Aston, Emily J. title: Effect of Pullet Vaccination on Development and Longevity of Immunity date: 2019-02-02 words: 7115.0 sentences: 321.0 pages: flesch: 45.0 cache: ./cache/cord-301810-vtgdqart.txt txt: ./txt/cord-301810-vtgdqart.txt summary: Because of the need to protect long-lived poultry against respiratory tract pathogens from an early age, vaccination programs for pullets typically involve serial administration of a variety of vaccines, including infectious bronchitis virus (IBV), Newcastle disease virus (NDV), and infectious laryngotracheitis virus (ILTV). At 5 days following challenge with IBV GA98, vaccinated/challenged birds had significantly lower RNA loads compared to positive controls at all collection times and in all tissue samples, with the exception of cecal tonsil at 24 WOA (Table 1 ). ILTV-specific IgG titers in serum collected 5 days post-challenge were significantly higher in vaccinated birds from both challenged and non-challenged groups, compared to the positive and negative controls ( Figure 6 ). ILTV-specific IgG titers in serum collected 5 days post-challenge were significantly higher in vaccinated birds from both challenged and non-challenged groups, compared to the positive and negative controls ( Figure 6 ). abstract: Avian respiratory disease causes significant economic losses in commercial poultry. Because of the need to protect long-lived poultry against respiratory tract pathogens from an early age, vaccination programs for pullets typically involve serial administration of a variety of vaccines, including infectious bronchitis virus (IBV), Newcastle disease virus (NDV), and infectious laryngotracheitis virus (ILTV). Often the interval between vaccinations is only a matter of weeks, yet it is unknown whether the development of immunity and protection against challenge when vaccines are given in short succession occurs in these birds, something known as viral interference. Our objective was to determine whether serially administered, live attenuated vaccines against IBV, NDV, and ILTV influence the development and longevity of immunity and protection against challenge in long-lived birds. Based on a typical pullet vaccination program, specific-pathogen-free white leghorns were administered multiple live attenuated vaccines against IBV, NDV, and ILTV until 16 weeks of age (WOA), after which certain groups were challenged with IBV, NDV, or ILTV at 20, 24, 28, 32, and 36 WOA. Five days post-challenge, viral load, clinical signs, ciliostasis, tracheal histopathology, and antibody titers in serum and tears were evaluated. We demonstrate that pullets serially administered live attenuated vaccines against IBV, NDV, and ILTV were protected against homologous challenge with IBV, NDV, or ILTV for at least 36 weeks, and conclude that the interval between vaccinations used in this study (at least 2 weeks) did not interfere with protection. This information is important because it shows that a typical pullet vaccination program consisting of serially administered live attenuated vaccines against multiple respiratory pathogens can result in the development of protective immunity against each disease agent. url: https://doi.org/10.3390/v11020135 doi: 10.3390/v11020135 id: cord-001768-8vljd5cv author: Awad, Faez title: Protection conferred by live infectious bronchitis vaccine viruses against variant Middle East IS/885/00-like and IS/1494/06-like isolates in commercial broiler chicks date: 2015-09-09 words: 3928.0 sentences: 212.0 pages: flesch: 55.0 cache: ./cache/cord-001768-8vljd5cv.txt txt: ./txt/cord-001768-8vljd5cv.txt summary: title: Protection conferred by live infectious bronchitis vaccine viruses against variant Middle East IS/885/00-like and IS/1494/06-like isolates in commercial broiler chicks At 30 days of age (on the day of challenge), vaccinated groups showed significantly higher levels of IBV ELISA antibody titre than the unvaccinated control group. The evaluation of protection conferred by live vaccines against the virulent IS/885 and IS/1494 isolates was assessed based on ciliary activity in the tracheal explants prepared from vaccinated-challenged chicks (Darbyshire 1980 , Andrade and others 1982 , Marquardt and others 1982 , Snyder and others 1983 , Cook and others 1999 and gross lesions in the trachea and kidneys following the challenge with the respective viruses. Challenge experiments to evaluate cross-protection induced at the trachea and kidney level by vaccine strains and Belgian nephropathogenic isolates of avian infectious bronchitis virus abstract: The ability of the infectious bronchitis H120 (a Massachusetts strain) and CR88 (a 793B strain) live attenuated vaccine viruses to protect from two Middle East infectious bronchitis virus isolates, IS/885/00-like (IS/885) and IS/1494/06-like (IS/1494) in broiler chicks was investigated. Day-old chicks were separated into three groups, (I) vaccinated with H120 at day-old followed by CR88 at 14 days-old, (II) vaccinated with H120 and CR88 simultaneously at day-old and again with CR88 at 14 days-old, (III) control unvaccinated. At 30 days-old, each of the groups was challenged with virulent IS/885 or IS/1494. Protection was evaluated based on the clinical signs, tracheal and kidney gross lesions and tracheal ciliostasis. Results showed that administering combined live H120 and CR88 vaccines simultaneously at day-old followed by CR88 vaccine at 14 days-old gave more than 80 per cent tracheal ciliary protection from both of the Middle East isolates. In addition, this programme conferred 100 per cent protection from clinical signs and tracheal or kidney lesions. The other vaccination programme, H120 at day-old followed by CR88 at 14 days-old, the tracheal ciliary protection conferred were 60 per cent and 80 per cent from IS/885/00-like and IS/1494/06-like, respectively. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4567785/ doi: 10.1136/vetreco-2014-000111 id: cord-296524-68gwusfe author: BARR, DA title: Isolation of infectious bronchitis virus from a flock of racing pigeons date: 2008-03-10 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/2844141/ doi: 10.1111/j.1751-0813.1988.tb14468.x id: cord-269024-re0hyolh author: Bande, Faruku title: Prediction and In Silico Identification of Novel B-Cells and T-Cells Epitopes in the S1-Spike Glycoprotein of M41 and CR88 (793/B) Infectious Bronchitis Virus Serotypes for Application in Peptide Vaccines date: 2016-09-07 words: 2566.0 sentences: 124.0 pages: flesch: 46.0 cache: ./cache/cord-269024-re0hyolh.txt txt: ./txt/cord-269024-re0hyolh.txt summary: title: Prediction and In Silico Identification of Novel B-Cells and T-Cells Epitopes in the S1-Spike Glycoprotein of M41 and CR88 (793/B) Infectious Bronchitis Virus Serotypes for Application in Peptide Vaccines Combination of antigenic B-cells and T-cells peptides that are conserved across many strains as approach to evoke humoral and CTL immune response will potentially lead to a broad-based vaccine that could reduce the challenges in using live attenuated vaccine technology in the control of IBV infection in poultry. This study predicted novel antigenic B-cells and T-cell epitopes within the S1 glycoprotein of M41 and CR88 IBV strains. The S1 glycoprotein but not the N or M proteins of avian infectious bronchitis virus induces protection in vaccinated chickens Two novel neutralizing antigenic epitopes of the s1 subunit protein of a QX-like avian infectious bronchitis virus strain Sczy3 as revealed using a phage display peptide library abstract: Bioinformatic analysis was used to predict antigenic B-cell and T-cell epitopes within the S1 glycoprotein of M41 and CR88 IBV strains. A conserved linear B-cell epitope peptide, YTSNETTDVTS(175–185), was identified in M41 IBV strains while three such epitopes types namely, VSNASPNSGGVD(279–290), HPKCNFRPENI(328–338), and NETNNAGSVSDCTAGT(54–69), were predicted in CR88 IBV strains. Analysis of MHCI binding peptides in M41 IBV strains revealed the presence of 15 antigenic peptides out of which 12 were highly conserved in 96–100% of the total M41 strains analysed. Interestingly three of these peptides, GGPITYKVM(208), WFNSLSVSI(356), and YLADAGLAI(472), relatively had high antigenicity index (>1.0). On the other hand, 11 MHCI binding epitope peptides were identified in CR88 IBV strains. Of these, five peptides were found to be highly conserved with a range between 90% and 97%. However, WFNSLSVSL(358), SYNISAASV(88), and YNISAASVA(89) peptides comparably showed high antigenicity scores (>1.0). Combination of antigenic B-cells and T-cells peptides that are conserved across many strains as approach to evoke humoral and CTL immune response will potentially lead to a broad-based vaccine that could reduce the challenges in using live attenuated vaccine technology in the control of IBV infection in poultry. url: https://doi.org/10.1155/2016/5484972 doi: 10.1155/2016/5484972 id: cord-298920-1lc2xf7u author: Bello-Perez, Melissa title: Canonical and Noncanonical Autophagy as Potential Targets for COVID-19 date: 2020-07-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The SARS-CoV-2 pandemic necessitates a review of the molecular mechanisms underlying cellular infection by coronaviruses, in order to identify potential therapeutic targets against the associated new disease (COVID-19). Previous studies on its counterparts prove a complex and concomitant interaction between coronaviruses and autophagy. The precise manipulation of this pathway allows these viruses to exploit the autophagy molecular machinery while avoiding its protective apoptotic drift and cellular innate immune responses. In turn, the maneuverability margins of such hijacking appear to be so narrow that the modulation of the autophagy, regardless of whether using inducers or inhibitors (many of which are FDA-approved for the treatment of other diseases), is usually detrimental to viral replication, including SARS-CoV-2. Recent discoveries indicate that these interactions stretch into the still poorly explored noncanonical autophagy pathway, which might play a substantial role in coronavirus replication. Still, some potential therapeutic targets within this pathway, such as RAB9 and its interacting proteins, look promising considering current knowledge. Thus, the combinatory treatment of COVID-19 with drugs affecting both canonical and noncanonical autophagy pathways may be a turning point in the fight against this and other viral infections, which may also imply beneficial prospects of long-term protection. url: https://www.ncbi.nlm.nih.gov/pubmed/32635598/ doi: 10.3390/cells9071619 id: cord-265681-ab8j4o1u author: Boroomand, Zahra title: Pathogenesis and Tissue Distribution of Avian Infectious Bronchitis Virus Isolate IRFIBV32 (793/B Serotype) in Experimentally Infected Broiler Chickens date: 2012-04-01 words: 3553.0 sentences: 219.0 pages: flesch: 53.0 cache: ./cache/cord-265681-ab8j4o1u.txt txt: ./txt/cord-265681-ab8j4o1u.txt summary: title: Pathogenesis and Tissue Distribution of Avian Infectious Bronchitis Virus Isolate IRFIBV32 (793/B Serotype) in Experimentally Infected Broiler Chickens The aim of this study was to investigate the distribution of avian infectious bronchitis virus isolate IRFIBV32 (793/B serotype) in experimentally infected chicken. Data indicated that the number of infected chickens and viral RNA detection from tissues was reduced with increasing antibody titer on day 20 PI. Gross lesions were recorded, and their trachea, lungs, kidneys, caecal tonsil, testes, and oviduct were aseptically collected for virus detection using RT-PCR assay ( Table 1) . In this study, the pathogenesis of the infectious bronchitis virus isolate IRFIBV32 which was recently isolated in Iran [12] , tissue tropism, and dissemination of the virus throughout the body were evaluated following intranasal (IN) inoculation of commercial broiler chickens by RT-PCR. Immunohistochemistry for detection of avian infectious bronchitis virus strain M41 in the proventriculus and nervous system of experimentally infected chicken embryos abstract: Infectious bronchitis (IB) is one of the most important viral diseases of poultry. The aim of this study was to investigate the distribution of avian infectious bronchitis virus isolate IRFIBV32 (793/B serotype) in experimentally infected chicken. Ninety-one-day-old commercial broilers were divided randomly into two groups (seventy in the experimental and twenty in the control group). Chicks in the experimental group were inoculated intranasally with 10(5) ELD50/0.1 mL of the virus at three weeks of age. The samples from various tissues were collected at1, 2, 3, 5, 7, 11, 13, 15, and 20 days postinoculation. Chickens exhibited mild respiratory signs and depression. Viral RNA was detected in the kidney, lung and tracheas on days 1 to 13 PI, in the oviduct between, days 3 and 13, in testes between days 1 and 11 PI, and in the caecal tonsil consistently up to day 20 PI. The most remarkable clinical signs and virus detection appeared on day 1 PI. Data indicated that the number of infected chickens and viral RNA detection from tissues was reduced with increasing antibody titer on day 20 PI. The results demonstrated that the IRFIBV32 virus has wide tissue distribution for respiratory, urogenital, and digestive systems. url: https://doi.org/10.1100/2012/402537 doi: 10.1100/2012/402537 id: cord-339235-8xslz4bs author: Boroomand, Zahra title: Molecular detection and phylogenetic properties of isolated infectious bronchitis viruses from broilers in Ahvaz, southwest Iran, based on partial sequences of spike gene date: 2018-09-15 words: 1978.0 sentences: 127.0 pages: flesch: 53.0 cache: ./cache/cord-339235-8xslz4bs.txt txt: ./txt/cord-339235-8xslz4bs.txt summary: title: Molecular detection and phylogenetic properties of isolated infectious bronchitis viruses from broilers in Ahvaz, southwest Iran, based on partial sequences of spike gene A phylogenetic tree (Fig. 2) , based on the hypervariable region of S1 gene sequences of four IBV isolates from the present study and other strains of IBV retrieved from GenBank, was generated. Infectious bronchitis virus is one of the main pathogens of commercial and backyard chickens with several serotypes and genotypes circulating in the world. Genotyping of Avian infectious bronchitis viruses in Iran (2015-2017) reveals domination of IS-1494 like virus Molecular characterization of infectious bronchitis viruses isolated from broiler chicken farms in Iran The pathogenesis of a new variant genotype and QX-like infectious bronchitis virus isolated from chickens in Thailand Isolation and molecular characterization of Sul/01/09 avian infectious bronchitis virus, indicates the emergence of a new genotype in the Middle East abstract: Infectious bronchitis (IB) is a highly contagious disease involving mostly upper respiratory tract in chickens, leading to significant economic losses in the poultry industry worldwide. One of the major concerns regarding to IB is the emergence of new types of infectious bronchitis viruses (IBVs). The purpose of this study was to identify the IBVs isolated from Iranian broiler chickens with respiratory symptoms. Twenty-five broiler flocks around Ahwaz (southwest of Iran) were examined for IBV. The specimens including trachea, lung, liver, kidney, and ceacal tonsil, were collected from diseased birds and inoculated into chicken embryonated eggs. Harvested allantoic fluids were subjected to reverse transcription polymerase chain reaction (RT-PCR) using primers in order to amplify spike 1 (S1) gene of IBV. The RT-PCR products of four IBV isolates were sequenced. The results showed that from 25 examined flocks with respiratory disease, 12 flocks (48.00%) were positive for IBV. In phylogenetic analysis, our isolates were closely related to the QX-like viruses such as PCRLab/06/2012 (Iran), QX, HC9, HC10, CK/CH/GX/NN11-1, CK/CH/JS/YC11-1, CK/CH/JS/2010/13, CK/CH/JS/2011/2 (China), QX/SGK-21, QX/SGK-11 (Iraq) with nucleotide homology up to 99.00%. This study indicates the role of IBVs in the respiratory disorders of broiler flocks located in southwest Iran, and also the existence of a variant of IBV, which is distinguishable from the other Iranian variants. url: https://doi.org/10.30466/vrf.2018.32089 doi: 10.30466/vrf.2018.32089 id: cord-265508-t1nfyzf5 author: Boursnell, M.E.G. title: Sequencing of coronavirus IBV genomic RNA: a 195-base open reading frame encoded by mRNA B date: 1984-08-31 words: 2130.0 sentences: 125.0 pages: flesch: 61.0 cache: ./cache/cord-265508-t1nfyzf5.txt txt: ./txt/cord-265508-t1nfyzf5.txt summary: authors: Boursnell, M.E.G.; Brown, T.D.K. title: Sequencing of coronavirus IBV genomic RNA: a 195-base open reading frame encoded by mRNA B Abstract DNA sequencing of genomic cDNA clones of avian infectious bronchitis virus (IBV) has been carried out. The organisation of the messenger RNAs and in vitro translation studies have led to the hypothesis that the 5''-most sequences of each mRNA, which are not present in the next smallest mRNA, contain the complete coding sequences for the major protein product produced by that messenger species (Stern and Kennedy, 1980b; Lai et al., 1981) . In this paper we report the nucleotide sequence of a cloned cDNA copy of IBV genomic RNA in the region corresponding to the 5'' end of mRNA B. The region of the IBV sequence presented in this paper contains the 5'' ends, on the viral genome, of mRNAs A and B. abstract: Abstract DNA sequencing of genomic cDNA clones of avian infectious bronchitis virus (IBV) has been carried out. 770 bases have been determined which include genomic sequences spanning the 5' termini of the two smallest mRNAs of the 3'-coterminal “nested” set: mRNA A and mRNA B. This region contains the complete coding sequences for mRNA B which are additional to those present in mRNA A. Two open reading frames are present, predicting proteins of M rs 7500 and 9500. url: https://www.ncbi.nlm.nih.gov/pubmed/6092234/ doi: 10.1016/0378-1119(84)90169-0 id: cord-295312-68b3zio6 author: Britton, Paul title: Genes 3 and 5 of Infectious Bronchitis Virus are Accessory Protein Genes date: 2006 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/17037560/ doi: 10.1007/978-0-387-33012-9_64 id: cord-307304-irji8owi author: Britton, Paul title: Generation of a recombinant avian coronavirus infectious bronchitis virus using transient dominant selection date: 2004-11-05 words: 4856.0 sentences: 219.0 pages: flesch: 52.0 cache: ./cache/cord-307304-irji8owi.txt txt: ./txt/cord-307304-irji8owi.txt summary: To demonstrate the feasibility of the method we exchanged the ectodomain of the Beaudette spike gene for the corresponding region from IBV M41 and generated two recombinant infectious bronchitis viruses (rIBVs) expressing the chimaeric S protein, validating the method as an alternative way for generating rIBVs. Avian infectious bronchitis virus (IBV), a group three member of the genus Coronavirus (order Nidovirales, family Coronaviridae), is a highly infectious pathogen of domestic fowl that replicates primarily in the respiratory tract but also in epithelial cells of the gut, kidney and oviduct (Cavanagh, 2001; Cavanagh and Naqi, 2003; Cook et al., 2001) . In an alternative strategy infectious IBV was recovered following transfection of restricted vaccinia virus DNA, containing the IBV full-length cDNA, into cells infected with recombinant fowlpox virus expressing T7 RNA polymerase (Casais et al., 2001) . abstract: A reverse genetics system for the avian coronavirus infectious bronchitis virus (IBV) has been described in which a full-length cDNA, corresponding to the IBV (Beaudette-CK) genome, was inserted into the vaccinia virus genome following in vitro assembly of three contiguous cDNAs [Casais, R., Thiel, V., Siddell, S.G., Cavanagh, D., Britton, P., 2001. Reverse genetics system for the avian coronavirus infectious bronchitis virus. J. Virol. 75, 12359–12369]. The method has subsequently been used to generate a recombinant IBV expressing a chimaeric S gene [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]. Use of vaccinia virus as a vector for the full-length cDNA of the IBV genome has the advantage that modifications can be made to the IBV cDNA using homologous recombination, a method frequently used to insert and delete sequences from the vaccinia virus genome. We describe the use of homologous recombination as a method for modifying the Beaudette full-length cDNA, within the vaccinia virus genome, without the requirement for in vitro assembly of the IBV cDNA. To demonstrate the feasibility of the method we exchanged the ectodomain of the Beaudette spike gene for the corresponding region from IBV M41 and generated two recombinant infectious bronchitis viruses (rIBVs) expressing the chimaeric S protein, validating the method as an alternative way for generating rIBVs. url: https://www.ncbi.nlm.nih.gov/pubmed/15620403/ doi: 10.1016/j.jviromet.2004.09.017 id: cord-273366-xd84f8ct author: Brownsword, Matthew J. title: Infectious Bronchitis Virus Regulates Cellular Stress Granule Signaling date: 2020-05-14 words: 8910.0 sentences: 520.0 pages: flesch: 47.0 cache: ./cache/cord-273366-xd84f8ct.txt txt: ./txt/cord-273366-xd84f8ct.txt summary: Interestingly, we found that IBV is able to inhibit multiple cellular stress granule signaling pathways, whilst at the same time, IBV replication also results in the induction of seemingly canonical stress granules in a proportion of infected cells. Moreover, IBV infection uncouples translational repression and stress granule formation and both processes are independent of eIF2α phosphorylation. Vero cells were infected with IBV and at the indicated time points, cells were fixed and labelled with anti-dsRNA to detect virus infection and with anti-G3BP1 to detect SG. Following identification of SG in IBV infected cells, the requirement for active virus replication in induction of granules was assessed. At 24 hpi, cells were fixed and labelled with anti-G3BP1 (red) to detect stress granules (SG) and IBV infected cells were detected with an anti-dsRNA antibody (green). Junin virus infection impairs stress-granule formation in Vero cells treated with arsenite via inhibition of eIF2alpha phosphorylation abstract: Viruses must hijack cellular translation machinery to express viral genes. In many cases, this is impeded by cellular stress responses. These stress responses result in the global inhibition of translation and the storage of stalled mRNAs, into RNA-protein aggregates called stress granules. This results in the translational silencing of the majority of mRNAs excluding those beneficial for the cell to resolve the specific stress. For example, the expression of antiviral factors is maintained during viral infection. Here we investigated stress granule regulation by Gammacoronavirus infectious bronchitis virus (IBV), which causes the economically important poultry disease, infectious bronchitis. Interestingly, we found that IBV is able to inhibit multiple cellular stress granule signaling pathways, whilst at the same time, IBV replication also results in the induction of seemingly canonical stress granules in a proportion of infected cells. Moreover, IBV infection uncouples translational repression and stress granule formation and both processes are independent of eIF2α phosphorylation. These results provide novel insights into how IBV modulates cellular translation and antiviral stress signaling. url: https://www.ncbi.nlm.nih.gov/pubmed/32422883/ doi: 10.3390/v12050536 id: cord-010608-eaa2znom author: Butt, Salman L. title: Real-time, MinION-based, amplicon sequencing for lineage typing of infectious bronchitis virus from upper respiratory samples date: 2020-03-05 words: 6846.0 sentences: 322.0 pages: flesch: 53.0 cache: ./cache/cord-010608-eaa2znom.txt txt: ./txt/cord-010608-eaa2znom.txt summary: title: Real-time, MinION-based, amplicon sequencing for lineage typing of infectious bronchitis virus from upper respiratory samples Sanger sequencing of the S1 subunit of the spike gene is currently used to genotype IBV; however, the universal S1 PCR was created to work from cultured IBV, and it is inefficient at detecting multiple viruses in a single sample. We describe herein a MinION-based, amplicon-based sequencing (AmpSeq) method that genetically categorized IBV from clinical samples, including samples with multiple IBVs. Total RNA was extracted from 15 tracheal scrapings and choanal cleft swab samples, randomly reverse transcribed, and PCR amplified using modified S1-targeted primers. Real-time data analysis, the lack of significant start-up cost investment or maintenance expenses, simultaneous and sequential multiplexing unique to MinION, and the ability to sequence long DNA molecules so that primers are in conserved regions while the product contains the variable region are the features that make the use of this technology highly feasible in disease diagnosis. abstract: Infectious bronchitis (IB) causes significant economic losses in the global poultry industry. Control of IB is hindered by the genetic diversity of the causative agent, infectious bronchitis virus (IBV), which has led to the emergence of several serotypes that lack complete serologic cross-protection. Although serotyping requires immunologic characterization, genotyping is an efficient means to identify IBVs detected in samples. Sanger sequencing of the S1 subunit of the spike gene is currently used to genotype IBV; however, the universal S1 PCR was created to work from cultured IBV, and it is inefficient at detecting multiple viruses in a single sample. We describe herein a MinION-based, amplicon-based sequencing (AmpSeq) method that genetically categorized IBV from clinical samples, including samples with multiple IBVs. Total RNA was extracted from 15 tracheal scrapings and choanal cleft swab samples, randomly reverse transcribed, and PCR amplified using modified S1-targeted primers. Amplicons were barcoded to allow for pooling of samples, processed per manufacturer’s instructions into a 1D MinION sequencing library, and then sequenced on the MinION. The AmpSeq method detected IBV in 13 of 14 IBV-positive samples. AmpSeq accurately detected and genotyped both IBV lineages in 3 of 5 samples containing 2 IBV lineages. Additionally, 1 sample contained 3 IBV lineages, and AmpSeq accurately detected 2 of the 3 lineages. Strain identification, including detection of different IBVs from the same lineage, was also possible with this AmpSeq method. Our results demonstrate the feasibility of using MinION-based AmpSeq for rapid and accurate identification and lineage typing of IBV from oral swab samples. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7201198/ doi: 10.1177/1040638720910107 id: cord-293651-96cmduez author: Callison, Scott A. title: Development and evaluation of a real-time Taqman RT-PCR assay for the detection of infectious bronchitis virus from infected chickens date: 2006-08-28 words: 4742.0 sentences: 216.0 pages: flesch: 56.0 cache: ./cache/cord-293651-96cmduez.txt txt: ./txt/cord-293651-96cmduez.txt summary: We also collected a total of 120 tracheal swabs at six different time points from birds experimentally infected with different dosages of IBV and found that, independent of the dose given, the viral load in the trachea plateau at 5 days post-inoculation. Molecular assays use the reverse transcriptase-polymerase chain reaction (RT-PCR) to detect viral RNA directly from a clinical sample or from virus isolated in a laboratory host system. Clinical samples consisting of 229 tracheal swabs from commercial chickens experiencing upper-respiratory disease, submitted as routine diagnostic cases to the Delaware (Georgetown, DE) and Maryland (Salisbury, MD) State Diagnostic Laboratories were tested by the real-time RT-PCR assay, as well as, by virus isolation at those laboratories (Gelb and Jackwood, 1998) . In this report we present the development and evaluation of a real-time Taqman ® -based RT-PCR assay for the detection and quantification of IBV genomic RNA directly from tracheal swabs. abstract: It is important to rapidly differentiate infectious bronchitis virus (IBV) from disease agents like highly pathogenic avian influenza virus and exotic Newcastle disease virus, which can be extremely similar in the early stages of their pathogenesis. In this study, we report the development and testing of a real-time RT-PCR assay using a Taqman(®)-labeled probe for early and rapid detection of IBV. The assay amplifies a 143-bp product in the 5′-UTR of the IBV genome and has a limit of detection and quantification of 100 template copies per reaction. All 15 strains of IBV tested as well as two Turkey coronavirus strains were amplified, whereas none of the other pathogens examined, tested positive. Evaluation of the assay was completed with 1329 tracheal swab samples. A total of 680 samples collected from IBV antibody negative birds were negative for IBV by the real-time RT-PCR assay. We tested 229 tracheal swabs submitted to two different diagnostic laboratories and found 79.04% of the tracheal swabs positive for IBV by real-time RT-PCR, whereas only 27.51% of the samples were positive by virus isolation, which is the reference standard test. We also collected a total of 120 tracheal swabs at six different time points from birds experimentally infected with different dosages of IBV and found that, independent of the dose given, the viral load in the trachea plateau at 5 days post-inoculation. In addition, an inverse relationship between the dose of virus given and the viral load at 14 days post-inoculation was observed. Finally, we tested 300 total tracheal swab samples, from a flock of commercial broilers spray vaccinated for IBV in the field. The percentage of birds infected with the IBV vaccine at 3, 7, and 14 days post-vaccination was 58%, 65%, and 83%, respectively, indicating that only slightly more than half the birds were initially infected then the vaccine was subsequently transmitted to other birds in the flock. This observation is significant because coronaviruses, which have a high mutation rate, can revert to pathogenicity when bird-to-bird transmission occurs. The real-time RT-PCR test described herein can be used to rapidly distinguish IBV from other respiratory pathogens, which is important for control of this highly infectious virus. The test was extremely sensitive and specific, and can be used to quantitate viral genomic RNA in clinical samples. url: https://api.elsevier.com/content/article/pii/S0166093406002734 doi: 10.1016/j.jviromet.2006.07.018 id: cord-330260-xuw31zfn author: Chen, Hui-Wen title: Identification of Taiwan and China-like recombinant avian infectious bronchitis viruses in Taiwan date: 2009-01-20 words: 3698.0 sentences: 238.0 pages: flesch: 58.0 cache: ./cache/cord-330260-xuw31zfn.txt txt: ./txt/cord-330260-xuw31zfn.txt summary: All of the recombinants showed chimeric IBV genome arrangements originated from Taiwan and China-like parental strains. Phylogenetic analyses were performed based on the nucleotide sequence alignment using each ORF from the S to N genes among eight Taiwan and reference strains (Fig. 1) . Phylogenetic analysis of partial S1 and N gene sequences of infectious bronchitis virus isolates from Italy revealed genetic diversity and recombination Recombinant avian infectious bronchitis virus expressing a heterologous spike gene demonstrates that the spike protein is a determinant of cell tropism A novel variant of avian infectious bronchitis virus resulting from recombination among three different strains Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus Genetic diversity of avian infectious bronchitis coronavirus strains isolated in China between Genetic grouping for the isolates of avian infectious bronchitis virus in Taiwan abstract: Infectious bronchitis virus (IBV) infections in poultry cause great economic losses to the poultry industry worldwide. The emergence of viral variants complicates disease control. The IBV strains in Taiwan were clustered into two groups, Taiwan group I and Taiwan group II, based on the S1 gene. A variant was previously identified and showed a distinct S1 gene homology with other local strains. This study investigated the 3′ 7.3 kb genome of eight Taiwan strains isolated from 1992 to 2007. The genes of interest were directly sequenced. Sequence analyses were performed to detect any recombination event among IBVs. The results demonstrated that all of the examined viruses maintained the typical IBV genome organization as 5′-S-3a-3b-E-M-5a-5b-N-UTR-3′. In the phylogenetic analyses, various genes from one strain were clustered into separate groups. Moreover, frequent recombination events were identified in the Simplot analyses among the Taiwan and China CK/CH/LDL/97I-type strains. Putative crossover sites were located in the S1, S2, 3b, M genes and the intergenic region between the M and 5a genes. All of the recombinants showed chimeric IBV genome arrangements originated from Taiwan and China-like parental strains. Field IBVs in Taiwan undergo genetic recombination and evolution. url: https://www.ncbi.nlm.nih.gov/pubmed/19100792/ doi: 10.1016/j.virusres.2008.11.012 id: cord-335310-61wibso4 author: Chen, Hui-Wen title: Synthetic virus-like particles prepared via protein corona formation enable effective vaccination in an avian model of coronavirus infection date: 2016-08-15 words: 5482.0 sentences: 264.0 pages: flesch: 40.0 cache: ./cache/cord-335310-61wibso4.txt txt: ./txt/cord-335310-61wibso4.txt summary: Herein, a facile approach to formulate synthetic virus-like particles (sVLPs) is demonstrated by exploiting the phenomenon of protein corona formation induced by the high-energy surfaces of synthetic nanoparticles. As compared to inoculation with free proteins, vaccination with the sVLPs showed enhanced lymphatic antigen delivery, stronger antibody titers, increased splenic T-cell response, and reduced infection-associated symptoms in an avian model of coronavirus infection. Comparison to a commercial whole inactivated virus vaccine also showed evidence of superior antiviral protection by the sVLPs. The study demonstrates a simple yet robust method in bridging viral antigens with synthetic nanoparticles for improved vaccine application; it has practical implications in the management of human viral infections as well as in animal agriculture. In the present study, vaccination with the sVLPs resulted in enhanced humoral and cellular immune responses, improving protection against an avian model of coronavirus infection as compared to free protein antigens and a commercial WIV vaccine. abstract: The ongoing battle against current and rising viral infectious threats has prompted increasing effort in the development of vaccine technology. A major thrust in vaccine research focuses on developing formulations with virus-like features towards enhancing antigen presentation and immune processing. Herein, a facile approach to formulate synthetic virus-like particles (sVLPs) is demonstrated by exploiting the phenomenon of protein corona formation induced by the high-energy surfaces of synthetic nanoparticles. Using an avian coronavirus spike protein as a model antigen, sVLPs were prepared by incubating 100 nm gold nanoparticles in a solution containing an optimized concentration of viral proteins. Following removal of free proteins, antigen-laden particles were recovered and showed morphological semblance to natural viral particles under nanoparticle tracking analysis and transmission electron microscopy. As compared to inoculation with free proteins, vaccination with the sVLPs showed enhanced lymphatic antigen delivery, stronger antibody titers, increased splenic T-cell response, and reduced infection-associated symptoms in an avian model of coronavirus infection. Comparison to a commercial whole inactivated virus vaccine also showed evidence of superior antiviral protection by the sVLPs. The study demonstrates a simple yet robust method in bridging viral antigens with synthetic nanoparticles for improved vaccine application; it has practical implications in the management of human viral infections as well as in animal agriculture. url: https://doi.org/10.1016/j.biomaterials.2016.08.018 doi: 10.1016/j.biomaterials.2016.08.018 id: cord-342354-j10m2dfh author: Chen, Huijie title: Protective effects of hypericin against infectious bronchitis virus induced apoptosis and reactive oxygen species in chicken embryo kidney cells date: 2019-12-31 words: 5865.0 sentences: 291.0 pages: flesch: 50.0 cache: ./cache/cord-342354-j10m2dfh.txt txt: ./txt/cord-342354-j10m2dfh.txt summary: title: Protective effects of hypericin against infectious bronchitis virus induced apoptosis and reactive oxygen species in chicken embryo kidney cells These results suggested that HY showed potential antiviral activities against IBV infection involving the inhibition of apoptosis and ROS generation in CEK cells. The aim of this study is to elucidate the antiviral activity and related mechanism of HY inhibiting IBV replication in chicken embryo kidney (CEK) cells, and provide alternative approach to prevent and treat IBV infection. The impact of HY on relative mRNA expression levels of IBV, apoptosis-related genes (including Fas, FasL, JNK, Bax, Bcl-2, Caspase 3, and Caspase 8), and ROS production in IBV-infected CEK cells were studied. Our results clearly demonstrated HY had potential antiviral activities against IBV infection involving the inhibition of apoptosis and ROS generation in CEK cells. The antiviral effect of HY was analyzed by the relative mRNA expression levels of IBV-N gene (Figure 2A ) and the virus titer ( Figure 2B ) in CEK cells. abstract: ABSTRACT Avian infectious bronchitis virus (IBV), a coronavirus, causes infectious bronchitis leading to enormous economic loss in the poultry industry worldwide. Hypericin (HY) is an excellent compound that has been investigated in antiviral, antineoplastic, and antidepressant. To investigate the inhibition effect of HY on IBV infection in chicken embryo kidney (CEK) cells, 3 different experimental designs: pre-treatment of cells prior to IBV infection, direct treatment of IBV-infected cells, and pre-treatment of IBV prior to cell infection were used. Quantitative real-time PCR (qRT-PCR), immunofluorescence assay (IFA), flow cytometry, and fluorescence microscopy were performed and virus titer was determined by TCID50. The results revealed that HY had a good anti-IBV effect when HY directly treated the IBV-infected cells, and virus infectivity decreased in a dose-dependent manner. Furthermore, HY inhibited IBV-induced apoptosis in CEK cells, and significantly reduced the mRNA expression levels of Fas, FasL, JNK, Bax, Caspase 3, and Caspase 8, and significantly increased Bcl-2 mRNA expression level in CEK cells. In addition, HY treatment could decrease IBV-induced reactive oxygen species (ROS) generation in CEK cells. These results suggested that HY showed potential antiviral activities against IBV infection involving the inhibition of apoptosis and ROS generation in CEK cells. url: https://doi.org/10.3382/ps/pez465 doi: 10.3382/ps/pez465 id: cord-356094-sbtigcfr author: Chen, Huijie title: Antiviral Activity Against Infectious Bronchitis Virus and Bioactive Components of Hypericum perforatum L. date: 2019-10-29 words: 8921.0 sentences: 485.0 pages: flesch: 55.0 cache: ./cache/cord-356094-sbtigcfr.txt txt: ./txt/cord-356094-sbtigcfr.txt summary: perforatum was ethyl acetate extraction section (HPE), and results showed that treatment with HPE significantly reduced the relative messenger ribonucleic acid (mRNA) expression and virus titer of IBV, and reduced positive green immunofluorescence signal of IBV in chicken embryo kidney (CEK) cells. The results of adaptation and replication in CEK cells, such as CPE, reverse transcription polymerase chain reaction (RT-PCR), and IBV growth curve determined by tissue culture infective dose (TCID 50 ) at different time were tested. The relative mRNA expression level of IBV-N gene was detected by qRT-PCR and the virus titer of IBV was determined by TCID 50 to analyze the antiviral effect of HPE, HPW and SEE (Figure 3) . FIgUre 8 | The effects of Hypericum perforatum ethyl acetate (HPE) on infectious bronchitis virus (IBV) messenger ribonucleic acid (mRNA) expression levels of trachea (A) and kidney (B). abstract: Hypericum perforatum L., also known as Saint John’s Wort, has been well studied for its chemical composition and pharmacological activity. In this study, the antiviral activities of H. perforatum on infectious bronchitis virus (IBV) were evaluated in vitro and in vivo for the first time. The results of in vitro experiments confirmed that the antiviral component of H. perforatum was ethyl acetate extraction section (HPE), and results showed that treatment with HPE significantly reduced the relative messenger ribonucleic acid (mRNA) expression and virus titer of IBV, and reduced positive green immunofluorescence signal of IBV in chicken embryo kidney (CEK) cells. HPE treatment at doses of 480–120 mg/kg for 5 days, reduced IBV induced injury in the trachea and kidney, moreover, reduced the mRNA expression level of IBV in the trachea and kidney in vivo. The mRNA expression levels of IL-6, tumor necrosis factor alpha (TNF-α), and nuclear factor kappa beta (NF-κB) significantly decreased, but melanoma differentiation-associated protein 5 (MDA5), mitochondrial antiviral signaling gene, interferon alpha (IFN-α), and interferon beta (IFN-β) mRNA levels significantly increased in vitro and in vivo. Our findings demonstrated that HPE had significant anti-IBV effects in vitro and in vivo, respectively. In addition, it is possible owing to up-regulate mRNA expression of type I interferon through the MDA5 signaling pathway and down-regulate mRNA expression of IL-6 and TNF-α via the NF-κB signaling pathway. Moreover, the mainly active compositions of HPE analyzed by high-performance liquid chromatography/electrospray ionization–mass spectroscopy (ESI-MS) are hyperoside, quercitrin, quercetin, pseudohypericin, and hypericin, and a combination of these compounds could mediate the antiviral activities. This might accelerate our understanding of the antiviral effect of H. perforatum and provide new insights into the development of effective therapeutic strategies. url: https://www.ncbi.nlm.nih.gov/pubmed/31736754/ doi: 10.3389/fphar.2019.01272 id: cord-305684-ipeup5mp author: Chen, Yuqiu title: Identification and molecular characterization of a novel serotype infectious bronchitis virus (GI-28) in China date: 2016-12-16 words: 5146.0 sentences: 311.0 pages: flesch: 58.0 cache: ./cache/cord-305684-ipeup5mp.txt txt: ./txt/cord-305684-ipeup5mp.txt summary: In this study, based on the results of S1 sequence analysis and virus cross-neutralization tests, IBV strain ck/CH/LGX/111119 was found to be genetically and antigenically different from other known IBV types, representing not only a novel genotype, but also a novel serotype (designated as GI-28). Further studies by complete genomic analysis showed that strain ck/CH/LGX/111119 may have originated from recombination events involving LX4 genotype IBVs and an as-yet-unidentified IBV donating a S1 gene, or from the result of accumulation of mutations and selections, especially in the S1 gene, from a LX4 genotype virus. In addition, the S1 gene sequences of 93 IBV reference strains with different genotypes were also selected for comparison in this study ( Fig. 1 ) (Valastro et al., 2016) . Genotyping based on the phylogenetic analysis of the S1 gene from our ck/CH/LGX/111119 and 99 reference IBV strains assigned the viruses into different clusters (Fig. 1) . abstract: Avian infectious bronchitis coronavirus (IBV) is a major poultry pathogen. A characteristic feature of IBV is the occurrence of many different strains belonging to different serotypes, which renders complete control of the disease by vaccination a challenging task due to the poor cross-protection between different serotypes. In this study, based on the results of S1 sequence analysis and virus cross-neutralization tests, IBV strain ck/CH/LGX/111119 was found to be genetically and antigenically different from other known IBV types, representing not only a novel genotype, but also a novel serotype (designated as GI-28). Viruses belonging to this novel serotype have been isolated from several regions in China in recent years, suggesting endemic circulation of the serotype in various geographic locations in China. Further studies by complete genomic analysis showed that strain ck/CH/LGX/111119 may have originated from recombination events involving LX4 genotype IBVs and an as-yet-unidentified IBV donating a S1 gene, or from the result of accumulation of mutations and selections, especially in the S1 gene, from a LX4 genotype virus. ck/CH/LGX/111119 is a nephropathogenic strain, although it had broader tissue tropism (respiratory, digestive, urinary, and reproductive tracts) among chickens challenged at one day old. Infection of the oviducts with ck/CH/LGX/111119 found in this study may have severe implications because the virus will likely induce the occurrence of false layers. url: https://www.ncbi.nlm.nih.gov/pubmed/28062000/ doi: 10.1016/j.vetmic.2016.12.017 id: cord-318400-l9kwxsq7 author: Chhabra, Rajesh title: Pathogenicity and tissue tropism of infectious bronchitis virus is associated with elevated apoptosis and innate immune responses date: 2016-01-15 words: 5153.0 sentences: 287.0 pages: flesch: 53.0 cache: ./cache/cord-318400-l9kwxsq7.txt txt: ./txt/cord-318400-l9kwxsq7.txt summary: To establish a characteristic host response to predict the pathogenicity and tissue tropism of infectious bronchitis viruses (IBV), we investigated innate immune responses (IIR) and apoptosis in chicken embryo kidney cells (CEKC) and tracheal organ cultures (TOC) infected with three IBV strains. In contrast, M41 infection caused greater expression of these genes than 885 or QX in TOCs. In summary, greater levels of apoptosis and elevated levels of TLR3, MDA5 and IFN-β expression are associated with increased pathogenicity of IBV strains in renal and tracheal tissues. In order to establish the characteristic host response to predict the tissue tropism and pathogenicity of IBVs, we investigated apoptosis and innate immune responses in chicken embryo kidney (CEK) cells and tracheal organ cultures (TOCs) following infection with IS/885/00-like, QX-like and M41 IBV strains. Nephropathogenic IBV strains 885 and QX resulted in significantly greater up-regulation of innate immune sensing genes namely TLR3 and MDA5 along with greater IFN-β mRNA levels in CEK cells at 9 h of infection when compared to M41 infection. abstract: To establish a characteristic host response to predict the pathogenicity and tissue tropism of infectious bronchitis viruses (IBV), we investigated innate immune responses (IIR) and apoptosis in chicken embryo kidney cells (CEKC) and tracheal organ cultures (TOC) infected with three IBV strains. Results showed nephropathogenic IBV strains 885 and QX induced greater apoptosis in CEKC than M41, which induced greater apoptosis in TOCs compared to 885 and QX. Elevated IIR is associated with tissue tropism of different IBV strains. Compared to M41, 885 and QX caused greater induction of toll like receptor 3 (TLR3), melanoma differentiation associated protein 5 (MDA5) and interferon beta (IFN-β) in CEKC. In contrast, M41 infection caused greater expression of these genes than 885 or QX in TOCs. In summary, greater levels of apoptosis and elevated levels of TLR3, MDA5 and IFN-β expression are associated with increased pathogenicity of IBV strains in renal and tracheal tissues. url: https://www.ncbi.nlm.nih.gov/pubmed/26655241/ doi: 10.1016/j.virol.2015.11.011 id: cord-006991-2q5ore6g author: Chi, X. title: Oral administration of tea saponins to relive oxidative stress and immune suppression in chickens date: 2017-06-15 words: 5200.0 sentences: 282.0 pages: flesch: 47.0 cache: ./cache/cord-006991-2q5ore6g.txt txt: ./txt/cord-006991-2q5ore6g.txt summary: The results showed that administration of tea saponins significantly increased total antioxidant capacity, total superoxide dismutase, catalase, glutathione peroxidase, glutathione, ascorbic acid, and α-tocopherol, and decreased malondialdehyde and protein carbonyl. Enhanced immune responses, such as lymphocyte proliferation induced by concanavalin A and lipopolysaccharides, and serum Newcastle disease virusand infectious bronchitis virus-specific antibodies were also observed in chickens injected with or without cyclophosphamide. At the present study, we evaluated the effect of TS on the antioxidative activities as well as the immune responses to a live bivalent vaccine of Newcastle disease virus (NDV) and infectious bronchitis virus (IBV) vaccine in chickens in oxidative stress induced by cyclophosphamide (Cy). In this study, injection of Cy generated oxidative stress and lowered immune responses by reducing antioxidant enzymes such as T-AOC, T-SOD, GSH, and CAT, as well as inhibiting lymphocyte proliferation and antibody responses to vaccination. abstract: The present study was designed to evaluate the effects of tea saponins on oxidative stress induced by cyclophosphamide in chickens. One hundred twenty chickens were randomly divided into 5 groups. Groups 3 to 4 received intramuscular injection of cyclophosphamide to induce oxidative stress and immunosuppression. After that, groups 2 and 4 were orally administered tea saponins in drinking water for 7 d. Then, groups 1 to 4 were immunized with a live, bivalent vaccine of Newcastle disease virus and infectious bronchitis virus. Blood samples were collected for analysis of oxidative parameters and specific antibody titers, and splenocytes were prepared for lymphocyte proliferative assay. The results showed that administration of tea saponins significantly increased total antioxidant capacity, total superoxide dismutase, catalase, glutathione peroxidase, glutathione, ascorbic acid, and α-tocopherol, and decreased malondialdehyde and protein carbonyl. Enhanced immune responses, such as lymphocyte proliferation induced by concanavalin A and lipopolysaccharides, and serum Newcastle disease virus- and infectious bronchitis virus-specific antibodies were also observed in chickens injected with or without cyclophosphamide. In addition, no side effects were found in chickens throughout the study. Therefore, tea saponins may be a potential agent to improve imunosuppression induced by oxidative stress in chickens. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7107189/ doi: 10.3382/ps/pex127 id: cord-343893-sophqqne author: Chu, Victor C title: Feline aminopeptidase N is not a functional receptor for avian infectious bronchitis virus date: 2007-02-26 words: 3972.0 sentences: 232.0 pages: flesch: 54.0 cache: ./cache/cord-343893-sophqqne.txt txt: ./txt/cord-343893-sophqqne.txt summary: Feline aminopeptidase N (fAPN) serves as a functional receptor for most group 1 coronaviruses including feline infectious peritonitis virus (FIPV), canine coronavirus, transmissible gastroenteritis virus (TGEV), and human coronavirus 229E (HCoV-229E). Group 1 CoVs -including human coronavirus-229E (HCoV-229E), feline infectious peritonitis virus (FIPV), transmissible gastroenteritis virus (TGEV) and canine coronavirus (CCV) -utilize human, feline, porcine, and canine aminopeptidase N (APN) as functional receptors during virus entry [10] [11] [12] [13] . We also cultured seven strains of IBV, including Arkansas 99, Arkansas_DPI, California 99, Connecticut 46, Holland 52, Iowa 97, and Massachusetts 41 (designated as Ark99, Ark_DPI, CA99, Conn46, H52, Iowa97, and Mass41) as candidates to test for fAPN utilization by group 3 avian CoVs. Surprisingly, expression of fAPN did not increase viral infection in any of the strains tested. To verify the functionality of fAPN as a coronavirus receptor, we first tested its ability to rescue FIPV-1146 and TGEV infection of non-permissive cells, as reported in previous studies [11] . abstract: BACKGROUND: Coronaviruses are an important cause of infectious diseases in humans, including severe acute respiratory syndrome (SARS), and have the continued potential for emergence from animal species. A major factor in the host range of a coronavirus is its receptor utilization on host cells. In many cases, coronavirus-receptor interactions are well understood. However, a notable exception is the receptor utilization by group 3 coronaviruses, including avian infectious bronchitis virus (IBV). Feline aminopeptidase N (fAPN) serves as a functional receptor for most group 1 coronaviruses including feline infectious peritonitis virus (FIPV), canine coronavirus, transmissible gastroenteritis virus (TGEV), and human coronavirus 229E (HCoV-229E). A recent report has also suggested a role for fAPN during IBV entry (Miguel B, Pharr GT, Wang C: The role of feline aminopeptidase N as a receptor for infectious bronchitis virus. Brief review. Arch Virol 2002, 147:2047–2056. RESULTS: Here we show that, whereas both transient transfection and constitutive expression of fAPN on BHK-21 cells can rescue FIPV and TGEV infection in non-permissive BHK cells, fAPN expression does not rescue infection by the prototype IBV strain Mass41. To account for the previous suggestion that fAPN could serve as an IBV receptor, we show that feline cells can be infected with the prototype strain of IBV (Mass 41), but with low susceptibility compared to primary chick kidney cells. We also show that BHK-21 cells are slightly susceptible to certain IBV strains, including Ark99, Ark_DPI, CA99, and Iowa97 (<0.01% efficiency), but this level of infection is not increased by fAPN expression. CONCLUSION: We conclude that fAPN is not a functional receptor for IBV, the identity of which is currently under investigation. url: https://www.ncbi.nlm.nih.gov/pubmed/17324273/ doi: 10.1186/1743-422x-4-20 id: cord-022378-ovxmy1as author: Cook, Jane K.A. title: Coronaviridae date: 2009-05-15 words: 4034.0 sentences: 192.0 pages: flesch: 50.0 cache: ./cache/cord-022378-ovxmy1as.txt txt: ./txt/cord-022378-ovxmy1as.txt summary: IBV also aff ects egg-laying performance, and renal damage associated with infectious bronchitis has become increasingly important, particularly in broilers. Economically, the most important aspects are the eff ects on egg production and quality in laying hens and production performance in broilers, where the initial respiratory infection is frequently exacerbated by secondary infections. In turkeys, coronaviruses (TCoV, also called Bluecomb disease virus and Turkey enteric coronavirus) are known to be associated with enteric disease, mortality and underperformance and to aff ect egg-laying performance in older birds. Th is is a new area of investigation and, while the coronaviruses detected in some gallinaceous and nongallinaceous birds have not so far been associated with disease, these species are potential carriers of IBV and other coronaviruses and could therefore play a role in global transmission of infection. In IBV infection of commercial layers or broiler breeders, respiratory signs may or may not be observed and the most common manifestation is the eff ect on egg production and egg quality. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155630/ doi: 10.1016/b978-0-7020-2862-5.50033-7 id: cord-329245-6tj2k1yn author: Corse, Emily title: The cytoplasmic tails of infectious bronchitis virus E and M proteins mediate their interaction date: 2003-07-20 words: 7414.0 sentences: 327.0 pages: flesch: 56.0 cache: ./cache/cord-329245-6tj2k1yn.txt txt: ./txt/cord-329245-6tj2k1yn.txt summary: Indeed, it has been shown that both the MHV E and the infectious bronchitis virus (IBV) E proteins are sufficient for formation of the virus-like particles (VLPs) described above (Corse and Machamer, 2000; Maeda et al., 1999) , although the efficiency probably varies with cell type and protein expression system. (B) IBV-infected Vero cells were labeled with [ 35 S]methionine-cysteine at 45 h postinfection, treated with DSP as indicated, lysed, and immunoprecipitated with anti-E or anti-M antibodies as described under Materials and methods. The E and M proteins of several coronaviruses are released from cotransfected cells in membrane-bound particles that are morphologically similar to virions (VLPs), suggesting that interactions between these proteins are an integral part of coronavirus assembly (Baudoux et al., 1998; Corse and Machamer, 2000; Godeke et al., 2000; Vennema et al., 1996) . abstract: Abstract Virus-like particle (VLP) formation by the coronavirus E and M proteins suggests that interactions between these proteins play a critical role in coronavirus assembly. We studied interactions between the infectious bronchitis virus (IBV) E and M proteins using in vivo crosslinking and VLP assembly assays. We show that IBV E and M can be crosslinked to each other in IBV-infected and transfected cells, indicating that they interact. The cytoplasmic tails of both proteins are important for this interaction. We also examined the ability of the mutant and chimeric E and M proteins to form VLPs. IBV M proteins that are missing portions of their cytoplasmic tails or transmembrane regions were not able to support VLP formation, regardless of their ability to be crosslinked to IBV E. Interactions between the E and M proteins and the membrane bilayer are likely to play an important role in VLP formation and virus budding. url: https://www.sciencedirect.com/science/article/pii/S0042682203001752 doi: 10.1016/s0042-6822(03)00175-2 id: cord-003334-ion97n4b author: De Silva Senapathi, Upasama title: The In Ovo Delivery of CpG Oligonucleotides Protects against Infectious Bronchitis with the Recruitment of Immune Cells into the Respiratory Tract of Chickens date: 2018-11-15 words: 5827.0 sentences: 266.0 pages: flesch: 54.0 cache: ./cache/cord-003334-ion97n4b.txt txt: ./txt/cord-003334-ion97n4b.txt summary: Although the delivery of CpG ODNs in ovo at embryo day (ED) 18 has been shown to reduce infectious bronchitis virus (IBV) loads in embryonic chicken lungs pre-hatch, whether in ovo delivered CpG ODNs are capable of protecting chickens against a post-hatch challenge is unknown. We found significantly higher survival rates and reduced IBV infection in the chickens following the pre-treatment of the ED 18 eggs with CpG ODNs. At 3 days post infection (dpi), we found an increased recruitment of macrophages, cluster of differentiation (CD)8α+ and CD4+ T lymphocytes, and an up-regulation of interferon (IFN)-γ mRNA in the respiratory tract of the chickens. Considering that we observed a significant reduction in the IBV induced morbidity and mortality of in ovo CpG ODN pre-treated birds correlating with varying degrees of increased macrophages, CD4+, and CD8α+ T cells in the tracheal and lung tissues, we needed to further elucidate the mechanisms by which these immune cells were efficiently recruited. abstract: The in ovo delivery of cytosine-guanosine (CpG) oligodeoxynucleotides (ODNs) protects chickens against many bacterial and viral infections, by activating the toll-like receptor (TLR)21 signaling pathway. Although the delivery of CpG ODNs in ovo at embryo day (ED) 18 has been shown to reduce infectious bronchitis virus (IBV) loads in embryonic chicken lungs pre-hatch, whether in ovo delivered CpG ODNs are capable of protecting chickens against a post-hatch challenge is unknown. Thus, our objectives were to determine the protective effect of the in ovo delivery of CpG ODNs at ED 18 against IBV infection encountered post-hatch and, then, to investigate the mechanisms of protection. We found significantly higher survival rates and reduced IBV infection in the chickens following the pre-treatment of the ED 18 eggs with CpG ODNs. At 3 days post infection (dpi), we found an increased recruitment of macrophages, cluster of differentiation (CD)8α+ and CD4+ T lymphocytes, and an up-regulation of interferon (IFN)-γ mRNA in the respiratory tract of the chickens. Overall, it may be inferred that CpG ODNs, when delivered in ovo, provide protection against IBV infection induced morbidity and mortality with an enhanced immune response. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6266937/ doi: 10.3390/v10110635 id: cord-313676-6rebpe57 author: De la Torre, David I. title: Enteric Virus Diversity Examined by Molecular Methods in Brazilian Poultry Flocks date: 2018-03-29 words: 5867.0 sentences: 295.0 pages: flesch: 55.0 cache: ./cache/cord-313676-6rebpe57.txt txt: ./txt/cord-313676-6rebpe57.txt summary: The most common enteric viruses affecting commercial flocks in Brazil include Fowl Adenovirus of group I (FAdV-I), Chicken Parvovirus (ChPV), Chicken Astrovirus (CAstV), Avian Nephritis Virus (ANV), Infectious Bronchitis Virus (IBV), Avian Reovirus (AReo), and Avian Rotavirus (ARtV). The main enteric viruses reported to cause enteric diseases are found in single and multiple infections and include the Fowl Adenovirus of group I (FAdV-I); Chicken Parvovirus (ChPV); two viruses from the Astroviridae family: Chicken Astrovirus (CAstV) and Avian Nephritis Virus (ANV); two viruses from the Reoviridae family: Avian Reovirus (AReo) and Avian Rotavirus (ARtV); and a member of the Coronaviridae family, Infectious Bronchitis Virus (IBV) [4, [6] [7] [8] [9] . The association of enteric virus with the age of broilers, breeders, and layers (Tables 4 and 5) showed that molecular diagnosis of these viruses can be performed at different stages of production, which can be useful in the control of vertical infections. abstract: Enteric viruses play an important role in the Brazilian poultry industry due to the economic impact of resulting low yields of broilers, layers, and breeders. The most common enteric viruses affecting commercial flocks in Brazil include Fowl Adenovirus of group I (FAdV-I), Chicken Parvovirus (ChPV), Chicken Astrovirus (CAstV), Avian Nephritis Virus (ANV), Infectious Bronchitis Virus (IBV), Avian Reovirus (AReo), and Avian Rotavirus (ARtV). The aim of this study was to identify single and multiple infections using data obtained from 270 samples from eleven Brazilian states, corresponding to the period between 2010 and 2017. This was accompanied by an analysis of the relationship between the age of birds, clinical signs, and geographical distribution, using Polymerase Chain Reaction (PCR) and Reverse Transcription-PCR (RT-PCR) techniques. Twenty-five profiles of virus combinations were detected. Single infections were encountered in 86.3% of samples, and multiple infections were present in the remaining 13.7%. Both single and multiple infections affected all kinds of commercial chickens with digestive problems, stunting syndrome, decreases in egg and meat production, increased mortality, and respiratory signs. FAdV-I, ChPV, CAstV, ANV, and ARtV were mostly detected in young broilers, in contrast with IBV, which was detected in hens from one to greater than 51 weeks of age. These results exhibit the complexity of enteric diseases and the still poorly understood role of each pathogen as a unique etiological agent. url: https://doi.org/10.3390/vetsci5020038 doi: 10.3390/vetsci5020038 id: cord-324324-8ybfiz8f author: Decaro, Nicola title: Novel human coronavirus (SARS-CoV-2): A lesson from animal coronaviruses date: 2020-04-14 words: 14927.0 sentences: 720.0 pages: flesch: 49.0 cache: ./cache/cord-324324-8ybfiz8f.txt txt: ./txt/cord-324324-8ybfiz8f.txt summary: In addition, the close contact between human beings and different animal species sold at the wet markets of East Asia represents the optimal situation for the host species jump and adaptation to humans of potentially zoonotic agents like CoVs. It is not a coincidence that two of the most severe zoonoses of the last two decades (highly pathogenic H5N1 avian influenza and SARS) have emerged in the same Chinese province of Guangdong where the contact between humans and animals is closer (Lorusso et al., 2020) . All these viruses as well as analogous IBV-like CoVs detected in other birds including penguins, pigeons, peafowl, parrots, waterfowl, teal, quail, duck and whooper swan (Cavanagh et al., 2002; Circella et al., 2007; Domanska-Blicharz et al., 2014; Torres et al., 2013; Hughes et al., 2009; Liu et al., 2005; Wille et al., 2016; Jordan et al., 2015; Bande et al., 2016; Suryaman et al., 2019) have been assigned to the same viral species known as Avian coronavirus (ACoV) within the subgenus Igacovirus of genus Gammacoronavirus. abstract: The recent pandemic caused by the novel human coronavirus, referrred to as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), not only is having a great impact on the health care systems and economies in all continents but it is also causing radical changes of common habits and life styles. The novel coronavirus (CoV) recognises, with high probability, a zoonotic origin but the role of animals in the SARS-CoV-2 epidemiology is still largely unknown. However, CoVs have been known in animals since several decades, so that veterinary coronavirologists have a great expertise on how to face CoV infections in animals, which could represent a model for SARS-CoV-2 infection in humans. In the present paper, we provide an up-to-date review of the literature currently available on animal CoVs, focusing on the molecular mechanisms that are responsible for the emergence of novel CoV strains with different antigenic, biologic and/or pathogenetic features. A full comprehension of the mechanisms driving the evolution of animal CoVs will help better understand the emergence, spreading, and evolution of SARS-CoV-2. url: https://www.sciencedirect.com/science/article/pii/S0378113520302935 doi: 10.1016/j.vetmic.2020.108693 id: cord-271897-9oqzsd70 author: Domanska-Blicharz, Katarzyna title: Molecular epidemiology of infectious bronchitis virus in Poland from 1980 to 2017 date: 2020-01-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The presence of infectious bronchitis virus (IBV) was identified for the first time in the poultry population in Poland at the end of the 1960s. From this time a few waves of epidemics caused by different IBV variants spread across the country. In order to gain more insight into the molecular epidemiology of IBV in Poland, in the present study the S1 coding region of 34 IBV isolates and nearly whole genome of 10 strains collected over a period of 38 years was characterized. Phylogenetic analysis showed that these strains belonged to five recently established IBV lineages: GI-1, GI-12, GI-13, GI-19 and GI-23. Additionally, two strains from 1989 and 1997 formed a separate branch of the phylogenetic tree categorized as unique early Polish variants, and one strain was revealed to be the recombinant of these and GI-1 lineage viruses. Irrespective of year of isolation and S1-dependent genotype, the genome sequences of Polish IBV strains showed the presence of six genes and 13 ORFs: 5′UTR-1a-1b-S-3a-3b-E-M-4b-4c-5a-5b-N-6b-3′UTR, however their individual genes and putative proteins had different lengths. The phylogenetic analyses performed on the genome of ten Polish IBV strains revealed that they cluster into different groups. The Polish GI-1, GI-19 and GI-23 strains cluster with other similar viruses of these lineages, with the exception of the two strains from 1989 and 1997 which are different. It seems that in Poland in the 1980s and 1990s IBV strains with a unique genome backbone circulated in the field, which were then replaced by other strains belonging to other IBV lineages with a genome backbone specific to these lineages. The recombination analysis showed that some Polish strains resulted from a recombination event involving different IBV lineages, most frequently GI-13 and GI-19. url: https://www.ncbi.nlm.nih.gov/pubmed/31917362/ doi: 10.1016/j.meegid.2020.104177 id: cord-265258-2rmtsyns author: Domanska‐Blicharz, K. title: Specific detection of GII‐1 lineage of infectious bronchitis virus date: 2017-07-03 words: 3393.0 sentences: 170.0 pages: flesch: 53.0 cache: ./cache/cord-265258-2rmtsyns.txt txt: ./txt/cord-265258-2rmtsyns.txt summary: The real-time RT-PCR assays seem to be effective tools for IBV-type identification and although S1 coding region is prone to mutations, methods aimed in this gene detection has been recently developed and used for GI-1 (Mass, Connecticut), GI-9 (Arkansas), GI-11 (SAI), G1-16 (ASAII) and GIV-1 (DE072/GA98) lineages (Acevedo et al. Here, we describe the development of a TaqMan probe-based real-time RT-PCR for the detection of GII-1 (D1466-like) IBV lineage. Moreover, the assay developed in the present study showed to be highly specific as no fluorescent signals were detected with other tested IBV lineages or chicken RNA viral pathogens. In conclusion, the TaqMan probe-based real-time RT-PCR assay described here is a time-saving, specific, sensitive and reliable method of detection of GII-1 lineage (D1466-like) of IBV which could successfully replace standard nested RT-PCR. Development and evaluation of a real-time Taqman RT-PCR assay for the detection of infectious bronchitis virus from infected chickens abstract: Infectious bronchitis virus (IBV) is a worldwide prevalent RNA virus that causes highly contagious and economically devastating disease in chicken. The virus exists in many different genetic forms which made the disease control very difficult. The present study describes the development and validation of TaqMan probe‐based real‐time reverse transcription‐polymerase chain reaction (real‐time RT‐PCR) targeting the S1 coding region of S gene characteristic for the GII‐1 lineage (formerly the D1466‐like variant) of IBV. These strains are quite different from other European IBV belonging to different lineages of the GI genotype. The developed method was 30‐fold more sensitive than used so far for standard nested RT‐PCR with detection limit of 56 RNA copies per reaction. The specificity of the assay was also evaluated with a panel of different poultry pathogens. Repeatability and reproducibility of the method was very high with coefficients of variation lower than 4%. One hundred and twenty‐seven IBV‐positive samples were tested by this method and GII‐1 strains were detected in four of them (3·15%) which indicate a decrease in the GII‐1 IBV prevalence in Poland. The assay was proven to be a valuable tool for rapid diagnosis of GII‐1 lineage of IBV strains and moreover it enabled the monitoring of viral loads which can be used to assess disease progression. SIGNIFICANCE AND IMPACT OF THE STUDY: This study reports a TaqMan probe‐based real‐time reverse transcription‐polymerase chain reaction (real‐time RT‐PCR) for rapid and accurate identification of GII‐1 lineage (formerly D1466‐like variant) of infectious bronchitis virus (IBV). The assay revealed to be more sensitive than standard nested RT‐PCR assay, previously used for this purpose. The developed assay has been tested on numerous field samples and revealed 3·15% prevalence of this lineage of IBV in Polish chicken population. Moreover, this new assay enables the assessment of viral load measurement which might be useful for epidemiology and pathogenesis studies. url: https://www.ncbi.nlm.nih.gov/pubmed/28493279/ doi: 10.1111/lam.12753 id: cord-265499-pbf11zy1 author: Dove, Brian K. title: Changes in nucleolar morphology and proteins during infection with the coronavirus infectious bronchitis virus date: 2006-03-03 words: 5026.0 sentences: 250.0 pages: flesch: 46.0 cache: ./cache/cord-265499-pbf11zy1.txt txt: ./txt/cord-265499-pbf11zy1.txt summary: In this study, using the avian infectious bronchitis coronavirus, we have shown that virus infection results in a number of changes to the nucleolus both in terms of gross morphology and protein content. Using IBV we tested the hypothesis that virus infection leads to perturbations in the morphology and proteins of the nucleolus which may have downstream consequences for host cell function. A change in the morphology of the nucleolus was observed in IBV-infected cells using EGFPnucleolin as a marker protein (e.g. Fig. 3B ), leading to the prediction that the levels of nucleolin might increase in virus-infected cells, which was observed in Fig. 4B . This study was undertaken with a higher resolution confocal microscope and we observed a third population of cells in which N protein was predominantly localized in the cytoplasm, but also was present in low levels in the nucleus and nucleolus (an example is shown in Fig. 7A) . abstract: The nucleolus is a dynamic subnuclear structure involved in ribosome subunit biogenesis, cell cycle control and mediating responses to cell stress, among other functions. While many different viruses target proteins to the nucleolus and recruit nucleolar proteins to facilitate virus replication, the effect of infection on the nucleolus in terms of morphology and protein content is unknown. Previously we have shown that the coronavirus nucleocapsid protein will localize to the nucleolus. In this study, using the avian infectious bronchitis coronavirus, we have shown that virus infection results in a number of changes to the nucleolus both in terms of gross morphology and protein content. Using confocal microscopy coupled with fluorescent labelled nucleolar marker proteins we observed changes in the morphology of the nucleolus including an enlarged fibrillar centre. We found that the tumour suppressor protein, p53, which localizes normally to the nucleus and nucleolus, was redistributed predominately to the cytoplasm. url: https://www.ncbi.nlm.nih.gov/pubmed/16819967/ doi: 10.1111/j.1462-5822.2006.00698.x id: cord-272666-3uidpr79 author: Doyle, Nicole title: Infectious Bronchitis Virus Nonstructural Protein 4 Alone Induces Membrane Pairing date: 2018-09-06 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Positive-strand RNA viruses, such as coronaviruses, induce cellular membrane rearrangements during replication to form replication organelles allowing for efficient viral RNA synthesis. Infectious bronchitis virus (IBV), a pathogenic avian Gammacoronavirus of significant importance to the global poultry industry, has been shown to induce the formation of double membrane vesicles (DMVs), zippered endoplasmic reticulum (zER) and tethered vesicles, known as spherules. These membrane rearrangements are virally induced; however, it remains unclear which viral proteins are responsible. In this study, membrane rearrangements induced when expressing viral non-structural proteins (nsps) from two different strains of IBV were compared. Three non-structural transmembrane proteins, nsp3, nsp4, and nsp6, were expressed in cells singularly or in combination and the effects on cellular membranes investigated using electron microscopy and electron tomography. In contrast to previously studied coronaviruses, IBV nsp4 alone is necessary and sufficient to induce membrane pairing; however, expression of the transmembrane proteins together was not sufficient to fully recapitulate DMVs. This indicates that although nsp4 is able to singularly induce membrane pairing, further viral or host factors are required in order to fully assemble IBV replicative structures. This study highlights further differences in the mechanism of membrane rearrangements between members of the coronavirus family. url: https://doi.org/10.3390/v10090477 doi: 10.3390/v10090477 id: cord-276755-ctzrgqe7 author: Emmott, Edward title: Elucidation of the avian nucleolar proteome by quantitative proteomics using SILAC and changes in cells infected with the coronavirus infectious bronchitis virus date: 2010-09-08 words: 2488.0 sentences: 120.0 pages: flesch: 35.0 cache: ./cache/cord-276755-ctzrgqe7.txt txt: ./txt/cord-276755-ctzrgqe7.txt summary: A recent quantitative analysis of the nucleolar proteome isolated from HeLa cells infected with the nuclear replicating DNA virus adenovirus identified 351 proteins, of which 24 proteins showed at least a twofold change in abundance, compared with nucleoli from mock-infected cells [14] . For example, in one such virus, avian infectious bronchitis virus (IBV), the virally encoded nucleocapsid (N) protein localized to the nucleolus in a cell cycle-dependent manner [15] and contained appropriate targeting motifs [16] [17] [18] . Several proteins were selected from the SILAC LC-MS/ MS analysis and their abundance and localization investigated in mock and IBV-infected cells using indirect immunofluorescence confocal microscopy (as described in [18, 19] ) in order to validate the quantitative proteomic approach (Supporting Information Fig. 1 ). Ingenuity Pathway Analysis was used to investigate the data sets to group together any proteins that shared similar functions in order to build an overview of the avian nucleolar proteome (Fig. 2) and potential roles of proteins in infectious and respiratory disease. abstract: The nucleolus is a dynamic subnuclear compartment involved in ribosome subunit biogenesis, regulation of cell stress and modulation of cellular growth and the cell cycle, among other functions. The nucleolus is composed of complex protein/protein and protein/RNA interactions. It is a target of virus infection with many viral proteins being shown to localize to the nucleolus during infection. Perturbations to the structure of the nucleolus and its proteome have been predicted to play a role in both cellular and infectious disease. Stable isotope labeling with amino acids in cell culture coupled to LC‐MS/MS with bioinformatic analysis using Ingenuity Pathway Analysis was used to investigate whether the nucleolar proteome altered in virus‐infected cells. In this study, the avian nucleolar proteome was defined in the absence and presence of virus, in this case the positive strand RNA virus, avian coronavirus infectious bronchitis virus. Data sets, potential protein changes and the functional consequences of virus infection were validated using independent assays. These demonstrated that specific rather than generic changes occurred in the nucleolar proteome in infectious bronchitis virus‐infected cells. url: https://doi.org/10.1002/pmic.201000139 doi: 10.1002/pmic.201000139 id: cord-260667-5aurua6o author: Falchieri, Marco title: Avian metapneumoviruses expressing Infectious Bronchitis virus genes are stable and induce protection date: 2013-05-24 words: 3817.0 sentences: 216.0 pages: flesch: 51.0 cache: ./cache/cord-260667-5aurua6o.txt txt: ./txt/cord-260667-5aurua6o.txt summary: The study investigates the ability of subtype A Avian metapneumovirus (AMPV) to accept foreign genes and be used as a vector for delivery of Infectious bronchitis virus (IBV) QX genes to chickens. First was a German field isolate (Virus A) passaged in Vero cells [9] and found avirulent in turkeys [12] , second was Virus AvF which contained an F gene modification found to better induce protection in turkeys [12] and third was 309/04, a virulent field isolate deriving from a subtype A vaccine and arising in field conditions [23] . When IBV MF recombinants were used to inoculate one-day-old chickens, many induced IBV protection of the trachea, yet serology and real time RT PCR virus detection indicated poor tracheal replication. Induction of protective immunity in chickens vaccinated with infectious bronchitis virus S1 glycoprotein expressed by a recombinant baculovirus abstract: The study investigates the ability of subtype A Avian metapneumovirus (AMPV) to accept foreign genes and be used as a vector for delivery of Infectious bronchitis virus (IBV) QX genes to chickens. Initially the GFP gene was added to AMPV at all gene junctions in conjunction with the development of cassetted full length DNA AMPV copies. After recombinant virus had been recovered by reverse genetics, GFP positions supporting gene expression while maintaining virus viability in vitro, were determined. Subsequently, either S1 or nucleocapsid (N) genes of IBV were positioned between AMPV M and F genes, while later a bivalent recombinant was prepared by inserting S1 and N at AMPV MF and GL junctions respectively. Immunofluorescent antibody staining showed that all recombinants expressed the inserted IBV genes in vitro and furthermore, all recombinant viruses were found to be highly stable during serial passage. Eyedrop inoculation of chickens with some AMPV-IBV recombinants at one-day-old induced protection against virulent IBV QX challenge 3 weeks later, as assessed by greater motility of tracheal cilia from chickens receiving the recombinants. Nonetheless evidence of AMPV/IBV seroconversion, or major recombinant tracheal replication, were largely absent. url: https://doi.org/10.1016/j.vaccine.2013.03.055 doi: 10.1016/j.vaccine.2013.03.055 id: cord-317587-rrx2r4n2 author: Fan, Wensheng title: Genetic Analysis of Avian Coronavirus Infectious Bronchitis Virus in Yellow Chickens in Southern China over the Past Decade: Revealing the Changes of Genetic Diversity, Dominant Genotypes, and Selection Pressure date: 2019-09-26 words: 9210.0 sentences: 479.0 pages: flesch: 58.0 cache: ./cache/cord-317587-rrx2r4n2.txt txt: ./txt/cord-317587-rrx2r4n2.txt summary: title: Genetic Analysis of Avian Coronavirus Infectious Bronchitis Virus in Yellow Chickens in Southern China over the Past Decade: Revealing the Changes of Genetic Diversity, Dominant Genotypes, and Selection Pressure In conclusion, the IBVs circulating in southern China over the past decade have experienced a remarkable change in genetic diversity, dominant genotypes, and selection pressure, indicating the importance of permanent monitoring of circulating strains and the urgency for developing new vaccines to counteract the emerging LX4-type and New-type IBVs. Infectious bronchitis (IB) is one of the major viral diseases affecting the poultry industry globally. Our results indicated that there was a remarkable change in genetic diversity, dominant genotypes, and selection pressure of IBV strains in southern China over the past decade compared with the previous period of 1985-2007. Molecular characterization of major structural protein genes of avian coronavirus infectious bronchitis virus isolates in southern China abstract: The high mutation rates of infectious bronchitis virus (IBV) pose economic threats to the poultry industry. In order to track the genetic evolutionary of IBV isolates circulating in yellow chickens, we continued to conduct the genetic analyses of the structural genes S1, E, M, and N from 64 IBV isolates in southern China during 2009–2017. The results showed that the dominant genotypes based on the four genes had changed when compared with those during 1985–2008. Based on the S1 gene phylogenetic tree, LX4-type (GI-19) was the most dominant genotype, which was different from that during 1985–2008. The second most dominant genotype was LDT3-A-type, but this genotype disappeared after 2012. New-type 1 (GVI-1) isolates showed increasing tendency and there were four aa (QKEP) located in the hypervariable region (HVR) III and one aa (S) insertion in all the New-type 1 isolates. Both the analyses of amino acid entropy and molecular evolutionary rate revealed that the variations from large to small were S1, E, M, and N. Purifying selection was detected in the S1, E, M, and N gene proteins, which was different from the positive selection during 1985–2008. Six isolates were confirmed to be recombinants, possibly generated from a vaccine virus of the 4/91-type or LDT3-A-type and a circulating virus. The estimated times for the most recent common ancestors based on the S1, E, M, and N genes were the years of 1744, 1893, 1940, and 1945, respectively. Bayesian skyline analysis revealed a sharp decrease in genetic diversity of all the four structural genes after 2010 and since late 2015, the viral population rapidly rose. In conclusion, the IBVs circulating in southern China over the past decade have experienced a remarkable change in genetic diversity, dominant genotypes, and selection pressure, indicating the importance of permanent monitoring of circulating strains and the urgency for developing new vaccines to counteract the emerging LX4-type and New-type IBVs. url: https://www.ncbi.nlm.nih.gov/pubmed/31561498/ doi: 10.3390/v11100898 id: cord-262226-7kwkla73 author: Fang, Shouguo title: Identification of two ATR-dependent phosphorylation sites on coronavirus nucleocapsid protein with nonessential functions in viral replication and infectivity in cultured cells date: 2013-07-09 words: 5629.0 sentences: 277.0 pages: flesch: 51.0 cache: ./cache/cord-262226-7kwkla73.txt txt: ./txt/cord-262226-7kwkla73.txt summary: authors: Fang, Shouguo; Xu, Linghui; Huang, Mei; Qisheng Li, Frank; Liu, D.X. title: Identification of two ATR-dependent phosphorylation sites on coronavirus nucleocapsid protein with nonessential functions in viral replication and infectivity in cultured cells Western blot analysis with antibodies against IBN N and ATM/ATR substrates showed that significantly less phosphorylated IBV N protein was detected in the UV-irradiated, transfected cells in the presence of 10 μM of SchB (Fig. 2d ). The results showed that the ATR-dependent phosphorylation of N protein was detected only in cells infected with wild type, Nm1 and Nm2 mutant viruses (Fig. 4a) . Western blot analysis of total cell lysates with antibodies against ATM/ATR substrates showed, once again, detection of the ATR-dependent phosphorylation of IBV N protein in cells infected with the virus (Fig. 4b) . abstract: Coronavirus encodes an extensively phosphorylated and highly basic nucleocapsid (N) protein. Previous studies have identified Ser190, Ser192, Thr378 and Ser379 as the phosphorylation sites for coronavirus infectious bronchitis virus (IBV) N protein. In this study, we show that phosphorylation at Thr378 and Ser379 sites is dependent on the ataxia-telangiectasia mutated (ATM) and Rad3-related (ATR), a kinase activated during IBV replication. Introduction of Ala substitutions at these two sites individually, in combination of the two and together with other two sites (Ser190 and Ser192) into an infectious IBV clone did not affect recovery of the recombinant viruses containing the mutations. A mutant virus (rIBV-Nm4) carrying the four Ala substitutions grew at a similar, if not better, growth rate as wild type virus. This study reveals a cellular kinase responsible for phosphorylation of a coronavirus N protein at two positions and the functional consequence of this modification on coronavirus replication. url: https://api.elsevier.com/content/article/pii/S0042682213003632 doi: 10.1016/j.virol.2013.06.014 id: cord-266585-jfjrk9gy author: Fang, Shouguo title: An arginine-to-proline mutation in a domain with undefined functions within the helicase protein (Nsp13) is lethal to the coronavirus infectious bronchitis virus in cultured cells date: 2007-02-05 words: 7152.0 sentences: 356.0 pages: flesch: 56.0 cache: ./cache/cord-266585-jfjrk9gy.txt txt: ./txt/cord-266585-jfjrk9gy.txt summary: During construction of an infectious clone from a Vero cell-adapted coronavirus infectious bronchitis virus (IBV), we found that a G–C point mutation at nucleotide position 15526, causing Arg-to-Pro mutation at amino acid position 132 of the helicase protein, is lethal to the infectivity of IBV on Vero cells. Further characterization of the in vitro-synthesized full-length transcripts containing the G15526C mutation demonstrated that this mutation blocks the transcription of subgenomic RNAs. Substitution mutation of the Arg132 residue to a positively charged amino acid (Lys) affected neither the infectivity of the in vitro-synthesized transcripts nor the growth properties of the rescued virus. To further demonstrate that the failure to rescue infectious virus from the G15526C mutant transcripts is due to a defect in subgenomic RNA transcription, the full-length clones with and without the G15526C mutation were used to generate recombinant IBV expressing the enhanced green fluorescent protein (EGFP) by replacing the 5a gene with EGFP. abstract: Genetic manipulation of the RNA genomes by reverse genetics is a powerful tool to study the molecular biology and pathogenesis of RNA viruses. During construction of an infectious clone from a Vero cell-adapted coronavirus infectious bronchitis virus (IBV), we found that a G–C point mutation at nucleotide position 15526, causing Arg-to-Pro mutation at amino acid position 132 of the helicase protein, is lethal to the infectivity of IBV on Vero cells. When the in vitro-synthesized full-length transcripts containing this mutation were introduced into Vero cells, no infectious virus was rescued. Upon correction of the mutation, infectious virus was recovered. Further characterization of the in vitro-synthesized full-length transcripts containing the G15526C mutation demonstrated that this mutation may block the transcription of subgenomic RNAs. Substitution mutation of the Arg132 residue to a positively charged amino acid Lys affected neither the infectivity of the in vitro-synthesized transcripts nor the growth properties of the rescued virus. However, mutation of the Arg132 residue to Leu, a conserved residue in other coronaviruses at the same position, reduced the recovery rate of the in vitro-synthesized transcripts. The recovered mutant virus showed much smaller-sized plaques. On the contrary, a G–C and a G–A point mutations at nucleotide positions 4330 and 9230, respectively, causing Glu–Gln and Gly–Glu mutations in or near the catalytic centers of the papain-like (Nsp3) and 3C-like (Nsp5) proteinases, did not show detectable detrimental effect on the rescue of infectious viruses and the infectivity of the rescued viruses. url: https://api.elsevier.com/content/article/pii/S0042682206005745 doi: 10.1016/j.virol.2006.08.020 id: cord-285942-mb1xwdqw author: Feng, K. Y. title: Molecular characteristic and pathogenicity analysis of a virulent recombinant avain infectious bronchitis virus isolated in China date: 2018-10-01 words: 6873.0 sentences: 318.0 pages: flesch: 59.0 cache: ./cache/cord-285942-mb1xwdqw.txt txt: ./txt/cord-285942-mb1xwdqw.txt summary: Sequence comparison among QY16 and other IBV strains was conducted and its results demonstrate that the S1 gene of QY16 has the highest nucleotide sequence identity with that of 4/91, and the other part of its genome is highly similar to that of YX10. The results of the sequence comparison and phylogenetic analysis show that QY16 has the highest identity with 4/91 in terms of the S1 gene and is located in the 1 10/10 4/10 0/10 0/10 4/7 6/6 6/6 7/7 5/6 3/6 2 9/10 4/10 3/10 9/10 8/8 6/6 6/6 8/8 4/6 2/6 3 4/10 2/10 4/10 10/10 9/9 8/8 8/8 5/9 2/8 1/8 Control 0/10 0/10 0/10 0/10 0/10 0/10 0/10 0/10 0/10 0/10 1 Chickens in groups 2 and 3 were vaccinated with H120 and 4/91 vaccines, respectively, and challenged with QY16. Complete genome sequence analysis of a predominant infectious bronchitis virus (IBV) strain in China Complete genome sequence of a recombinant nephropathogenic infectious bronchitis virus strain in china abstract: ABSTRACT A virulent infectious bronchitis virus (IBV), designated as CK/CH/GD/QY16 (referred as QY16), was isolated from a diseased chicken farm in Guangdong province, China, in 2016. The complete genome of the strain was sequenced and analyzed. The results show that the genome of QY16 consists of 27,670 nucleotides, excluding poly (A) tail, and that its genome organization is 5’ UTR-1a-1b-S-3a-3b-E-M-4b-4c-5a-5b-N-6b-3’ UTR-poly (A) tail. Sequence comparison among QY16 and other IBV strains was conducted and its results demonstrate that the S1 gene of QY16 has the highest nucleotide sequence identity with that of 4/91, and the other part of its genome is highly similar to that of YX10. The results of the phylogenic analysis show that the entire genome of QY16 and most of the QY16 genes are located in the same cluster as those of YX10, except for the S1 gene which is located in the same cluster with that of 4/91. It has been further confirmed by the RDP and SimPlot analysis that QY16 is a recombinant strain deriving from YX10 (as the major parental sequence) and 4/91 (as the minor parental sequence), and that the recombination occurs in a region which includes the 3’-terminal 1b sequence (85 nt) and the 5’-terminal S1 protein gene sequence (1,466 nt). The results of the vaccination-challenge test suggest that QY16 is a nephropathogenic strain of IBV and that the vaccine strains–H120 and 4/91—cannot provide effective protection against it. These results indicate that the continuing evolution of IBV strains by genetic drift and genetic recombination may lead to IBV outbreaks even among the vaccinated chickens in China. url: https://doi.org/10.3382/ps/pey237 doi: 10.3382/ps/pey237 id: cord-310536-u30cufg7 author: Finger, Paula Fonseca title: Combined use of ELISA and Western blot with recombinant N protein is a powerful tool for the immunodiagnosis of avian infectious bronchitis date: 2018-12-12 words: 4663.0 sentences: 242.0 pages: flesch: 52.0 cache: ./cache/cord-310536-u30cufg7.txt txt: ./txt/cord-310536-u30cufg7.txt summary: title: Combined use of ELISA and Western blot with recombinant N protein is a powerful tool for the immunodiagnosis of avian infectious bronchitis This study examined the combined use of an ELISA and Western blot (WB) to detect antibodies against the nucleocapsid protein (N) of IBV. Serum samples scored as negative with the commercial kit but as positive with the ELISA-rN were further analysed by Western blot analyses using the rN protein as an antigen. The aim of the current study was to evaluate the combined use of an ELISA and Western blot (WB) to detect antibodies against the nucleocapsid protein of IBV. Recombinant nucleocapsid protein based single serum dilution ELISA for the detection of antibodies to infectious bronchitis virus in poultry Development of a multiepitope antigen of S protein-based ELISA for antibodies detection against infectious bronchitis virus abstract: BACKGROUND: The avian infectious bronchitis virus (IBV) remains a significant source of loss in the poultry industry and early diagnosis is required to prevent the disease from spreading. This study examined the combined use of an ELISA and Western blot (WB) to detect antibodies against the nucleocapsid protein (N) of IBV. The coding sequence for N was amplified by RT-PCR and expressed in Escherichia coli. A soluble recombinant N protein (rN) of approximately 50 kDa was obtained. A total of 389 sera were tested against the rN in ELISA and the results were compared with those of the commercial IDEXX IBV Ab test. ELISA-rN achieved a 90.34% sensitivity and 90.16% specificity. WB confirmed all false negative sera in ELISA-rN or IDEXX test as truly positive. The current study indicate that the combined use of rN in ELISA and WB is a powerful tool for the immunodiagnosis of avian infectious bronchitis. METHODS: Constructed recombinant pAE/n expression vectors were used to transform E. coli BL21(DE3) Star competent cells (Invitrogen). The rN of infectious bronchitis virus was purified by affinity chromatography using HisTrap HP 1 mL columns pre-packed with pre-charged Ni Sepharose in the ÄKTAprime Automated Liquid Chromatography system (GE Healthcare). A total of 389 serum samples from chickens were used to develop and evaluate the ELISA-rN test. To standardize the indirect ELISA development, serum dilutions (1:100, 1:200 and 1:400) and different concentrations of purified rN antigen (50, 100 and 200 ng/well) were tested. Positive and negative sera for IBV were used as controls. The results were compared with those obtained from a commercial kit. Serum samples scored as negative with the commercial kit but as positive with the ELISA-rN were further analysed by Western blot analyses using the rN protein as an antigen. The results of the ELISA-rN were compared to the commercial kit results using receiver-operating characteristics curves, area under the curve, and confidence intervals with the software GraphPad Prism version 6.0 for Windows (GraphPad Software, USA). RESULTS: The expected cDNA fragment of approximately 1240 bp was successfully amplified by PCR using primers designed to select for the coding region of the N protein. The rN was expressed as a soluble protein to avoid the refolding steps and, after purification a yield of 10 mg/L of rN was obtained. The SDS-PAGE results demonstrated the presence of two distinct bands that had a molecular mass of approximately 45 and 50 KDa. Out of 244 sera that scored positive in the commercial ELISA IDEXX IBV Ab Test, 220 were also positive in the ELISA-rN, yielding an ELISA-rN test sensitivity of 90.16%. Out of 145 sera that scored negative in the IDEXX IBV Ab Test, 131 also scored negative in the ELISA-rN, indicating a specificity of 90.34%. Sera that tested negative in the ELISA-rN and positive in the commercial test also reacted with the rN protein in Western blot. CONCLUSIONS: The association between the ELISA and Western blot techniques developed in this study with a subunit of IBV (rN) were able to detect antibodies that the commercial ELISA did not detect suggesting that the ELISA-rN has greater sensitivity. url: https://doi.org/10.1186/s12985-018-1096-2 doi: 10.1186/s12985-018-1096-2 id: cord-330057-3vucm0s1 author: Franzo, Giovanni title: Phylodynamic analysis and evaluation of the balance between anthropic and environmental factors affecting IBV spreading among Italian poultry farms date: 2020-04-29 words: 5537.0 sentences: 280.0 pages: flesch: 40.0 cache: ./cache/cord-330057-3vucm0s1.txt txt: ./txt/cord-330057-3vucm0s1.txt summary: In the present study, 361 IBV QX (the most relevant field genotype in Italy) sequences were obtained between 2012 and 2016 from the two main Italian integrated poultry companies. Finally, the different viral population pattern observed in the two companies over the same time period supports the pivotal role of management and control strategies on IBV epidemiology. Almost identical results were obtained including a third "ghost" deme (i.e. an estimated deme for which no sequences were available, representative of other unsampled companies and farms) in the analysis or using the "traditional" coalescent approach. In the particular Italian QX scenario, the serially sampled (i.e. with known collection date) strains were used to infer the migration rate and history between the two integrated poultry companies (i.e. considered as different demes) over time. abstract: Infectious bronchitis virus (IBV) control is mainly based on wide vaccine administration. Although effective, its efficacy is not absolute, the viral circulation is not prevented and some side effects cannot be denied. Despite this, the determinants of IBV epidemiology and the factors affecting its circulation are still largely unknown and poorly investigated. In the present study, 361 IBV QX (the most relevant field genotype in Italy) sequences were obtained between 2012 and 2016 from the two main Italian integrated poultry companies. Several biostatistical and bioinformatics approaches were used to reconstruct the history of the QX genotype in Italy and to assess the effect of different environmental, climatic and social factors on its spreading patterns. Moreover, two structured coalescent models were considered in order to investigate if an actual compartmentalization occurs between the two integrated poultry companies and the role of a third “ghost” deme, representative of minor industrial poultry companies and the rural sector. The obtained results suggest that the integration of the poultry companies is an effective barrier against IBV spreading, since the strains sampled from the two companies formed two essentially-independent clades. Remarkably, the only exceptions were represented by farms located in the high densely populated poultry area of Northern Italy. The inclusion of a third deme in the model revealed the likely role of other poultry companies and rural farms (particularly concentrated in Northern Italy) as sources of strain introduction into one of the major poultry companies, whose farms are mainly located in the high densely populated poultry area of Northern Italy. Accordingly, when the effect of different environmental and urban parameters on IBV geographic spreading was investigated, no factor seems to contribute to IBV dispersal velocity, being poultry population density the only exception. Finally, the different viral population pattern observed in the two companies over the same time period supports the pivotal role of management and control strategies on IBV epidemiology. Overall, the present study results stress the crucial relevance of human action rather than environmental factors, highlighting the direct benefits that could derive from improved management and organization of the poultry sector on a larger scale. url: https://doi.org/10.1038/s41598-020-64477-4 doi: 10.1038/s41598-020-64477-4 id: cord-009487-7xb4huyz author: GODWIN, IR title: Simple rapid method of rumen cannulation date: 2008-03-10 words: 1299.0 sentences: 80.0 pages: flesch: 63.0 cache: ./cache/cord-009487-7xb4huyz.txt txt: ./txt/cord-009487-7xb4huyz.txt summary: Previous methods of rumen cannulation in sheep have involved 2-stage operations in which the rumen is sutured to the skin, through dissected abdominal muscles, and then several days later an incision is made through the skin and rumen wall to form a permanent fistula, and a cannula fitted (Jarrett 1948 Hecker (1969) adapted a method previously used for cattle (Balch and Cowie 1962) . A siplple one-stage operation, requiring no suturing of the rumen''wall and an incision smaller than the neck of the Australian Veterinary Journal, Vol. 65, NO. We report the isolation of IBV from a flock of racing pigeons and assess its significance. Four 4-week-old CSIRO SPF chickens and four 8-week-old meat pigeons that were housed in the same cage were each inoculated by intranasal, intraocular and oral routes with allantoic fluid containing 10'' EID,, of IBV. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7159126/ doi: 10.1111/j.1751-0813.1988.tb14467.x id: cord-273846-l0elcfe8 author: Ganapathy, Kannan title: Effects of cold storage on detection of avian infectious bronchitis virus in chicken carcasses and local antibodies in tracheal washes date: 2005-02-24 words: 2440.0 sentences: 134.0 pages: flesch: 59.0 cache: ./cache/cord-273846-l0elcfe8.txt txt: ./txt/cord-273846-l0elcfe8.txt summary: title: Effects of cold storage on detection of avian infectious bronchitis virus in chicken carcasses and local antibodies in tracheal washes In order to test the survivability of infectious bronchitis virus (IBV) in dead chicken carcasses during 24 h of cold storage, 7 week-old specific-pathogen-free chickens were infected with virulent IBV Massachusetts strain M41, and were killed humanely 10 days later. Trachea, lung, kidney and rectum were collected for virus isolation by tracheal organ culture (TOC) or embryonated chicken eggs (ECE), and detection by nested reverse-transcriptase polymerase chain reaction (RT-PCR). Diagnosis of infectious bronchitis virus (IBV) is confirmed by isolation of the virus using either chicken embryonated eggs (ECE) or tracheal organ culture (TOC) and detection by reverse-transcriptase polymerase chain reaction (RT-PCR) (Cavanagh and Naqi, 2003; Gelb and Jackwood, 1998) . The use of chicken tracheal organ cultures for the isolation and assay of avian infectious bronchitis virus abstract: In order to test the survivability of infectious bronchitis virus (IBV) in dead chicken carcasses during 24 h of cold storage, 7 week-old specific-pathogen-free chickens were infected with virulent IBV Massachusetts strain M41, and were killed humanely 10 days later. Carcasses were stored in a cold room at 4 °C. After 1, 3, 6, 9, 12 or 24 h of storage, necropsies were carried out. Trachea, lung, kidney and rectum were collected for virus isolation by tracheal organ culture (TOC) or embryonated chicken eggs (ECE), and detection by nested reverse-transcriptase polymerase chain reaction (RT-PCR). IBV was detected by RT-PCR at all sampling times, except for 1 and 6 h of storage in kidney and 9 h of storage in kidney and rectum. For ECE, isolation was obtained at all sampling points, except at 1 and 24 h of storage in lungs. Isolation by tracheal organ cultures was less successful, except from rectum. In addition to sampling for virus, tracheal washes were collected from each carcass to measure the ability to detect local antibodies after storage. Levels of IgA in tracheal washes remained high for up to 9 h of storage, suggesting that accurate sampling for research purposes when required must be carried out within this time. url: https://www.ncbi.nlm.nih.gov/pubmed/15847923/ doi: 10.1016/j.jviromet.2005.01.024 id: cord-306976-p2521bl4 author: Gao, Mengying title: Serotype, antigenicity, and pathogenicity of a naturally recombinant TW I genotype infectious bronchitis coronavirus in China date: 2016-08-15 words: 5087.0 sentences: 232.0 pages: flesch: 57.0 cache: ./cache/cord-306976-p2521bl4.txt txt: ./txt/cord-306976-p2521bl4.txt summary: Furthermore, neither the vaccine strains nor the attenuated viruses could provide complete respiratory protection of chickens against a challenge with the ck/CH/LDL/140520 strain, indicating that it is necessary to develop new live vaccines or to evaluate the use of established vaccines in combination to control naturally recombinant TW I-type IBV strains in the future. Our results showed that strain ck/CH/LDL/140520 is very pathogenic, and that it is able to cause cystic oviducts in a high percentage of birds, as well as mortality due to nephritis and respiratory distress with complete tracheal ciliostasis, especially in chickens infected at 1 day of age. In contrast, respiratory signs (sneezing, nasal discharge, and tracheal rales) developed at 3-4 dpc and lasted until 10 dpc in some of the chickens in the groups that were vaccinated with the H120, 4/91, and Conn vaccines, and the attenuated LSD/120720 and LGX/ 100508 viruses when challenged with the nrTW I IBV strain at 20 days of age. abstract: Since 2009, strains of the naturally recombinant TW I genotype of infectious bronchitis virus (IBV) have caused considerable damage to the Chinese poultry industry. To better understand the antigenicity and pathogenesis of this genotype, the characteristics of the ck/CH/LDL/140520 strain were compared to those of four commercial IB vaccine strains that are used commonly in China, as well as four attenuated viruses that represent two types of IBV strains, which are believed to have originated in China and are the predominant IBV types circulating in chicken flocks in China and many other parts of the world. The results showed that all eight strains were genetically and serotypically different from the strain ck/CH/LDL/140520. Furthermore, neither the vaccine strains nor the attenuated viruses could provide complete respiratory protection of chickens against a challenge with the ck/CH/LDL/140520 strain, indicating that it is necessary to develop new live vaccines or to evaluate the use of established vaccines in combination to control naturally recombinant TW I-type IBV strains in the future. Our results showed that strain ck/CH/LDL/140520 is very pathogenic, and that it is able to cause cystic oviducts in a high percentage of birds, as well as mortality due to nephritis and respiratory distress with complete tracheal ciliostasis, especially in chickens infected at 1 day of age. url: https://doi.org/10.1016/j.vetmic.2016.05.018 doi: 10.1016/j.vetmic.2016.05.018 id: cord-286473-sl5zy8nj author: Gomaa, M.H. title: Complete genomic sequence of turkey coronavirus date: 2008-05-12 words: 7980.0 sentences: 411.0 pages: flesch: 61.0 cache: ./cache/cord-286473-sl5zy8nj.txt txt: ./txt/cord-286473-sl5zy8nj.txt summary: Turkey coronavirus (TCoV), one of the least characterized of all known coronaviruses, was isolated from an outbreak of acute enteritis in young turkeys in Ontario, Canada, and the full-length genomic sequence was determined. The RdRp motif was highly conserved among all coronaviruses, and TCoV-MG10 also showed a high degree of sequence identity for RdRp by 64%, 62%, 94% at the amino acid level to HCoV-229E, BCoV, IBV, respectively. The M gene seemed to be highly conserved within group III coronaviruses since TCoV M showed a 94% nucleotide identity to IBV M. This ORF is unique to TCoV and IBV, the only Group III coronaviruses for which sequence data in this region of the genome are available. In addition, we have identified a putatively functional gene (ORF-X) shared among all sequenced IBV and TCoV strains that may be a shared feature of all group III coronaviruses. abstract: Turkey coronavirus (TCoV), one of the least characterized of all known coronaviruses, was isolated from an outbreak of acute enteritis in young turkeys in Ontario, Canada, and the full-length genomic sequence was determined. The full-length genome was 27,632 nucleotides plus the 3′ poly(A) tail. Two open reading frames, ORFs 1a and 1b, resided in the first two thirds of the genome, and nine additional downstream ORFs were identified. A gene for hemagglutinin-esterase was absent in TCoV. The region between the membrane (M) and nucleocapsid (N) protein genes contained three potential small ORFs: ORF-X, a previously uncharacterized ORF with an associated putative TRS within the M gene (apparently shared among all group III coronaviruses), and previously described ORFs 5a and 5b. The TCoV genome is organized as follows: 5′ UTR – replicase (ORFs 1a, 1b) – spike (S) protein – ORF3 (ORFs 3a, 3b) – small envelop (E or 3c) protein – membrane (M) protein – ORF5 (ORFs X, 5a, 5b) – nucleocapsid (N) protein −3′ UTR – poly(A). TCoV genome structure and sequence was most similar, but distinct from, avian infectious bronchitis virus (IBV). This is the first complete genome sequence for a TCoV and confirms that TCoV belongs to group III coronaviruses. url: https://api.elsevier.com/content/article/pii/S0168170208001317 doi: 10.1016/j.virusres.2008.03.020 id: cord-341541-3l6tjf3t author: Hajijafari Anaraki, Mozafar title: Molecular characterization of infectious bronchitis virus based on RNA‐dependent RNA polymerase gene date: 2020-05-26 words: 1276.0 sentences: 87.0 pages: flesch: 49.0 cache: ./cache/cord-341541-3l6tjf3t.txt txt: ./txt/cord-341541-3l6tjf3t.txt summary: title: Molecular characterization of infectious bronchitis virus based on RNA‐dependent RNA polymerase gene Extensive rate of variations in in spike glycoprotein subunit gene of infectious bronchitis virus (IBV) caused challenges for counting variants for differentiation of infected from vaccinated birds and addressing the variants of unknown significance. The study aimed at investigating the possibility use of RNA‐dependent RNA polymerase gene (RdRp) as a target for molecular characterization of IBV strains in Iran. Phylogenetic analysis of RdRp gene sequences resulted in clustering the IBV strains related to each area. Using RdRp, as a genetic marker eliminates the challenges arise from the enormous variations that making difficult the discrimination between field and vaccine strains as well as affiliation of certain variants to various geographical areas. Based on the RT-PCR detection and sequence analysis of IBV RdRp gene, an overall prevalence of field strains estimated as 44.2%. abstract: Extensive rate of variations in in spike glycoprotein subunit gene of infectious bronchitis virus (IBV) caused challenges for counting variants for differentiation of infected from vaccinated birds and addressing the variants of unknown significance. The study aimed at investigating the possibility use of RNA‐dependent RNA polymerase gene (RdRp) as a target for molecular characterization of IBV strains in Iran. Samples collected from commercial broiler flocks (n= 52) showing respiratory syndrome. Specific polymerase chain reaction (PCR) primers were designed for a variable region locates in RdRp gene, flanked by highly conserved regions. Reverse transcriptase PCR (RT‐PCR) followed by sequencing and sequence analysis could identified 8 IBV variants in an overall prevalence of 44.2%. Deduced nucleotide and amino acid sequences were compared with published sequences for IBV strains. Due to the long‐distance similarities, the field samples could be discriminated from vaccine strains. Phylogenetic analysis of RdRp gene sequences resulted in clustering the IBV strains related to each area. Using RdRp, as a genetic marker eliminates the challenges arise from the enormous variations that making difficult the discrimination between field and vaccine strains as well as affiliation of certain variants to various geographical areas. This article is protected by copyright. All rights reserved. url: https://doi.org/10.1111/1348-0421.12825 doi: 10.1111/1348-0421.12825 id: cord-309623-2ngr682l author: Han, Xiaoxiao title: Infectious Bronchitis Virus Infection Induces Apoptosis during Replication in Chicken Macrophage HD11 Cells date: 2017-07-26 words: 5618.0 sentences: 317.0 pages: flesch: 46.0 cache: ./cache/cord-309623-2ngr682l.txt txt: ./txt/cord-309623-2ngr682l.txt summary: Previous studies have reported that infectious bronchitis virus (IBV) infection can produce cytopathic effects (CPE) and apoptosis in some mammalian cells and primary cells. The Beaudette strains were used previously to study the resistance of IBV to the antiviral state induced by type I interferon (IFN) [7] , induction of apoptosis through endoplasmic reticulum stress in Vero cells by IBV infection [8] and activate autophagy by IBV nonstructural protein (NSP) 6 [9] . The rate of apoptosis significantly increased at 12 h.p.i. in virus-infected cells when compared with the mockInfection of HD11 cells with IBV Beaudette caused cell death in a time-and dose-dependent manner, as tested by CCK-8 assay. The results also showed that activation of caspase-9 in IBV Beaudette-infected cells was regulated by decreased expression of Bcl-2 and increased expression of Bax. The caspase-3 activation and virus-induced apoptosis might be triggered through both extrinsic and intrinsic pathways. abstract: Avian infectious bronchitis has caused huge economic losses in the poultry industry. Previous studies have reported that infectious bronchitis virus (IBV) infection can produce cytopathic effects (CPE) and apoptosis in some mammalian cells and primary cells. However, there is little research on IBV-induced immune cell apoptosis. In this study, chicken macrophage HD11 cells were established as a cellular model that is permissive to IBV infection. Then, IBV-induced apoptosis was observed through a cell viability assay, morphological changes, and flow cytometry. The activity of caspases, the inhibitory efficacy of caspase-inhibitors and the expression of apoptotic genes further suggested the activation of apoptosis through both intrinsic and extrinsic pathways in IBV-infected HD11 cells. Additionally, ammonium chloride (NH(4)Cl) pretreated HD11 cells blocked IBV from entering cells and inhibited IBV-induced apoptosis. UV-inactivated IBV also lost the ability of apoptosis induction. IBV replication was increased by blocking caspase activation. This study presents a chicken macrophage cell line that will enable further analysis of IBV infection and offers novel insights into the mechanisms of IBV-induced apoptosis in immune cells. url: https://www.ncbi.nlm.nih.gov/pubmed/28933760/ doi: 10.3390/v9080198 id: cord-303794-fn3jkiil author: Hassan, Kareem E. title: Experimental co-infection of infectious bronchitis and low pathogenic avian influenza H9N2 viruses in commercial broiler chickens date: 2017-06-30 words: 3787.0 sentences: 202.0 pages: flesch: 52.0 cache: ./cache/cord-303794-fn3jkiil.txt txt: ./txt/cord-303794-fn3jkiil.txt summary: title: Experimental co-infection of infectious bronchitis and low pathogenic avian influenza H9N2 viruses in commercial broiler chickens Avian influenza H9N2 and H5N1 subtypes, Infectious bronchitis virus (IBV), and virulent Newcastle disease virus (vNDV) have been frequently isolated from different broiler chicken flocks (Hassan et al., 2016) . Experimentally infected commercial broilers with classical and variant IBV and vaccine IBV strains in presence or absence of AIV-H9N2N2 infection were monitored for clinical outcomes, virus shedding, postmortem and histopathological lesions. Histopathologically, trachea in all mixed infection groups including the AIV-H9N2 with vaccine IBV strain showed severe changes comparable to the milder changes in single classical or variant IBV challenged groups (Purcell et al., 1976) . Similarly, in this study, significant increases of AIV-H9N2 virus shedding with classical IBV infection especially at 2 and 5 DPI and with the variant and vaccine IBV strains co-infections up to 7 DPI were observed. abstract: In this study, commercial broilers were experimentally infected with single (classical IBV, variant IBV or AIV-H9N2) or mixed AIV-H9N2 with classical, variant or vaccine strains of IBV. Birds were monitored for clinical and pathological outcomes and virus shedding for 10 days post infection (DPI). Clinical signs were limited to the respiratory tract in all challenged groups and varied from mild to moderate mouth breathing to severe respiratory signs with snorting sound and extended head. Mortalities were only recorded in mixed AIV-H9N2/variant IBV challenge group. AIV-H9N2 challenge caused tracheal petechial hemorrhage that progressed to tracheal congestion and caseation. In mixed AIV-H9N2/IBV vaccine challenge, severe tracheitis with bronchial cast formation was observed. In mixed AIV-H9N2/variant IBV challenge severe congestion of the tracheal mucosa and excessive exudates with a tendency to form tubular casts were observed. Kidney ureate deposition was only observed in variant IBV challenge group. Histopathologically, tracheal congestion, severe degeneration, and deciliation were noticed in all groups of mixed infection. Interestingly, hemorrhage and atrophy were observed in thymus gland of birds challenged with single AIV-H9N2 or mixed AIV-H9N2/IBV. There was no difference in the tracheal shedding level of variant IBV between single and mixed infected groups while classical IBV shedding increased in mixed infection group. Interestingly, the AIV-H9N2 showed constantly high shedding titers till 7DPI with variant or vaccine IBV co-infection. In conclusion, co-infection of IBV and AIV-H9N2 induced severe clinical outcome and high mortality. Also, IBV co-infection increased the shedding of AIV-H9N2 in experimentally infected birds. url: https://api.elsevier.com/content/article/pii/S003452881730022X doi: 10.1016/j.rvsc.2017.06.024 id: cord-300104-855iw9wi author: Hennion, Ruth M. title: The Preparation of Chicken Kidney Cell Cultures for Virus Propagation date: 2014-12-18 words: 1487.0 sentences: 112.0 pages: flesch: 76.0 cache: ./cache/cord-300104-855iw9wi.txt txt: ./txt/cord-300104-855iw9wi.txt summary: Chicken kidney (CK) cell cultures have historically proved useful for the assay of a number of viruses including coronaviruses. A technique for the preparation of such cell cultures, using a combination of manual and trypsin disaggregation of kidneys dissected from 2to 3-week-old birds is described. When all the kidneys required have been removed from the birds, agitate them in the beaker and discard the PBSa. Repeat this process until the wash PBSa looks clear ( see Note 6 ). 5. Dilute cell suspension in growth medium to the cell concentration required, seed culture fl asks and place in incubator until intact monolayer forms ( see Note 10 ). 6. Whilst some kidney cells may be lost in this process, it is an effective way of removing many of the red blood cells that are still present at this stage of the preparation. abstract: Chicken kidney (CK) cell cultures have historically proved useful for the assay of a number of viruses including coronaviruses. A technique for the preparation of such cell cultures, using a combination of manual and trypsin disaggregation of kidneys dissected from 2- to 3-week-old birds is described. This technique routinely gives high cell yield together with high viability and the resultant adherent primary cultures can be used for virus growth and plaque formation. url: https://www.ncbi.nlm.nih.gov/pubmed/25720471/ doi: 10.1007/978-1-4939-2438-7_6 id: cord-346516-lal35iyr author: Hughes, Laura A. title: Genetically Diverse Coronaviruses in Wild Bird Populations of Northern England date: 2009-07-17 words: 1490.0 sentences: 91.0 pages: flesch: 51.0 cache: ./cache/cord-346516-lal35iyr.txt txt: ./txt/cord-346516-lal35iyr.txt summary: Coronavirus RNA was detected in 7 fecal sample pools (Table 2) , giving an individual animal-level prevalence estimate of 1.6% (95% confidence interval 0.7-3.1). Phylogenetic analysis showed that coronavirus sequences detected by this study were genetically diverse. Virus sequences from 3 pools of fecal samples from ducks and whooper swans shared high nucleotide sequence identity with sequence from the IBV H120 vaccine strain, which is commonly used for the vaccination of commercial chickens worldwide. These viIt would be useful to determine the number and genome position of accessory genes of the coronaviruses detected in wild birds and to compare them with those of IBV. Minimum-evolution tree (11) of coronaviruses based on a 146-bp fragment of the 3′ untranslated region of infectious bronchitis virus (IBV). Detection of a coronavirus from turkey poults in Europe genetically related to infectious bronchitis virus of chickens abstract: Infectious bronchitis virus (IBV) causes a costly respiratory viral disease of chickens. The role of wild birds in the epidemiology of IBV is poorly understood. We detected diverse coronaviruses by PCR in wildfowl and wading birds in England. Sequence analysis showed some viruses to be related to IBV. url: https://doi.org/10.3201/eid1507.090067 doi: 10.3201/eid1507.090067 id: cord-271568-qgpi2kcs author: Jackwood, M.W. title: Avian coronavirus infectious bronchitis virus susceptibility to botanical oleoresins and essential oils in vitro and in vivo date: 2010-01-21 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Anti-coronaviral activity of a mixture of oleoresins and essential oils from botanicals, designated QR448(a), was examined in vitro and in vivo. Treatment of avian infectious bronchitis virus (IBV) with QR448(a) reduced the virus titer as measured in two laboratory host systems, Vero E6 cells and embryonating eggs. The effect of QR448(a) on IBV in chickens was also investigated. Administering QR448(a) to chickens at a 1:20 dilution by spray, 2 h before challenge with IBV was determined to be the most effective treatment. Treatment decreased the severity of clinical signs and lesions in the birds, and lowered the amount of viral RNA in the trachea. Treatment with QR448(a) protected chickens for up to 4 days post-treatment from clinical signs of disease (but not from infection) and decreased transmission of IBV over a 14-day period. Anti-IBV activity of QR448(a) was greater prior to virus attachment and entry indicating that the effect is virucidal. In addition, QR448(a) had activity against both Massachusetts and Arkansas type IB viruses, indicating that it can be expected to be effective against IBV regardless of serotype. To our knowledge, this is the first report on the in vivo use of a virucidal mixture of compounds effective against the coronavirus IBV. url: https://doi.org/10.1016/j.virusres.2010.01.006 doi: 10.1016/j.virusres.2010.01.006 id: cord-285323-473d7zvg author: Jang, Hyesun title: Altered pro-inflammatory cytokine mRNA levels in chickens infected with infectious bronchitis virus date: 2013-09-01 words: 4802.0 sentences: 228.0 pages: flesch: 49.0 cache: ./cache/cord-285323-473d7zvg.txt txt: ./txt/cord-285323-473d7zvg.txt summary: The KIIa genotype (Kr/ADL110002/2011) induced clinical signs accompanied by the excessive production of pro-inflammatory cytokines and a higher viral load. In chickens infected with this isolate, simultaneous peaks in the viral copy number and cytokine production were observed at 7 dpi in the trachea and 9 d postinoculation in the kidney. In chickens infected with this isolate, simultaneous peaks in the viral copy number and cytokine production were observed at 7 dpi in the trachea and 9 d postinoculation in the kidney. In this study, we observed changes in the transcriptional levels of 3 pro-inflammatory cytokines that are known to be involved in the innate immune response in chickens (Hong et al., 2006; Davison et al., 2008) after inoculation with 2 IB isolates. On the other hand, an active infection of the ChVI genotype isolate kr/ADL120003/2012, which resulted in an increase in serum AGP level at 9 dpi (Table 3) , evoked only a limited range of pro-inflammatory responses. abstract: Infectious bronchitis virus (IBV) replicates primarily in the respiratory tract and grows in various organs in chickens, with or without pathological effects. The diversity of this virus has been verified by sequence analysis of the S1 glycoprotein gene, but this method must be supplemented with further analysis for characterization of the agent. To increase our understanding of the pathogenesis of the disease caused by this virus, we investigated the response of chickens to 2 IBV with different genotypes, KIIa and ChVI. The clinical signs induced by the viruses were observed. In addition, the mRNA levels of the pro-inflammatory cytokines, IL-6, IL-1β, and lipopolysaccharide-induced tumor necrosis factor-α factor and the serum levels of α(1)-acid glycoprotein, which is a major acute phase protein, were measured. The KIIa genotype (Kr/ADL110002/2011) induced clinical signs accompanied by the excessive production of pro-inflammatory cytokines and a higher viral load. In chickens infected with this isolate, simultaneous peaks in the viral copy number and cytokine production were observed at 7 dpi in the trachea and 9 d postinoculation in the kidney. On the other hand, the chickens infected with the ChVI genotype (Kr/ADL120003/2012) did not show a response other than a mild upregulation of cytokines at 1 d postinoculation, which appears to indicate the invasion of the virus. In summary, we confirmed a differential innate response following infection with distinct IBV. We hypothesize that an excessive innate response contributes to the scale of the pathophysiologic effect in chickens. url: https://api.elsevier.com/content/article/pii/S0032579119394404 doi: 10.3382/ps.2013-03116 id: cord-310372-qc6941pm author: Ji, Jun title: Phylogenetic distribution and predominant genotype of the avian infectious bronchitis virus in China during 2008-2009 date: 2011-04-22 words: 3554.0 sentences: 169.0 pages: flesch: 47.0 cache: ./cache/cord-310372-qc6941pm.txt txt: ./txt/cord-310372-qc6941pm.txt summary: The genetic characterization of recent IBV field isolates in China was performed by sequencing the whole S1 genes, sequence alignment and phylogenetic analysis compared with other reference strains. The results of virus recovery in chicks indicated 87.5% (70/80) isolates caused serious kidney lesions, which were presented with swollen specked kidney and distended ureters filled with uric acid were nephropathogenic type, and the other ten isolates in the study caused respiratory system signs, which were consistent with the clinical record of each strain (Table 1) . In the present study, nucleotide and derived amino acid sequences of S1 protein genes of the 80 field strains were aligned and compared to the representative strains, to determine the relationship of circulating field isolates, vaccine strains and previously described variant strains. Isolation and genetic analysis revealed no predominant new strains of avian infectious bronchitis virus circulating in South China during abstract: BACKGROUND: The nephropathogenic avian infectious bronchitis (IB) caused unprecedented economic losses to the commercial chicken industry of China in 2008-2009. To investigate the prevalence of nephropathogenic IB in China, eighty IBV isolates from different provinces during 2008-2009 were identified by dwarf embryo test and RT-PCR. RESULTS: The strains were mostly isolated in winter and spring with a wide age range of IB outbreaks, from 4 to 69 days. By the virus recovery trials, 70/80 of the strains resulted in the deaths or distresses of birds from nephritis. To learn more about the molecular evolutionary characteristics of the circulating field strains, the coding region of major spike 1 (S1) protein gene of these strains was RT-PCR amplified and sequenced. Compared to the published representative strains, nucleotides and amino acids sequence analysis indicated that the S1 genes of these strains and the reference strains displayed homologies ranging from 75.1% to 99.8% and from 73.1% to 99.8% respectively. S1 protein of the major pandemic strains contained 540 or 542 amino acids with the cleavage site of HRRRR or RRFRR. Phylogenetic analysis revealed that recent field isolates of IBV in China were mostly belonged to A2-branch (QXIBV-branch) and HN08-branch, only one isolate was belonged to Gray-branch and M41-branch respectively. Most of the 80 strains showed evolutionarily distant from vaccine strains. CONCLUSIONS: The results of this study suggested that nephropathogenic IBVs were mainly A2-like strains in China during 2008-2009. url: https://doi.org/10.1186/1743-422x-8-184 doi: 10.1186/1743-422x-8-184 id: cord-316153-wet0go35 author: Jia, W. title: A novel variant of avian infectious bronchitis virus resulting from recombination among three different strains date: 1995 words: 3917.0 sentences: 232.0 pages: flesch: 61.0 cache: ./cache/cord-316153-wet0go35.txt txt: ./txt/cord-316153-wet0go35.txt summary: An antigenic variant of avian infectious bronchitis virus (IBV), a coronavirus, was isolated and characterized. Therefore, several recently reported diagnostic and serotyping methods of IBV which are based on dot-blot hybridization, restriction fragment length polymorphism (RFLP), and polymerase chain reaction (PCR), may not reveal the true antigenic and/or genetic nature of IBV isolates, and may in fact yield misleading information. More recently, two American field isolates were found to contain fragments of Mass-like sequences in the S1 gene, which were 94% to 95% homologous to IBV strain Mass41 [38] . Sequence data were obtained from cDNA clones, except for the first 1100 bases of the S gene, the last 200 bases of the N gene, the 3'' end non-coding region of CU-T2, and the partial Gene3 of Ark99 and Ho1152, which were obtained from direct sequencing of IBV genomic RNA. Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus abstract: An antigenic variant of avian infectious bronchitis virus (IBV), a coronavirus, was isolated and characterized. This strain, CU-T2, possesses a number of unusual features, which have not been previously observed in IBV. The S1 glycoprotein of CU-T2 carries virus-neutralizing and serotype-specific epitopes of two IBV serotypes, Arkansas (Ark) and Massachusetts (Mass). Sequence analysis revealed that the virus, originally an Ark serotype, has acquired the Mass-specific epitope by mutation(s). This provides evidence that point mutations may lead to generation of IBV antigenic variants in the field. It was further observed that two independent recombination events involving three different IBV strains had occurred in the S2 glycoprotein gene and N protein gene of CU-T2, indicating that genomic RNA recombination in IBV may occur in multiple genes in nature. It was especially significant that a sequence of Holland 52 (a vaccine strain) had replaced half of the N gene of CU-T2. This proves that recombination among vaccine strains is contributing to the generation of IBV variants in the field. Based on these observations it is predicted that every IBV field isolate could have unique genetic nature. Therefore, several recently reported diagnostic and serotyping methods of IBV which are based on dot-blot hybridization, restriction fragment length polymorphism (RFLP), and polymerase chain reaction (PCR), may not reveal the true antigenic and/or genetic nature of IBV isolates, and may in fact yield misleading information. url: https://www.ncbi.nlm.nih.gov/pubmed/7710354/ doi: 10.1007/bf01309861 id: cord-286658-9kco7qad author: Jiang, Lei title: Characterization of the complete genome, antigenicity, pathogenicity, tissue tropism, and shedding of a recombinant avian infectious bronchitis virus with a ck/CH/LJL/140901-like backbone and an S2 fragment from a 4/91-like virus date: 2018-01-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: In this study, we isolated an infectious bronchitis virus, designated I1101/16, from broiler breeders in China. Analysis of the S1 gene showed that isolate I1101/16 was genetically close to strain ck/CH/LJL/140901, which belongs to the TW I genotype (also known as lineage GI-7 based on the recent IBV classification), however the S2 gene showed genetic diversity comparing to that of S1 gene. Comparison of the genomic sequences showed that the genome of isolate I1101/16 was similar to that of strain ck/CH/LJL/140901 from the 5′ end of the genome to the 5′ end of the S2 gene and from the 5′ end of the 3a gene to the end of the genome, whereas the remaining parts of the genome sequences were more closely related to those of strain 4/91 than those of ck/CH/LJL/140901, thereby suggesting that recombination might have occurred during the origin of the virus. SimPlot and Bootscan analysis of the complete genomic sequence confirmed this hypothesis, where it showed that isolate I1101/16 arose through recombination events between ck/CH/LJL/140901- and 4/91-like viruses. Isolate I1101/16 and strain ck/CH/LJL/140901 shared identical amino acids in almost all five of their B cell epitopes, but the two viruses had a serotype relatedness value of 65, which is well below 80, i.e., the lower cutoff value for viruses of the same serotype. In addition, pathogenicity tests demonstrated that isolate I1101/16 was more pathogenic to 1-day-old specific-pathogen-free chickens than strain ck/CH/LJL/140901, according to analysis of the clinical signs, whereas strain ck/CH/LJL/140901 exhibited prolonged replication and shedding after challenge compared with isolate I1101/16. This study did not provide evidence that recombination can directly alter the antigenicity, virulence, replication, shedding, and tissue tropism of a virus, but it did show that recombination events are likely to be major determinants of viral evolution. url: https://api.elsevier.com/content/article/pii/S0168170217307098 doi: 10.1016/j.virusres.2017.11.007 id: cord-291510-jh2fdks4 author: Jiang, Yi title: Recombinant infectious bronchitis coronavirus H120 with the spike protein S1 gene of the nephropathogenic IBYZ strain remains attenuated but induces protective immunity date: 2020-02-11 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Infectious bronchitis (IB) is a highly infectious viral disease responsible for major economic losses in the poultry industry. A reverse genetic vaccine is a safe, rapid, and effective method of achieving IB prevention and control. In this study, we constructed the recombinant strain, rH120-S1/YZ, using a reverse genetic system, based on the backbone of the H120 vaccine strain, with the S1 gene replaced with that of the QX-like nephropathogenic strain, ck/CH/IBYZ/2011, isolated in China. The results of dwarf chicken embryos, growth kinetics, and viral titration in the embryos demonstrated that the biological characteristics of the recombinant virus remained unchanged. Like the rH120-infected group and in contrast to the rIBYZ-infected group, no mortality, clinical signs, or lesions were observed in the lungs or kidneys of young chickens inoculated with rH120-S1/YZ. The viral loads in various tissues, cloacal, and oral swabs was lower in most types of samples, indicating that the rH120-S1/YZ strain was highly safe in chicks. Compared to rH120 vaccination group, when the efficacy of this strain was evaluated against the QX-like IBV strain, better protection, with 100% survival rate and no disease symptom or gross lesion was observed in the chickens vaccinated with rH120-S1/YZ. Increased levels of IBV-specific antibodies were detected in the serum of the rH120-S1/YZ-vaccinated animals 14 days post-vaccination. Collectively, our results suggest that the recombinant strain, rH120-S1/YZ, may represent a promising vaccine candidate against QX-like IBVs. url: https://doi.org/10.1016/j.vaccine.2020.01.001 doi: 10.1016/j.vaccine.2020.01.001 id: cord-331740-yjt3q9ph author: Jones, R. M. title: Development and Validation of RT‐PCR Tests for the Detection and S1 Genotyping of Infectious Bronchitis Virus and Other Closely Related Gammacoronaviruses Within Clinical Samples date: 2011-04-07 words: 5863.0 sentences: 257.0 pages: flesch: 49.0 cache: ./cache/cord-331740-yjt3q9ph.txt txt: ./txt/cord-331740-yjt3q9ph.txt summary: This real-time RT-PCR test was used to examine a panel of field samples and its performance compared to virus isolation in embryonated fowls'' eggs. Design and calibration of IBV real-time RT-PCR To confirm that the modified test was suitable for detecting contemporary UK field strains of IBV, a panel of laboratory isolates of IBV representing the major genotypes currently circulating in the UK was tested . The validity of the result obtained for 38 of the 173 real-time RT-PCR positive, virus isolation negative samples could be confirmed by sequencing of the amplicon generated by the diagnostic RT-PCR. Infectious bronchitis virus RNA has been detected in tracheal swab samples by other real-time RT-PCRs for at least 21 days post-vaccination (Callison et al., 2006) and has been isolated from faecal samples in some infected birds as long as 227 days post-infection Gough, 1977, 1978) , making it essential to be able to differentiate between vaccine and field strains for diagnostic purposes. abstract: Two tests were developed that allow the detection and genotyping of infectious bronchitis virus (IBV) and other closely related gammacoronaviruses. The first test employs a one‐step, reverse transcription‐polymerase chain reaction (RT‐PCR) assay in which the amplification is monitored in real time using a TaqMan(®) probe. This real‐time RT‐PCR test was used to examine a panel of field samples and its performance compared to virus isolation in embryonated fowls’ eggs. A total of 323 field samples were tested; 176 samples were positive using the real‐time RT‐PCR method, but only three were positive by virus isolation. Sequencing was used to confirm the positive real‐time RT‐PCR results for a subset of samples. The test is suitable for swabs and post‐mortem samples and has been shown to be highly sensitive and specific. The second test, a genotyping method, was developed for identification of the strain of IBV present in field samples based on nucleotide variations within the gene encoding the S1 subunit of the surface spike (S) glycoprotein. This method was developed to provide a tool to inform vaccination decisions and for ongoing surveillance to detect new and emerging strains of IBV within the UK. The performance of the test was evaluated using laboratory isolates of IBV and field samples. Both tests are suitable for use in a high‐throughput diagnostic laboratory. url: https://doi.org/10.1111/j.1865-1682.2011.01222.x doi: 10.1111/j.1865-1682.2011.01222.x id: cord-285052-aql0vrzv author: Kamble, Nitin Machindra title: Evolutionary and bioinformatic analysis of the spike glycoprotein gene of H120 vaccine strain protectotype of infectious bronchitis virus from India date: 2016-02-12 words: 2820.0 sentences: 129.0 pages: flesch: 50.0 cache: ./cache/cord-285052-aql0vrzv.txt txt: ./txt/cord-285052-aql0vrzv.txt summary: The complete spike gene of Indian AIB vaccine strain was amplified and sequenced using a conventional reverse transcription polymerase chain reaction and is submitted to the GenBank (accession no KF188436). Nucleotide and amino acid sequence comparisons have shown that the reported spike gene from Indian isolates have 71.8%–99% and 71.4%–96.9% genetic similarity with the sequenced H120 strain. Genotyping of IBV strains can also be done by genetic characterization of the spike glycoprotein gene by reverse transcription polymerase chain reaction (RT-PCR), restriction fragment length polymorphism, and nucleotide sequencing, which for the most part correlates with the viral serotype [10, 11] . The deduced amino acid sequences of the spike glycoprotein from the Indian IBV vaccine strain and previously reported Indian isolates exhibited 71.4%-96.9% homology. In this study, we carried out propagation, amplification, sequencing, and bioinformatic analysis of the complete spike gene from the Indian vaccine strain, routinely used for vaccination of poultry birds. abstract: The infectious bronchitis virus is a causative agent of avian infectious bronchitis (AIB), and is is an important disease that produces severe economic losses to the poultry industry worldwide. Recent AIB outbreaks in India have been associated with poor growth in broilers, drop in egg production, and thin egg shells in layers. The complete spike gene of Indian AIB vaccine strain was amplified and sequenced using a conventional reverse transcription polymerase chain reaction and is submitted to the GenBank (accession no KF188436). Phylogenetic analysis revealed that the vaccine strain currently used belongs to H120 genotype, an attenuated strain of Massachusetts (Mass) serotype. Nucleotide and amino acid sequence comparisons have shown that the reported spike gene from Indian isolates have 71.8%–99% and 71.4%–96.9% genetic similarity with the sequenced H120 strain. The study identifies live attenuated IBV vaccine strain, which is routinely used for vaccination, for the first time. Based on nucleotide and amino acid relatedness studies of the vaccine strain with reported IBV sequences from India, it is shown that the current vaccine strain is efficient in controlling the IBV infection. Continuous monitoring of IBV outbreaks by sequencing for genotyping and in vivo cross protection studies for serotyping is not only important for epidemiological investigation but also for evaluation of efficacy of the current vaccine. url: https://doi.org/10.1002/bab.1298 doi: 10.1002/bab.1298 id: cord-260042-cs0wp99n author: Khan, Samiullah title: Genes involved in mitochondrial biogenesis and function may not show synchronised responses to mitochondria in shell gland of laying chickens under infectious bronchitis virus challenge date: 2019-04-01 words: 6931.0 sentences: 362.0 pages: flesch: 47.0 cache: ./cache/cord-260042-cs0wp99n.txt txt: ./txt/cord-260042-cs0wp99n.txt summary: The present study aimed to: a) determine mitochondrial counts in the cells of oviduct segments in laying hens at different time-points of egg formation in relation to the requirement of energy for egg production during IBV challenge; b) to determine the expression of nuclear DNA encoded genes in the shell gland to gain insights into their responses to IBV infection and time-points of egg-shell formation. Based on the lack of significant differences in mitochondrial count in the cells between the challenged and control groups for the magnum and isthmus, we focused further on shell gland tissue and studied the expression level of genes involved in mitochondrial density, biogenesis and fission. The lack of any significant difference in the relative expression levels of all of the genes except SDHA, between the control and IBV T challenged groups, may indicate that mitochondrial function may have been enhanced and thus overall egg quality may not have been affected by fewer mitochondria in the shell gland cells of IBV T infected hens. abstract: BACKGROUND: Egg formation takes place in the oviduct of laying hens over a 24 h period. Infectious bronchitis virus (IBV) causes pathological lesions in the chicken oviduct. In the current study, mitochondrial counts were determined in three different segments of the oviduct during egg formation in laying chickens challenged with IBV T strain. Nuclear DNA encoded genes that are involved in mitochondrial biogenesis, fission and function were studied in the shell gland of the oviduct undergoing virus multiplication. RESULTS: In the shell gland, the mitochondrial count was significantly lower (P < 0.05) in the challenged group, compared with the control group. However, it did not vary in response to IBV challenge in the isthmus and magnum regions of the oviduct. The gene succinate dehydrogenase complex, subunit A, flavoprotein variant (SDHA) was down-regulated in the shell gland by IBV challenge (P < 0.05), while other genes being studied did not show responses to the challenge (P > 0.05). Differential expression of the genes was observed at different time-points of egg-shell formation. The expression levels of citrate synthase (CS), cytochrome C, somatic (CYC, S) and sodium-potassium adenosine triphosphatase (Na(+)-K(+)ATPase) genes were significantly higher, while those of SDHA and dynamin related protein 1 (Drp1) genes were significantly lower, at 15 h compared with 5 h following oviposition of the previous egg. The expression level of peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α) did not show significant change at different time-points. CONCLUSIONS: It was concluded that IBV T strain infection in laying hens reduced mitochondrial counts only in the shell gland region of the oviduct. The genes involved in mitochondrial biogenesis or function may not show synchronised responses to that of mitochondria in the shell gland of chickens under T strain of IBV challenge. url: https://doi.org/10.1186/s12860-019-0190-7 doi: 10.1186/s12860-019-0190-7 id: cord-257064-iafm3pcc author: Kint, Joeri title: Quantification of Infectious Bronchitis Coronavirus by Titration In Vitro and In Ovo date: 2014-12-18 words: 1809.0 sentences: 156.0 pages: flesch: 63.0 cache: ./cache/cord-257064-iafm3pcc.txt txt: ./txt/cord-257064-iafm3pcc.txt summary: During a titration assay, tissue cultures or embryonated eggs are incubated with tenfold serial dilutions of a virus containing sample and several days later the cytopathic effect is scored. The virus titer is defined as the reciprocal of the dilution at which 50 % of the inoculated embryos or tissue cultures show CPE. Passaging of IBV in either embryonated eggs or primary cell cultures leads to attenuation of the virus in vivo [10] [11] [12] . IBV strains which have been adapted to grow in cultures of primary chicken cells can be titrated on these cells using either the TCID 50 method or plaque titration. Virus titers in the original sample, expressed as 10 log EID 50 /ml are calculated using the method described by Spearman and Kaerber [6, 7] , using the following formula: Plaque formation by infectious bronchitis virus in chicken embryo kidney cell cultures Growth kinetics of embryo-and organ-culture adapted Beaudette strain of infectious bronchitis virus in embryonated chicken eggs abstract: Quantification of the number of infectious viruses in a sample is a basic virological technique. In this chapter we provide a detailed description of three techniques to estimate the number of viable infectious avian coronaviruses in a sample. All three techniques are serial dilution assays, better known as titrations. url: https://doi.org/10.1007/978-1-4939-2438-7_9 doi: 10.1007/978-1-4939-2438-7_9 id: cord-342176-tewfm8it author: Kjærup, Rikke M. title: Adjuvant effects of mannose-binding lectin ligands on the immune response to infectious bronchitis vaccine in chickens with high or low serum mannose-binding lectin concentrations date: 2013-11-08 words: 8381.0 sentences: 479.0 pages: flesch: 62.0 cache: ./cache/cord-342176-tewfm8it.txt txt: ./txt/cord-342176-tewfm8it.txt summary: title: Adjuvant effects of mannose-binding lectin ligands on the immune response to infectious bronchitis vaccine in chickens with high or low serum mannose-binding lectin concentrations Chickens from two inbred lines (L10H and L10L) selected for high or low MBL serum concentrations, respectively, were vaccinated against IBV with or without the addition of the MBL ligands mannan, chitosan and fructooligosaccharide (FOS). Studies using these chicken sublines as well as outbred chickens have shown an inverse relationship between the MBL concentrations and the pathogen-specific antibody response (Juul-Madsen et al. However, MBL has an influence as the difference was more pronounced for the L10H chickens than L10L chickens for both the IBV-specific IgG antibody titres and the numbers of CD4−CD8␣+ and CD4−CD8␣− cells. Mannan-binding lectin (MBL) serum concentration in relation to propagation of infectious bronchitis virus (IBV) in chickens Crosstalk between innate and adaptive immune responses to infectious bronchitis virus after vaccination and challenge of chickens varying in serum mannose-binding lectin concentrations abstract: Mannose-binding lectin (MBL) plays a major role in the immune response as a soluble pattern-recognition receptor. MBL deficiency and susceptibility to different types of infections have been subject to extensive studies over the last decades. In humans and chickens, several studies have shown that MBL participates in the protection of hosts against virus infections. Infectious bronchitis (IB) is a highly contagious disease of economic importance in the poultry industry caused by the coronavirus infectious bronchitis virus (IBV). MBL has earlier been described to play a potential role in the pathogenesis of IBV infection and the production of IBV-specific antibodies, which may be exploited in optimising IBV vaccine strategies. The present study shows that MBL has the capability to bind to IBV in vitro. Chickens from two inbred lines (L10H and L10L) selected for high or low MBL serum concentrations, respectively, were vaccinated against IBV with or without the addition of the MBL ligands mannan, chitosan and fructooligosaccharide (FOS). The addition of MBL ligands to the IBV vaccine, especially FOS, enhanced the production of IBV-specific IgG antibody production in L10H chickens, but not L10L chickens after the second vaccination. The addition of FOS to the vaccine also increased the number of circulating CD4+ cells in L10H chickens compared to L10L chickens. The L10H chickens as well as the L10L chickens also showed an increased number of CD4−CD8α−γδ T-cells when an MBL ligand was added to the vaccine, most pronouncedly after the first vaccination. As MBL ligands co-administered with IBV vaccine induced differences between the two chicken lines, these results indirectly suggest that MBL is involved in the immune response to IBV vaccination. Furthermore, the higher antibody response in L10H chickens receiving vaccine and FOS makes FOS a potential adjuvant candidate in an IBV vaccine. url: https://api.elsevier.com/content/article/pii/S0171298513001964 doi: 10.1016/j.imbio.2013.10.013 id: cord-259505-7hiss0j3 author: Kong, Qingming title: Proteomic analysis of purified coronavirus infectious bronchitis virus particles date: 2010-06-09 words: 6907.0 sentences: 355.0 pages: flesch: 44.0 cache: ./cache/cord-259505-7hiss0j3.txt txt: ./txt/cord-259505-7hiss0j3.txt summary: It is an important prerequisite for the functional studies to know the protein composition of the purified viral particles, as it allows the analysis of specific proteins and their roles during the virus life cycle, resulting in better understanding of the infection process and the pathogenesis of viruses. To date, there have been no reports about TENP associated with virus, but it''s an enriched and abundant protein identified in purified infectious bronchitis particles which suggests to us that it may be a requisite host protein in IBV life cycles. The present study 1) provides the first proteomic analysis of infectious bronchitis particles, 2) establishes the most comprehensive proteomic index of IBV and 3) shows that most of the virion incorporated host proteins have central roles in virus life cycle. abstract: BACKGROUND: Infectious bronchitis virus (IBV) is the coronavirus of domestic chickens causing major economic losses to the poultry industry. Because of the complexity of the IBV life cycle and the small number of viral structural proteins, important virus-host relationships likely remain to be discovered. Toward this goal, we performed two-dimensional gel electrophoresis fractionation coupled to mass spectrometry identification approaches to perform a comprehensive proteomic analysis of purified IBV particles. RESULTS: Apart from the virus-encoded structural proteins, we detected 60 host proteins in the purified virions which can be grouped into several functional categories including intracellular trafficking proteins (20%), molecular chaperone (18%), macromolcular biosynthesis proteins (17%), cytoskeletal proteins (15%), signal transport proteins (15%), protein degradation (8%), chromosome associated proteins (2%), ribosomal proteins (2%), and other function proteins (3%). Interestingly, 21 of the total host proteins have not been reported to be present in virions of other virus families, such as major vault protein, TENP protein, ovalbumin, and scavenger receptor protein. Following identification of the host proteins by proteomic methods, the presence of 4 proteins in the purified IBV preparation was verified by western blotting and immunogold labeling detection. CONCLUSIONS: The results present the first standard proteomic profile of IBV and may facilitate the understanding of the pathogenic mechanisms. url: https://www.ncbi.nlm.nih.gov/pubmed/20534109/ doi: 10.1186/1477-5956-8-29 id: cord-264716-igl25jhg author: Koo, B.S. title: Molecular survey of enteric viruses in commercial chicken farms in Korea with a history of enteritis date: 2013-11-01 words: 4979.0 sentences: 240.0 pages: flesch: 47.0 cache: ./cache/cord-264716-igl25jhg.txt txt: ./txt/cord-264716-igl25jhg.txt summary: A molecular survey was performed to determine the presence of a broad range of enteric viruses, namely chicken astrovirus (CAstV), avian nephritis virus (ANV), chicken parvovirus (ChPV), infectious bronchitis virus (IBV), avian rotavirus (AvRV), avian reovirus (ARV), and fowl adenovirus (FAdV), in intestinal samples derived from 34 commercial chicken flocks that experienced enteritis outbreaks between 2010 and 2012. Several enteric viruses have been identified in a high proportion of chickens suffering from RSS in the fields using molecular surveys, including chicken astrovirus (CAstV), avian nephritis virus (ANV), chicken parvovirus (ChPV), infectious bronchitis virus (IBV), avian rotavirus (AvRV), avian reovirus (ARV), and fowl adenovirus (FAdV; Yu et al., 2001; Otto et al., 2006; Smyth et al., 2009; Hewson et al., 2010; Palade et al., 2011; Canelli et al., 2012) . In this study, a molecular survey was performed for a broad range of enteric viruses including CAstV, ANV, ChPV, IBV, AvRV, ARV, and FAdV in intestine samples from commercial chicken flocks suffering from enteritis. abstract: Several enteric viruses have increasingly received attention as potential causative agents of runting-stunting syndrome (RSS) in chickens. A molecular survey was performed to determine the presence of a broad range of enteric viruses, namely chicken astrovirus (CAstV), avian nephritis virus (ANV), chicken parvovirus (ChPV), infectious bronchitis virus (IBV), avian rotavirus (AvRV), avian reovirus (ARV), and fowl adenovirus (FAdV), in intestinal samples derived from 34 commercial chicken flocks that experienced enteritis outbreaks between 2010 and 2012. Using techniques such as PCR and reverse-transcription PCR, enteric viruses were identified in a total of 85.3% of investigated commercial chicken flocks in Korea. Furthermore, diverse combinations of 2 or more enteric viruses were simultaneously identified in 51.7% of chicken farms positive for enteric viruses. The rank order of positivity for enteric viruses was as follows: ANV (44.1%), CAstV (38.2%), ChPV (26.5%), IBV (20.6%), ARV (8.8%), AvRV (5.9%), and FAdV (2.9%). Additionally, other pathogens such as Escherichia coli, Salmonella spp., Eimeria spp., and FAdV were detected in 79% of chicken flocks positive for enteric viruses using PCR, bacterial isolation, and microscopic examination. The results of our study indicate the presence of several enteric viruses with various combinations in commercial chicken farms that experienced enteritis outbreaks. Experimental studies are required to further understand the roles of enteric viruses in RSS in commercial chickens. url: https://doi.org/10.3382/ps.2013-03280 doi: 10.3382/ps.2013-03280 id: cord-255619-5h3l6nh6 author: Kuo, Shu-Ming title: Evolution of infectious bronchitis virus in Taiwan: Positively selected sites in the nucleocapsid protein and their effects on RNA-binding activity date: 2013-03-23 words: 6329.0 sentences: 326.0 pages: flesch: 55.0 cache: ./cache/cord-255619-5h3l6nh6.txt txt: ./txt/cord-255619-5h3l6nh6.txt summary: title: Evolution of infectious bronchitis virus in Taiwan: Positively selected sites in the nucleocapsid protein and their effects on RNA-binding activity This study illustrates that the N protein of the current TW IBV variant has been shaped by both RNA recombination and positive selection and that the latter may promote viral survival and fitness, potentially by increasing the RNA-binding capacity of the N protein. This study illustrates that the N protein of the current TW IBV variant has been shaped by both RNA recombination and positive selection and that the latter may promote viral survival and fitness, potentially by increasing the RNAbinding capacity of the N protein. In this study, we showed that substituting either of the positively selected residues with the amino acid present in most CH IBVs dramatically reduced the binding capacity of the N protein for synthetic TRS repeats (Fig. 4) . abstract: RNA recombination has been shown to underlie the sporadic emergence of new variants of coronavirus, including the infectious bronchitis virus (IBV), a highly contagious avian pathogen. We have demonstrated that RNA recombination can give rise to a new viral population, supported by the finding that most isolated Taiwanese (TW) IBVs, similar to Chinese (CH) IBVs, exhibit a genetic rearrangement with the American (US) IBV at the 5’ end of the nucleocapsid (N) gene. Here, we further show that positive selection has occurred at two sites within the putative crossover region of the N-terminal domain (NTD) of the TW IBV N protein. Based on the crystal structure of the NTD, the stereographic positions of both predicted selected sites do not fall close to the RNA-binding groove. Surprisingly, converting either of the two residues to the amino acid present in most CH IBVs resulted in significantly reduced affinity of the N protein for the synthetic RNA repeats of the viral transcriptional regulatory sequence. These results suggest that modulating the amino acid residue at either selected site may alter the conformation of the N protein and affect the viral RNA–N interaction. This study illustrates that the N protein of the current TW IBV variant has been shaped by both RNA recombination and positive selection and that the latter may promote viral survival and fitness, potentially by increasing the RNA-binding capacity of the N protein. url: https://www.sciencedirect.com/science/article/pii/S0378113512005597 doi: 10.1016/j.vetmic.2012.10.020 id: cord-321261-3lp54mmu author: Kuo, Shu-Ming title: Evolution of infectious bronchitis virus in Taiwan: Characterisation of RNA recombination in the nucleocapsid gene date: 2010-08-26 words: 3884.0 sentences: 208.0 pages: flesch: 57.0 cache: ./cache/cord-321261-3lp54mmu.txt txt: ./txt/cord-321261-3lp54mmu.txt summary: Putative IBV genetic recombination in the S gene has been documented in different field isolates, including a Japanese strain (KB8523), European Avian infectious bronchitis virus (IBV) belongs to the Coronaviridae family and causes significant economic loss in Taiwan (TW), even in flocks that have been extensively immunised with Massachusetts (Mass)-serotype vaccines. No major difference was observed between the results from the BI and those from the ML test (Fig. 4B , D and F), confirming that RNA recombination probably occurred between TW and US IBVs in the 5 0terminal region of the N gene and that the phylogenetic incongruence was not caused by point mutation or variation in local evolutionary rates. We here show that the recombinant N gene was detected in all the isolated TW IBVs, supporting the participation of recombination in viral evolution and showing that a recombinant RNA virion can emerge as a local dominant strain. Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus abstract: Avian infectious bronchitis virus (IBV) belongs to the Coronaviridae family and causes significant economic loss in Taiwan (TW), even in flocks that have been extensively immunised with Massachusetts (Mass)-serotype vaccines. Phylogenetic analysis of all non-structural and most structural genes shows that TW IBV is genetically distinct from the US strain and more similar to Chinese (CH) IBV. In contrast, the nucleocapsid (N) gene of TW IBV presents phylogenetic incongruence. RNA recombination at the 5′ end of the N gene between TW and US IBV is shown to be responsible for this discordance. Surprisingly, the recombinant N gene is found in all of tested TW IBV isolates, suggesting that a recombination event gave origin to a founder lineage. Our data indicate that RNA recombination in the recombinant 5′ end of the N gene may have caused the emergence of the current IBV population in Taiwan. url: https://www.ncbi.nlm.nih.gov/pubmed/20299165/ doi: 10.1016/j.vetmic.2010.02.027 id: cord-288309-6pw7t512 author: Kusters, J. G. title: Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus date: 1990-12-31 words: 1972.0 sentences: 164.0 pages: flesch: 68.0 cache: ./cache/cord-288309-6pw7t512.txt txt: ./txt/cord-288309-6pw7t512.txt summary: J.; Niesters, H.G.M.; van der Zeijst, B.A.M. title: Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus Nucleotide sequences of eight IBV isolates in a region of the genome suspected to contain recombination, were aligned and compared. To address the question of the frequency of recombination in the generation of new field isolates the nucleotide sequences in five windows of homologous sequences of the genomes of eight IBV strains have been compared. With the murine coronavirus MHV a high frequency of recombination was found both in vitro and in mouse brain after infection with a ts mutant of MHV strain A59 and wild type JHM-virus 18''19 Phylogenetic trees constructed from five different windows of the genomes of eight IBV strains were used to detect crossover events. Cloning and sequencing of genes encoding structural proteins of avian infectious bronchitis virus abstract: Abstract Under laboratory conditions coronaviruses were shown to have a high frequency of recombination. In The Netherlands, vaccination against infectious bronchitis virus (IBV) is performed with vaccines that contain several life-attenuated virus strains. These highly effective vaccines may create ideal conditions for recombination, and could therefore be dangerous in the long term. This paper addresses the question of the frequency of recombination of avian coronavirus IBV in the field. A method was sought to detect and quantify recombination from sequence data. Nucleotide sequences of eight IBV isolates in a region of the genome suspected to contain recombination, were aligned and compared. Phylogenetic trees were constructed for different sections of this region. Differences in topology between these trees were observed, suggesting that in three out of eight strains in vivo RNA recombinant had occurred. url: https://api.elsevier.com/content/article/pii/0264410X9090018H doi: 10.1016/0264-410x(90)90018-h id: cord-298078-uqrwq5qk author: Kwak, Hoyun title: Annexin A2 Binds RNA and Reduces the Frameshifting Efficiency of Infectious Bronchitis Virus date: 2011-08-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Annexin A2 (ANXA2) is a protein implicated in diverse cellular functions, including exocytosis, DNA synthesis and cell proliferation. It was recently proposed to be involved in RNA metabolism because it was shown to associate with some cellular mRNA. Here, we identified ANXA2 as a RNA binding protein (RBP) that binds IBV (Infectious Bronchitis Virus) pseudoknot RNA. We first confirmed the binding of ANXA2 to IBV pseudoknot RNA by ultraviolet crosslinking and showed its binding to RNA pseudoknot with ANXA2 protein in vitro and in the cells. Since the RNA pseudoknot located in the frameshifting region of IBV was used as bait for cellular RBPs, we tested whether ANXA2 could regulate the frameshfting of IBV pseudoknot RNA by dual luciferase assay. Overexpression of ANXA2 significantly reduced the frameshifting efficiency from IBV pseudoknot RNA and knockdown of the protein strikingly increased the frameshifting efficiency. The results suggest that ANXA2 is a cellular RBP that can modulate the frameshifting efficiency of viral RNA, enabling it to act as an anti-viral cellular protein, and hinting at roles in RNA metabolism for other cellular mRNAs. url: https://doi.org/10.1371/journal.pone.0024067 doi: 10.1371/journal.pone.0024067 id: cord-256444-grw5s2pf author: Lai, Michael M.C. title: The Molecular Biology of Coronaviruses date: 1997-12-31 words: 35222.0 sentences: 1753.0 pages: flesch: 51.0 cache: ./cache/cord-256444-grw5s2pf.txt txt: ./txt/cord-256444-grw5s2pf.txt summary: Publisher Summary This chapter discusses the manipulation of clones of coronavirus and of complementary DNAs (cDNAs) of defective-interfering (DI) RNAs to study coronavirus RNA replication, transcription, recombination, processing and transport of proteins, virion assembly, identification of cell receptors for coronaviruses, and processing of the polymerase. This decade has seen the manipulation of these clones, and of complementary DNAs (cDNAs) of defective-interfering (DI) RNAs, to study coronavirus RNA replication, transcription, recombination, processing and transport of proteins, virion assembly, identification of cell receptors for coronaviruses, and processing of the polymerase. The species and tissue specificity of a coronavirus infection is a t least partially dictated by the nature and distribution of cellular receptors and other related molecules that regulate virus entry, as evidenced by the viral replication that results when viral RNA is directly introduced into cell types of other animal species. abstract: Publisher Summary This chapter discusses the manipulation of clones of coronavirus and of complementary DNAs (cDNAs) of defective-interfering (DI) RNAs to study coronavirus RNA replication, transcription, recombination, processing and transport of proteins, virion assembly, identification of cell receptors for coronaviruses, and processing of the polymerase. The nature of the coronavirus genome is nonsegmented, single-stranded, and positive-sense RNA. Its size ranges from 27 to 32 kb, which is significantly larger when compared with other RNA viruses. The gene encoding the large surface glycoprotein is up to 4.4 kb, encoding an imposing trimeric, highly glycosylated protein. This soars some 20 nm above the virion envelope, giving the virus the appearance-with a little imagination-of a crown or coronet. Coronavirus research has contributed to the understanding of many aspects of molecular biology in general, such as the mechanism of RNA synthesis, translational control, and protein transport and processing. It remains a treasure capable of generating unexpected insights. url: https://api.elsevier.com/content/article/pii/S0065352708602869 doi: 10.1016/s0065-3527(08)60286-9 id: cord-306380-msk9p1yy author: Lee, C.-W. title: Evidence of genetic diversity generated by recombination among avian coronavirus IBV date: 2000 words: 2796.0 sentences: 146.0 pages: flesch: 58.0 cache: ./cache/cord-306380-msk9p1yy.txt txt: ./txt/cord-306380-msk9p1yy.txt summary: Phylogenetic analysis of selected regions of the genome of the DE072 serotype field isolates further support those results and indicate that isolates within the same serotype may have different amounts of nucleotide sequence similarity with each other in individual genes other than the S gene. Further, we conducted sequence analysis of six isolates of the DE072 serotype in order to determine if recombination is frequently occurring in this region in field isolates of IBV. We conducted phylogenetic analysis by dividing 3.8 kb of the 3 end of the genome among five IBV strains at the IG sequences. However, these 6 isolates had a much different level of nucleotide sequence similarity with each other in gene 3 and gene 4, and clustered randomly with other serotypes of IBV (Fig. 3) . Sequence analysis of gene 3, gene 4 and gene 5 of avian infectious bronchitis virus strain CU-T2 Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus abstract: Previously, we demonstrated that the DE072 strain of IBV is a recombinant which has an IBV strain D1466-like sequence in the S gene. Herein, we analyzed the remaining 3.8 kb 3′ end of the genome, which includes Gene 3, Gene 4, Gene 5, Gene 6, and the 3′ non-coding region of the DE072 and D1466 strains. Those two viruses had high nucleotide similarity in Gene 4. However, the other individual genes had a much different level of sequence similarity with the same gene of the other IBV strains. The genome of five IBV strains, of which the complete sequence of the 3′ end of the genome has been determined, were divided at an intergenic (IG) consensus sequence (CTGAACAA or CTTAACAA) and compared phylogenetically. Phylogenetic trees of different topology indicated that the consensus IG sequences and the highly conserved sequence around this regions may serve as recombination ‘hot spots’. Phylogenetic analysis of selected regions of the genome of the DE072 serotype field isolates further support those results and indicate that isolates within the same serotype may have different amounts of nucleotide sequence similarity with each other in individual genes other than the S gene. Presumably this occurs because the consensus IG sequence serves as the template switching site for the viral encoded polymerase. url: https://www.ncbi.nlm.nih.gov/pubmed/11087096/ doi: 10.1007/s007050070044 id: cord-345630-bam3pa70 author: Lee, Han-Jung title: The complete sequence (22 kilobases) of murine coronavirus gene 1 encoding the putative proteases and RNA polymerase date: 1991-02-28 words: 5973.0 sentences: 418.0 pages: flesch: 65.0 cache: ./cache/cord-345630-bam3pa70.txt txt: ./txt/cord-345630-bam3pa70.txt summary: authors: Lee, Han-Jung; Shieh, Chien-Kou; Gorbalenya, Alexander E.; Koonin, Eugene V.; La Monica, Nicola; Tuler, Jeremy; Bagdzhadzhyan, Anush; Lai, Michael M.C. title: The complete sequence (22 kilobases) of murine coronavirus gene 1 encoding the putative proteases and RNA polymerase Third, the 3''-half of the gene 1 sequences of IBV and MHV-A59 contains the sequence motifs for RNA polymerase and helicase, which are the activities expected to be involved in RNA synthesis Gorbalenya et a/., 198913; Bredenbeek et a/., 1990) . The alignment of amino acids in ORF la of MHV-JHM and IBV showed that there are four possible stretches of moderate homology which are separated by highly diverged sequences (Fig. 8) . Although ORF la is highly diverged between MHV-JHM and IBV, common functional domains could be identified in this ORF of both viruses by detailed amino acid sequence analysis (see Materials and Methods) (Fig. 9 ). abstract: Abstract The 5′-most gene, gene 1, of the genome of murine coronavirus, mouse hepatitis virus (MHV), is presumed to encode the viral RNA-dependent RNA polymerase. We have determined the complete sequence of this gene of the JHM strain by cDNA cloning and sequencing. The total length of this gene is 21,798 nucleotides long, which includes two overlapping, large open reading frames. The first open reading frame, ORF 1 a, is 4488 amino acids long. The second open reading frame, ORF 1 b, overlaps ORF 1 a for 75 nucleotides, and is 2731 amino acids long. The overlapping region may fold into a pseudoknot RNA structure, similar to the corresponding region of the RNA of avian coronavirus, infectious bronchitis virus (IBV). The in vitro transcription and translation studies of this region indicated that these two ORFs were most likely translated into one polyprotein by a ribosomal frameshifting mechanism. Thus, the predicted molecular weight of the gene 1 product is more than 800,000 Da. The sequence of ORF 1 b is very similar to the corresponding ORF of IBV. In contrast, the ORF 1 a of these two viruses differ in size and have a high degree of divergence. The amino acid sequence analysis suggested that ORF 1 a contains several functional domains, including two hydrophobic, membrane-anchoring domains, and three cysteine-rich domains. It also contains a picornaviral 3C-like protease domain and two papain-like protease domains. The presence of these protease domains suggests that the polyprotein is most likely processed into multiple protein products. In contrast, the ORF 1b contains polymerase, helicase, and zinc-finger motifs. These sequence studies suggested that the MHV gene 1 product is involved in RNA synthesis, and that this product is processed autoproteolytically after translation. This study completes the sequence of the MHV genome, which is 31 kb long, and constitutes the largest viral RNA known. url: https://api.elsevier.com/content/article/pii/004268229190071I doi: 10.1016/0042-6822(91)90071-i id: cord-004810-g0y7ied0 author: Lee, S. K. title: S1 glycoprotein gene analysis of infectious bronchitis viruses isolated in Korea date: 2003-11-13 words: 3750.0 sentences: 190.0 pages: flesch: 59.0 cache: ./cache/cord-004810-g0y7ied0.txt txt: ./txt/cord-004810-g0y7ied0.txt summary: The S1 glycoprotein gene of IBV isolates were amplified by reverse transcriptase – polymerase chain reaction (RT-PCR) and analyzed by restriction fragment length polymorphism (RFLP) analysis. And these IBV isolates showed different patterns from each other and non-Korean IBV isolates in reverse transcriptase-polymerase chain reaction-restriction fragment length polymorphism (RT-PCR-RFLP) analysis [29] . Amplified S1 genes were first classified by RFLP analysis and then the representative strains were cloned, sequenced and compared to other non-Korean published IBV sequences. Phylogenetic trees were constructed from the nucleotide and deduced amino acid sequences of the S1 glycoprotein genes of Korean IBV isolates and non-Korean IBV strains (Fig. 3) . Korean IBV K281-01 and K210-02 isolates formed distinct clusters that were related to non-Korean IBV Ark99, Ark DPI, Gray and JMK strains although K281-01 and K210-02 isolates were classified into the Arkansas type by PCR-RFLP analysis. abstract: Fifteen isolates of Infectious bronchitis virus (IBV) were obtained from the kidney, trachea, and cecal tonsil of IB suspected chickens between 2001 and 2002 years in Korea. The S1 glycoprotein gene of IBV isolates were amplified by reverse transcriptase – polymerase chain reaction (RT-PCR) and analyzed by restriction fragment length polymorphism (RFLP) analysis. Fifteen Korean IBV isolates were classified into 4 groups by their RFLP patterns using restriction enzymes, HaeIII, BstYI, and XcmI. The RFLP patterns for 3, 1, and 1 of 15 isolates corresponded to the patterns of IBV Arkansas, Connecticut, and Massachusetts strains, respectively. Ten of 15 isolates generated unique KM91 RFLP pattern that was observed in the IBV KM 91 strain previously isolated in Korea. To confirm genetic diversity in the S1 genes of IBV isolates, viral RNAs of representative 9 of 15 IBV isolates were amplified, cloned, sequenced and compared with published sequences for non-Korean IBV strains. Korean IBV isolates showed amino acid sequence similarity between 61.8% (K446-01 and K161-02) and 96.1% (K281-01 and K210-02) with each other and they showed amino acid sequence similarity between 42.9% (K161-02 and GA980470) and 96.5% (K203-02 and KB8523) compared to non-Korean IBV strains. By phylogenetic tree analysis, Korean IBV field isolates were branched into five clusters in which 3 clusters were differentiated from non-Korean IBV strains. Especially, Korean IBV isolates K069-01, K507-01, K774-01 and K142-02 formed a separate cluster. It seems that IBVs continue to evolve and IBVs showing various genetic differences may cocirculate in Korea. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087141/ doi: 10.1007/s00705-003-0225-3 id: cord-290638-7ro72sv3 author: Lenstra, Johannes A. title: Antigenicity of the peplomer protein of infectious bronchitis virus date: 1989-01-31 words: 3960.0 sentences: 230.0 pages: flesch: 53.0 cache: ./cache/cord-290638-7ro72sv3.txt txt: ./txt/cord-290638-7ro72sv3.txt summary: Abstract To study the antigenic structure of the peplomer protein of the avian coronavirus infectious bronchitis virus, fragments from the peplomer gene were generated by restriction-enzyme cleavage or by limited DNase digestion and inserted in the Escherichia coli expression plasrnid pEX (Stanley and Luzio, 1984). Recombinants expressing the IBV gene fragments were selected by immunoscreening with a rabbit antiserum or, when the expression product was not recognized antigenically, by hybridization followed by gel electrophoresis of the protein expression products. Figure 2 (C) shows a Western blot of hybrid proteins screened with this MAb. The strong binding to fragments p2, s4, psl and ps2 localizes the epitope of MAb 26.1 between residues 390 and 612, the same region that is recognized by all polyclonal sera. The localization of epitopes within stretches of 10-20 residues in several coronaviruses (Fig. 4 , unpublished results) demonstrates that the binding of antibody does not depend on particular flanking sequences, and that any nativelike folding of the epitope in the hybrid protein is confined to the same small region. abstract: Abstract To study the antigenic structure of the peplomer protein of the avian coronavirus infectious bronchitis virus, fragments from the peplomer gene were generated by restriction-enzyme cleavage or by limited DNase digestion and inserted in the Escherichia coli expression plasrnid pEX (Stanley and Luzio, 1984). The antigenicity of the expression products was tested using a number of polyclonal antisera and monoclonal antibodies. The polyclonal antisera recognized different sets of epitopes in the 1162-residue sequence. The N-terminal region of one of the two subunits, S2, was recognized by all polyclonal sera and by two monoclonal antibodies. This clearly immunodominant region contains at least two adjacent or overlapping epitopes, one of which has been localized within 18 residues. The epitopes found as antigenic pEX expression products do not coincide with the regions in the S1 subunit that have been found to contain hypervariable sequences. We suggest that these regions constitute conformation dependent neutralization epitopes that cannot be detected in the pEX system. The relevance of our finclings for vaccine development is discussed. url: https://api.elsevier.com/content/article/pii/016158908990014X doi: 10.1016/0161-5890(89)90014-x id: cord-259480-1tqfoecc author: Li, Huixin title: Recombinant duck enteritis viruses expressing major structural proteins of the infectious bronchitis virus provide protection against infectious bronchitis in chickens date: 2016-03-02 words: 6015.0 sentences: 300.0 pages: flesch: 54.0 cache: ./cache/cord-259480-1tqfoecc.txt txt: ./txt/cord-259480-1tqfoecc.txt summary: To design an alternative vaccine for control of infectious bronchitis in chickens, three recombinant duck enteritis viruses (rDEVs) expressing the N, S, or S1 protein of infectious bronchitis virus (IBV) were constructed using conventional homologous recombination methods, and were designated as rDEV-N, rDEV-S, and rDEV-S1, respectively. After challenge with a homologous virulent IBV strain at 21 days post-immunization, vaccinated groups showed significant differences in the percentage of birds with clinical signs, as compared to the control group (p < 0.01), as the two covalent-vaccination groups and the rDEV-S group provided better protection than the rDEV-Nor rDEV-S1-vaccinated group. The N phosphoprotein is conserved among different IBV serotypes and can induce high titers of cross-reactive antibodies and cell-mediated immunity that protects chickens from acute infection, thus it is used as a target protein in designing vaccines against IB (Williams et al., 1992; Collisson et al., 2000; Seo et al., 1997) . Antibody responses of chickens vaccinated with recombinant duck enteritis viruses expressing the N, S or S1 gene of infectious bronchitis virus (IBV). abstract: To design an alternative vaccine for control of infectious bronchitis in chickens, three recombinant duck enteritis viruses (rDEVs) expressing the N, S, or S1 protein of infectious bronchitis virus (IBV) were constructed using conventional homologous recombination methods, and were designated as rDEV-N, rDEV-S, and rDEV-S1, respectively. Chickens were divided into five vaccinated groups, which were each immunized with one of the rDEVs, covalent vaccination with rDEV-N & rDEV-S, or covalent vaccination with rDEV-N & rDEV-S1, and a control group. An antibody response against IBV was detectable and the ratio of CD4(+)/CD8(+) T-lymphocytes decreased at 7 days post-vaccination in each vaccinated group, suggesting that humoral and cellular responses were elicited in each group as early as 7 days post-immunization. After challenge with a homologous virulent IBV strain at 21 days post-immunization, vaccinated groups showed significant differences in the percentage of birds with clinical signs, as compared to the control group (p < 0.01), as the two covalent-vaccination groups and the rDEV-S group provided better protection than the rDEV-N- or rDEV-S1-vaccinated group. There was less viral shedding in the rDEV-N & rDEV-S- (2/10) and rDEV-N & rDEV-S1- (2/10) vaccinated groups than the other three vaccinated groups. Based on the clinical signs, viral shedding, and mortality rates, rDEV-N & rDEV-S1 covalent vaccination conferred better protection than use of any of the single rDEVs. url: https://doi.org/10.1016/j.antiviral.2016.03.003 doi: 10.1016/j.antiviral.2016.03.003 id: cord-293081-40pa5g89 author: Li, Jun title: Preliminary crystallographic analysis of avian infectious bronchitis virus main protease date: 2006-12-16 words: 1510.0 sentences: 95.0 pages: flesch: 61.0 cache: ./cache/cord-293081-40pa5g89.txt txt: ./txt/cord-293081-40pa5g89.txt summary: IBV belongs to group III (Lai & Holmes, 2001) , which only infects avian species, and leads to a highly contagious disease affecting the respiratory, reproductive, neurological and renal systems of chickens, resulting in a drop in egg production in adult birds and damaging the developing reproductive system in young birds. To date, several crystal structures of coronavirus M pro s have been reported for group I and II coronaviruses, which mostly infect mammals (Anand et al., 2002 Yang et al., 2003) . The crystals belong to space group P6 1 22, with unit-cell parameters a = b = 119.1, c = 270.7 Å , = = 90, = 120 (see Table 1 Typical crystals of IBV M pro grown by the hanging-drop method in 2.5% PEG 4000, 12% 2-propanol, 0.1 M sodium cacodylate pH 6.5. abstract: Infectious bronchitis virus (IBV) is the prototype of the genus Coronavirus. It causes a highly contagious disease which affects the respiratory, reproductive, neurological and renal systems of chickens, resulting great economic losses in the poultry industry worldwide. The coronavirus (CoV) main protease (M(pro)), which plays a pivotal role in viral gene expression and replication through a highly complex cascade involving the proteolytic processing of replicase polyproteins, is an attractive target for antiviral drug design. In this study, IBV M(pro) was overexpressed in Escherichia coli. Crystals suitable for X-ray crystallography have been obtained using microseeding techniques and belong to space group P6(1)22. X-ray diffraction data were collected in-house to 2.7 Å resolution from a single crystal. The unit-cell parameters were a = b = 119.1, c = 270.7 Å, α = β = 90, γ = 120°. Three molecules were predicted to be present in the asymmetric unit from a calculated self-rotation function. url: http://europepmc.org/articles/pmc2330114?pdf=render doi: 10.1107/s1744309106052341 id: cord-004680-u3cnsdl8 author: Lin, Z. title: Typing of recent infectious bronchitis virus isolates causing nephritis in chicken date: 1991 words: 860.0 sentences: 47.0 pages: flesch: 57.0 cache: ./cache/cord-004680-u3cnsdl8.txt txt: ./txt/cord-004680-u3cnsdl8.txt summary: Four isolates of infectious bronchitis viruses (IBV) from chickens with nephritis, were characterized by polymerase chain reaction (PCR) and restriction enzyme fragment length polymorphism (RFLP), and were found to be genetically different from the other twelve strains which we previously studied. HinfI digested pUC 19 DNA was used as the molecular size markers (3//), and their sizes are indicated in base pairs (bp) on the left In this study, essentially the same procedure was used in an attempt to characterize four IBV isolates F-88, Y-4, M-l, and NI-1 from chickens with nephritis in different endemic areas of Japan between 1988 and 1989. The results of the present study, indicate that the four recently obtained IBV isolates causing nephritis are, by our genetic criteria, similar to each other but different from previous isolates, hence are classified together into a new subtype (group VI). Serological comparisons of strains of infectious bronchitis virus using plaque-purified isolants abstract: Four isolates of infectious bronchitis viruses (IBV) from chickens with nephritis, were characterized by polymerase chain reaction (PCR) and restriction enzyme fragment length polymorphism (RFLP), and were found to be genetically different from the other twelve strains which we previously studied. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086593/ doi: 10.1007/bf01310957 id: cord-258379-v3lceirh author: Liu, D. X. title: Association of the infectious bronchitis virus 3c protein with the virion envelope date: 1991-12-31 words: 2868.0 sentences: 121.0 pages: flesch: 53.0 cache: ./cache/cord-258379-v3lceirh.txt txt: ./txt/cord-258379-v3lceirh.txt summary: There was considerably less evidence of contaminating cellular proteins in this gradient, and the relative proportion of the 12K protein to the other virion proteins appeared similar to that observed at the previous stage in purification, strongly supporting the idea of a specific association between the 12K protein and virus particles. In order to establish the identity of the 12K polypeptide as the product of the 3c gene, and to examine the possibility that IBV virions might contain other new virus polypeptides in amounts too small to detect directly, we next carried out immunoprecipitation experiments using monospecific antisera directed against the predicted products of the 3a, 3b, 3c, 5a, and 5b ORFs (17, 18, 23) . Messenger RNA 4 of mouse hepatitis virus (MHV) is known to encode a 15K polypeptide, the predicted amino acid sequence of which contains a highly hydrophobic region from residues 8 to 41 (9, 22) , although the protein has not so far been found in virions. abstract: Abstract A highly purified radiolabeled preparation of the coronavirus infectious bronchitis virus (IBV) was analyzed, by immunoprecipitation with monospecific antisera, for the presence of a series of small virus proteins recently identified as the products of I BV mRNAs 3 and 5. One of these, 3c, a 12.4K protein encoded by the third open reading frame of the tricistronic mRNA3 was clearly detectable and was found to cofractionate with virion envelope proteins on detergent disruption of virus particles. These results, together with the hydrophobic nature of 3c and its previously demonstrated association with the membranes of infected cells, suggest strongly that 3c represents a new virion envelope protein, which may have counterparts in other coronaviruses. url: https://www.ncbi.nlm.nih.gov/pubmed/1962461/ doi: 10.1016/0042-6822(91)90572-s id: cord-262940-eyejnexx author: Liu, Genmei title: Assembly and immunogenicity of coronavirus-like particles carrying infectious bronchitis virus M and S proteins date: 2013-11-12 words: 3853.0 sentences: 175.0 pages: flesch: 49.0 cache: ./cache/cord-262940-eyejnexx.txt txt: ./txt/cord-262940-eyejnexx.txt summary: In the present study, we assembled IBV VLPs containing M and S proteins using a baculovirus expression system and we further evaluated the VLPs immune responses in mice and chickens. The results showed that, 2 weeks after the primary vaccination (day 14), both of VLPs and inactivated H120 groups could not detected serum IgG titers, and the differences between these and PBS groups were not statistically significant (P > 0.05); but following the second immunization (day 28), the IgG titers of the VLPs and inactivated H120 groups increased (Fig. 6 ) and were significantly higher (P < 0.01) than the PBS group. The results showed that VLPs and inactivated H120 groups had statistically significantly higher neutralizing antibody titers (P < 0.01) than the PBS group (Fig. 7) . Virus like particles (VLPs) and inactivated H120 groups had significantly higher neutralizing antibody titers (P < 0.01) than the PBS group. abstract: Infectious bronchitis virus (IBV) as an avian coronavirus is still posing a persistent and imminent threat to the poultry industry worldwide. Here we report that transfection of Sf9 cells with a single recombinant baculovirus encoding M and S proteins resulted in the assembly of IBV VLPs; this is the first report that S protein plus M protein alone were able to be assembled into VLPs for coronaviruses. We further showed that the generated IBV VLPs could induce humoral immune responses in a level comparable to that of inactivated IBV vaccine, and more importantly the IBV VLPs could elicit significantly higher cellular immune responses than the inactivated IBV vaccine. In summary, the assembly of IBV VLPs with M and S proteins provided a simple strategy for generating VLPs for coronaviruses, and the generated IBV VLPs laid a feasible foundation for the development of an effective vaccine against infection of IBV in the future. url: https://www.sciencedirect.com/science/article/pii/S0264410X13012656 doi: 10.1016/j.vaccine.2013.09.024 id: cord-256859-7ixegm72 author: Liu, S. W. title: Genetic diversity of avian infectious bronchitis coronavirus strains isolated in China between 1995 and 2004 date: 2006-01-09 words: 5156.0 sentences: 266.0 pages: flesch: 56.0 cache: ./cache/cord-256859-7ixegm72.txt txt: ./txt/cord-256859-7ixegm72.txt summary: Except for isolates in genotype V, which included the Mass-type strains, none of the Chinese IBV isolates examined in this study shared more than 83% amino acid similarity in the S1 protein with the H120 vaccine strain. Furthermore, almost all of the Chinese IBV isolates contained deletions and insertions except for those of the Mass-type IBV, which were included in genotype V in this study, and had amino acid sequences similar to those of the H120 strain ( Table 4 ). The low identities (<83%) of amino acid sequences between Chinese IBV isolates and H120, except for those of the Mass-type IBV, which were included in genotype V in this study, may account for the prevalence of the viruses during the past ten years in spite of the extensive use of Mass-type vaccines in the field in China. abstract: Twenty-six avian infectious bronchitis (IB) viruses (IBV) were isolated from outbreaks in chickens in China between 1995 and 2004. They were characterized by comparison with twenty-six Chinese reference strains and five other IBV strains. Chinese IBVs, which were mainly nephropathogenic, were placed into seven genotypes. Fourteen Chinese IBV isolates were placed in genotype I, having small evolutionary distances from each other. Genotype II included 6 strains that were isolated in the 1990s in China. Genotype III consisted of eight Chinese isolates that showed close relationship with Korean IBV isolates. Another eight IBV isolates clustered in genotype IV and showed larger evolutionary distances. The Massachusetts serotype was present in China in 1990s and was in a separate genotype. Two isolates, HN99 and CK/CH/LHN/00I, which might be a reisolation of vaccine strains, clustered into genotype VI. Four Chinese IBV isolates formed another genotype and showed larger evolutionary distances from other Chinese IBV genotypes (genotype VII). IBVs in same genotypes showed more than 90% amino acid sequence similarities, whereas most of the viruses in different genotypes showed less than 90%. The results showed that IBVs in China came from genetic changes both in IBV populations that existed before the advent of vaccination and in the viruses that were introduced through live vaccines. IBVs showing various genetic differences are cocirculating in China. url: https://www.ncbi.nlm.nih.gov/pubmed/16397751/ doi: 10.1007/s00705-005-0695-6 id: cord-022187-7c3wz6c6 author: Liu, Shengwang title: A new genotype of nephropathogenic infectious bronchitis virus circulating in vaccinated and non-vaccinated flocks in China date: 2010-10-19 words: 3520.0 sentences: 195.0 pages: flesch: 60.0 cache: ./cache/cord-022187-7c3wz6c6.txt txt: ./txt/cord-022187-7c3wz6c6.txt summary: title: A new genotype of nephropathogenic infectious bronchitis virus circulating in vaccinated and non-vaccinated flocks in China Five strains of infectious bronchitis virus (IBV) were isolated from five layer flocks that had nephropathogenic infection in four provinces in China. Virulence studies indicated that the five Chinese IBV isolates caused 10 to 30% mortality in 15-day-old specific pathogen free chickens and gross lesions were mainly confined to the kidneys in all of the dead chickens. In order to investigate whether there are other genotype(s) of nephropathogenic IBV besides the Massachusetts type in flocks in China, we tested five IBV isolates from layer flocks showing clinical signs of IB by sequencing and analysis of the S1 protein genes. In the present study, we isolated three IBV strains from H120-vaccinated flocks and two from non-vaccinated flocks of layer chickens that experienced nephropathogenic infection in four provinces of north China. abstract: Five strains of infectious bronchitis virus (IBV) were isolated from five layer flocks that had nephropathogenic infection in four provinces in China. Among them, three of the five flocks had been vaccinated against infectious bronchitis. Virulence studies indicated that the five Chinese IBV isolates caused 10 to 30% mortality in 15-day-old specific pathogen free chickens and gross lesions were mainly confined to the kidneys in all of the dead chickens. Two oligonucleotide pairs, S1Uni2 and S1Oligo3′ or S1Oligo5′ and S1Oligo3′, were used after propagation of the isolates in embryonated eggs to amplify the S1 protein genes of the spike protein. The cDNA derived by reverse transcriptase-polymerase chain reaction was cloned and sequenced. The nucleotide and amino acid sequence of S1 protein gene had a similar degree of identity (≥92%) among the five Chinese IBV isolates. The nucleotide and amino acid identity of the S1 protein gene between the five Chinese IBV isolates and 16 strains of other IBVs varied from 60 to 81%. This clearly showed that the five Chinese IBV isolates comprised a separate genotype. These results demonstrated, for the first time, that there is a new genotype of nephropathogenic IBV circulating in vaccinated and non-vaccinated flocks in China. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7154297/ doi: 10.1080/0307945042000220697 id: cord-255870-gmq5zs2d author: Liu, Shengwang title: Identification of the avian infectious bronchitis coronaviruses with mutations in gene 3 date: 2008-04-15 words: 5685.0 sentences: 258.0 pages: flesch: 56.0 cache: ./cache/cord-255870-gmq5zs2d.txt txt: ./txt/cord-255870-gmq5zs2d.txt summary: All the IBV field and vaccine strains were propagated once in 9 to 11-day-old embryonated chicken-specific pathogen-free (SPF) eggs (Harbin Veterinary Research Institute, China) and confirmed using negative contrast electronic microscopy (JEM-1200, EX) in the allantoic fluids of inoculated eggs as described previously (Liu and Kong, 2004) , before being used in sequence analysis. Each of the nine 9-day-old SPF chicken embryos was inoculated with the isolates CK/CH/LLN/98, CK/CH/LSD/03I, CK/CH/LJL/04I, CK/CH/LDL/97I, and CK/CH/LGD/04II passage level 3 (the latter 3 virus strains, each representing different IBV serotypes in China, were used as controls) with 10 2 EID 50 per embryo in 0.1 ml inoculum into the allantoic cavity. This mutation resulted in the virus lacking ORF 3a and changed the primary structure of the 3′-encoding regions of CK/CH/LLN/98I, leading to a novel genomic organization of the avian coronavirus that had the S-3b-3c-M-5a-5b-N gene order from the 5′-end to the 3′-end, instead of the typical gene order in the 3′-encoding regions of group 3 coronaviruses isolated from chicken (IBV) (Boursnell et al., 1987) , turkey (Breslin et al., 1999; Cavanagh et al., 2001; Lin et al., 2002) , and pheasants (Cavanagh et al., 2002) . abstract: The sequence of a 6.0-kb fragment was compared in the 3′-encoding region of the genome in 27 infectious bronchitis virus (IBV) strains. All these strains have the same S-3-M-5-N gene order, as is the case for other IBVs. However, the sizes of the corresponding open reading frames (ORFs) of some genes varied among the virus strains. Phylogenetic analysis and sequence alignments demonstrated that recombination events had occurred in the origin and evolution of the strains CK/CH/LSD/03I and CK/CH/LLN/98I and the possible recombinant junction sites might be located at the 3c and M genes, respectively. The normal product of ORF 3a is 57 amino acids long, whereas a 43-bp deletion at the 3′-end of the CK/CH/LSD/03I 3a gene was detected, resulting in a frameshift event and C-terminally truncated protein with 47 amino acids. Comparison of the growth ability in embryos and replication and pathogenicity in chickens with IBV carrying the normal 3a gene indicated that this deleted sequence in the 3a gene of CK/CH/LSD/03I was not necessary for viral pathogenesis and replication either in vitro or in vivo. Occurrence of a mutation at the corresponding position of the CK/CH/LLN/98I start codon in the 3a gene led to the absence of ORF 3a in this virus, resulting in a novel genomic organization at the 3′-encoding regions: S-3b, 3c-M-5a, 5b-N. Comparison with other viruses carrying the normal 3a gene revealed that CK/CH/LLN/98I had replication and pathogenicity abilities in vivo similar to those of other IBVs; however, its growth ability in embryos was lower, although the relationship between the lower growth ability and the ORF 3a defect requires further confirmation. url: https://api.elsevier.com/content/article/pii/S037811190800005X doi: 10.1016/j.gene.2008.01.004 id: cord-260145-grz0fe9l author: Liu, Shengwang title: Altered pathogenicity, immunogenicity, tissue tropism and 3′-7 kb region sequence of an avian infectious bronchitis coronavirus strain after serial passage in embryos date: 2009-07-23 words: 7486.0 sentences: 366.0 pages: flesch: 51.0 cache: ./cache/cord-260145-grz0fe9l.txt txt: ./txt/cord-260145-grz0fe9l.txt summary: title: Altered pathogenicity, immunogenicity, tissue tropism and 3′-7 kb region sequence of an avian infectious bronchitis coronavirus strain after serial passage in embryos In this study, we attenuated a Chinese LX4-type nephropathogenic infectious bronchitis virus (IBV) strain, CK/CH/LHLJ/04V, by serial passage in embryonated chicken eggs. At the age of 15 days, groups 1-4 were inoculated intranasally with 0.1 ml per chick containing 10 4.7 -10 4.8 median embryo infectious doses (EID 50 ) at passage level 3 of strains CH/CK/LHLJ/04V, CK/CH/LDL/04II, CK/CH/LXJ/02I and CK/CH/LSHH/03I. The CH/CK/LHLJ/04V strain was serially passaged 110 times by inoculating 9-day-old SPF chicken eggs by the allantoic cavity route as described previously [19] . Virus titrations were performed in 9-day-old embryonated chicken SPF eggs via the allantoic cavity route of inoculation, and titers were expressed as 50% (median) embryo infectious doses (EID 50 ) [9, 37] . abstract: In this study, we attenuated a Chinese LX4-type nephropathogenic infectious bronchitis virus (IBV) strain, CK/CH/LHLJ/04V, by serial passage in embryonated chicken eggs. Based on sequence analysis of the 3′-7 kb region, the CK/CH/LHLJ/04V virus population contained subpopulations with a mixture of genetic mutants. The titers of the virus increased gradually during serial passage, but the replication capacity decreased in chickens. The virus was partially attenuated at passage 40 (P40) and P70, and was fully attenuated at P110. It lost immunogenicity and kidney tropism at P110 and P70, respectively. Amino acid substitutions were found in the 3′-7 kb region, primarily in the spike (S) protein. Substitutions in the S1 subunit occurred between P3 and P40 and all subpopulations in a virus passage showed the same substitutions. Other substitutions that occurred between P70 and P110, however, were found only in some subpopulations of the virus passages. A 109-bp deletion in the 3′-UTR was observed in most subpopulations of P70 and P110, and might be related to virus replication, transcription and pathogenicity. The changes described in the 3′-7 kb region of the virus are possibly responsible for virus attenuation, immunogenicity decrease and tissue tropism changes; however, we cannot exclude the possibility that other parts of the genome may also be involved in those changes. url: https://doi.org/10.1016/j.vaccine.2009.05.072 doi: 10.1016/j.vaccine.2009.05.072 id: cord-279495-zxerb7de author: Liu, Xiaoli title: Comparative analysis of four Massachusetts type infectious bronchitis coronavirus genomes reveals a novel Massachusetts type strain and evidence of natural recombination in the genome date: 2012-11-21 words: 5235.0 sentences: 258.0 pages: flesch: 56.0 cache: ./cache/cord-279495-zxerb7de.txt txt: ./txt/cord-279495-zxerb7de.txt summary: Four Massachusetts-type (Mass-type) strains of infectious bronchitis coronavirus (IBV) were compared genetically with the pathogenic M41 and H120 vaccine strains using the complete genomic sequences. Phylogenetic analysis, and pairwise comparison of full-length genomes and the nine genes, identified the occurrence of recombination events in the genome of strain CK/VH/LHLJ/07VII, which suggests that this virus originated from recombination events between M41and H120-like strains at the switch site located at the 3′ end of the nucleocapsid (N) genes. Herein, we sequenced the complete genome of four IBV Mass-type strains that showed S1 gene diversity (Liu et al., 2009; Ma et al., 2012; Sun et al., 2011) , and we present evidence for in-field recombination between pathogenic and vaccinal strains. Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus abstract: Four Massachusetts-type (Mass-type) strains of infectious bronchitis coronavirus (IBV) were compared genetically with the pathogenic M41 and H120 vaccine strains using the complete genomic sequences. The results revealed that strains ck/CH/LNM/091017 and ck/CH/LDL/101212 were closely related to the H120 vaccine, which suggests that they might represent re-isolations of vaccine strains or variants of vaccine strains that have resulted from the accumulated point mutations after several passages in chickens. In contrast, strains ck/CH/LHLJ/07VII and ck/CH/LHLJ/100902 had a close genetic relationship with the pathogenic M41 strain. In addition, molecular markers have been identified that distinguish between field and vaccine (or vaccine-like) Mass-type viruses, which may be able to differentiate between field and vaccine strains for diagnostic purposes. Phylogenetic analysis, and pairwise comparison of full-length genomes and the nine genes, identified the occurrence of recombination events in the genome of strain CK/VH/LHLJ/07VII, which suggests that this virus originated from recombination events between M41- and H120-like strains at the switch site located at the 3′ end of the nucleocapsid (N) genes. To our knowledge, this is the first time that evidence for the evolution and natural recombination under field conditions between Mass-type pathogenic and vaccinal IBV strains has been documented. These findings provide insights into the emergence and evolution of the Mass-type IB coronaviruses and may help to explain the emergence of Mass-type IBV in chicken flocks all over the world. url: https://api.elsevier.com/content/article/pii/S1567134812003292 doi: 10.1016/j.meegid.2012.09.016 id: cord-017894-8iahlshj author: Loa, Chien Chang title: A Multiplex Polymerase Chain Reaction for Differential Detection of Turkey Coronavirus from Chicken Infectious Bronchitis Virus and Bovine Coronavirus date: 2015-09-10 words: 1306.0 sentences: 93.0 pages: flesch: 55.0 cache: ./cache/cord-017894-8iahlshj.txt txt: ./txt/cord-017894-8iahlshj.txt summary: title: A Multiplex Polymerase Chain Reaction for Differential Detection of Turkey Coronavirus from Chicken Infectious Bronchitis Virus and Bovine Coronavirus A multiplex polymerase chain reaction (PCR) method for differential detection of turkey coronavirus (TCoV), infectious bronchitis virus (IBV), and bovine coronavirus (BCoV) is presented in this chapter. Primers are designed from the conserved or variable regions of nucleocapsid (N) or spike (S) protein genes of TCoV, IBV, and BCoV and used in the same PCR reaction. There is a close antigenic and genomic relationship between TCoV and infectious bronchitis virus (IBV) according to studies of immunofl uorescent antibody assay ( IFA ), enzyme-linked immunosorbent assay ( ELISA ), and sequence analysis in our and other laboratories [ 3 -8 ] . Nucleocapsid protein gene sequence analysis reveals close genomic relationship between turkey coronavirus and avian infectious bronchitis virus Differential detection of turkey coronavirus, infectious bronchitis virus, and bovine coronavirus by a multiplex polymerase chain reaction abstract: A multiplex polymerase chain reaction (PCR) method for differential detection of turkey coronavirus (TCoV), infectious bronchitis virus (IBV), and bovine coronavirus (BCoV) is presented in this chapter. Primers are designed from the conserved or variable regions of nucleocapsid (N) or spike (S) protein genes of TCoV, IBV, and BCoV and used in the same PCR reaction. Reverse transcription followed by PCR reaction is used to amplify a portion of N or S gene of the corresponding coronaviruses. Two PCR products, a 356-bp band corresponding to N gene and a 727-bp band corresponding to S gene, are obtained for TCoV. In contrast, one PCR product of 356 bp corresponding to a fragment of N gene is obtained for IBV strains and one PCR product of 568 bp corresponding to a fragment of S gene is obtained for BCoV. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122580/ doi: 10.1007/978-1-4939-3414-0_12 id: cord-349149-nqsohp9h author: Lounas, A. title: The first evidence of a new genotype of nephropathogenic infectious bronchitis virus circulating in vaccinated and unvaccinated broiler flocks in Algeria date: 2018-11-29 words: 3700.0 sentences: 191.0 pages: flesch: 52.0 cache: ./cache/cord-349149-nqsohp9h.txt txt: ./txt/cord-349149-nqsohp9h.txt summary: title: The first evidence of a new genotype of nephropathogenic infectious bronchitis virus circulating in vaccinated and unvaccinated broiler flocks in Algeria BACKGROUND AND AIM: Avian infectious bronchitis virus (IBV) frequently infects broilers and is responsible for severe economic losses to the poultry industry worldwide. MATERIALS AND METHODS: 14 clinically diseased broiler flocks from Western and Central Algeria were sampled and analyzed by hemagglutination inhibition (HI) test and reverse transcriptase-polymerase chain reaction (RT-PCR) followed by phylogenic analysis. Clinically diseased broiler flocks were sampled and analyzed by the hemagglutination inhibition (HI) test and reverse transcriptase-polymerase chain reaction (RT-PCR) followed by phylogenic analysis. Phylogenetic analysis of avian infectious bronchitis virus S1 glycoprotein regions reveals emergence of a new genotype in Moroccan broiler chicken flocks S1 gene sequence analysis of a nephropathogenic strain of avian infectious bronchitis virus in Egypt Isolation and genetic analysis revealed no predominant new strains of avian infectious bronchitis virus circulating in South China during abstract: BACKGROUND AND AIM: Avian infectious bronchitis virus (IBV) frequently infects broilers and is responsible for severe economic losses to the poultry industry worldwide. It has also been associated with kidney damage in the broiler flocks. The aim of the present study is to determine the presence of IBV and its possible involvement in kidney damage of broiler chicks. MATERIALS AND METHODS: 14 clinically diseased broiler flocks from Western and Central Algeria were sampled and analyzed by hemagglutination inhibition (HI) test and reverse transcriptase-polymerase chain reaction (RT-PCR) followed by phylogenic analysis. RESULTS: The QX (100%) and 4/91 (60%) IBV serotypes were the most prevalent in the kidney damaged broilers regardless of vaccination status. The molecular detection of avian IBV by RT-PCR identified six samples as positive, of which only two isolates were typable by sequencing. We identified a novel IBDZ13a genotype which showed 93% sequence homology to the partial-S1 gene sequence of the IB 4/91 commercial vaccine strain. Sequencing analysis characterized this virus as a novel and divergent IB 4/91 field virus with eight amino acid substitutions that might have resulted in altered immunogenicity. CONCLUSION: The isolation of a new IBV strain (IBDZ13a) from vaccinated broiler flocks may explain the failure of the vaccination programs against IBV field strains. Combination of the HI test and RT-PCR indicated that the nephropathogenic IB outbreaks in broilers are related to this novel strain. url: https://www.ncbi.nlm.nih.gov/pubmed/30587900/ doi: 10.14202/vetworld.2018.1630-1636 id: cord-321602-88b2h06y author: Lv, Chenfei title: Construction of an infectious bronchitis virus vaccine strain carrying chimeric S1 gene of a virulent isolate and its pathogenicity analysis date: 2020-08-19 words: 4902.0 sentences: 266.0 pages: flesch: 58.0 cache: ./cache/cord-321602-88b2h06y.txt txt: ./txt/cord-321602-88b2h06y.txt summary: The full-length genomic cDNA of IBV vaccine strain H120 was constructed in pBAC vector from four IBV fragment subcloning vectors by homologous recombination, which contained the CMV promoter at the 5′ end and the hepatitis D virus ribozyme (HDVR) sequence and bovine growth hormone polyadenylation (BGH) sequence after the polyA tail at the 3′ end of the full-length cDNA. To construct the full-length cDNA of IBV H120 strain, total RNA was extracted from the allantoic fluid of SPF chicken embryonated eggs infected with H120 and transcribed to cDNA by reverse transcriptase using the Thermo Scientific RevertAid First-Strand cDNA Synthesis Kit (Thermo Fisher, USA). The SC021202 S1 gene containing same homology arms to those of the H120F4 was amplified from total RNA of allantoic fluid of SPF chicken embryonated eggs infected with IBV SC021202 by RT-PCR with the primers SCS1-F and SCS1-R listed in Table 1 and was then inserted into pBAC-F4-△S1 by the same homologous recombination process using the ClonExpress one-step cloning kit (Vazyme Biotechnology, China). abstract: ABSTRACT: Infectious bronchitis virus (IBV) is a member of genus gamma-coronavirus in the family Coronaviridae, causing serious economic losses to the poultry industry. Reverse genetics is a common technique to study the biological characteristics of viruses. So far, there is no BAC reverse genetic system available for rescue of IBV infectious clone. In the present study, a new strategy for the construction of IBV infectious cDNA clone was established. The full-length genomic cDNA of IBV vaccine strain H120 was constructed in pBAC vector from four IBV fragment subcloning vectors by homologous recombination, which contained the CMV promoter at the 5′ end and the hepatitis D virus ribozyme (HDVR) sequence and bovine growth hormone polyadenylation (BGH) sequence after the polyA tail at the 3′ end of the full-length cDNA. Subsequently, using the same technique, another plasmid pBAC-H120/SCS1 was also constructed, in which S1 gene from IBV H120 strain was replaced with that of a virulent SC021202 strain. Recombinant virus rH120 and rH120/SCS1 were rescued by transfecting the plasmids into BHK cells and passaged in embryonated chicken eggs. Finally, the pathogenicity of both the recombinant virus strains rH120 and rH120/SCS1 was evaluated in SPF chickens. The results showed that the chimeric rH120/SCS1 strain was not pathogenic compared with the wild-type IBV SC021202 strain and the chickens inoculated with rH120/SCS1 could resist challenge infection by IBV SC021202. Taken together, our results indicate that BAC reverse genetic system could be used to rescue IBV in vitro and IBV S1 protein alone might not be the key factor for IBV pathogenicity. KEY POINTS: • BAC vector was used to construct IBV full-length cDNA by homologous recombination. • Based on four subcloning vectors, a recombinant chimeric IBV H120/SCS1 was constructed and rescued. • Pathogenicity of H120/SCS1 was similar to that of H120, but different to that of SC021202. url: https://www.ncbi.nlm.nih.gov/pubmed/32813067/ doi: 10.1007/s00253-020-10834-2 id: cord-331020-lyxje82u author: M. Najimudeen, Shahnas title: Infectious Bronchitis Coronavirus Infection in Chickens: Multiple System Disease with Immune Suppression date: 2020-09-24 words: 6966.0 sentences: 349.0 pages: flesch: 37.0 cache: ./cache/cord-331020-lyxje82u.txt txt: ./txt/cord-331020-lyxje82u.txt summary: The evolution of new strains of IBV during the last nine decades against vaccine-induced immune response and changing clinical and pathological manifestations emphasize the necessity of the rational development of intervention strategies based on a thorough understanding of IBV interaction with the host. For example, chickens infected with certain strains of IBV such as Mass, QX-like strain or Aust T at ages of 1-14 days develop cystic oviducts without impaired ovarian functions, which leads to false layer syndrome with no egg production [15, [63] [64] [65] . One of the immune cell types that bridges innate and adaptive host responses is the macrophages, and the available data show that certain IBV serotypes (i.e., Mass and Conn) target respiratory tract macrophages and replicate within them, thus leading to a productive infection [59, 88] . abstract: In the early 1930s, infectious bronchitis (IB) was first characterized as a respiratory disease in young chickens; later, the disease was also described in older chickens. The etiology of IB was confirmed later as being due to a coronavirus: the infectious bronchitis virus (IBV). Being a coronavirus, IBV is subject to constant genome change due to mutation and recombination, with the consequence of changing clinical and pathological manifestations. The potential use of live attenuated vaccines for the control of IBV infection was demonstrated in the early 1950s, but vaccine breaks occurred due to the emergence of new IBV serotypes. Over the years, various IBV genotypes associated with reproductive, renal, gastrointestinal, muscular and immunosuppressive manifestations have emerged. IBV causes considerable economic impacts on global poultry production due to its pathogenesis involving multiple body systems and immune suppression; hence, there is a need to better understand the pathogenesis of infection and the immune response in order to help developing better management strategies. The evolution of new strains of IBV during the last nine decades against vaccine-induced immune response and changing clinical and pathological manifestations emphasize the necessity of the rational development of intervention strategies based on a thorough understanding of IBV interaction with the host. url: https://doi.org/10.3390/pathogens9100779 doi: 10.3390/pathogens9100779 id: cord-296611-ma32oz4o author: Ma, Tianxin title: Novel genotype of infectious bronchitis virus isolated in China date: 2019-01-29 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Recombination events are known to contribute to the emergence of novel infectious bronchitis virus (IBV) genotypes. In this study, we carried out detailed phylogenetic analysis and sequence comparisons based on 74 complete nucleotide sequences of the IBV S1 gene, including strain I0636/16 and 73 representative sequences from each genotype and lineage. The results showed that strain I0636/16 represented a novel genotype, designated as lineage 1 within genotype VII (GVII-1). Further comparative genomic analysis revealed at least two recombination sites that replaced the spike gene in a lineage 18 within genotype I (GI-18)-like virus with an as-yet-unidentified sequence, likely derived from another IBV strain, resulting a novel serotype with a lower affinity to the respiratory tract in chickens. To the best of our knowledge, this provides the first evidence for recombination leading to replacement of the complete spike gene and the emergence of a novel genotype/serotype with a lower affinity to the respiratory tract in chickens comparing to one of its parental virus ck/CH/LGX/111119. These results emphasize the importance of limiting exposure to novel IBVs that may serve as a source of genetic material for emerging viruses, as well as the importance of IBV surveillance in chicken flocks. url: https://www.ncbi.nlm.nih.gov/pubmed/30827386/ doi: 10.1016/j.vetmic.2019.01.020 id: cord-322516-wekvet6f author: Maceyka, Michael title: Ceramide Accumulation Uncovers a Cycling Pathway for the cis-Golgi Network Marker, Infectious Bronchitis Virus M Protein date: 1997-12-15 words: 6173.0 sentences: 326.0 pages: flesch: 53.0 cache: ./cache/cord-322516-wekvet6f.txt txt: ./txt/cord-322516-wekvet6f.txt summary: Short-term treatment with two inhibitors of sphingolipid synthesis had no effect on localization of IBV M or other Golgi markers. Treatment of cells with 100 M PDMP for 1 h had no effect on the localization of either protein (Fig. 4) , suggesting that the morphology of the Golgi was not greatly altered. Pretreatment with the earlier inhibitors reduced the PDMP-induced slowing of anterograde traffic by about half, suggesting that accumulation of newly synthesized ceramide at least partially mediates this effect. The pretreatment experiments suggested that increased levels of ceramide mediate the PDMP-induced effects on IBV M localization. However, neither ␤CA nor FB1 had an effect on the rate of anterograde traffic of VSV G or the localization of IC, CGN, or Golgi stack proteins. However, the glucosylceramide analogue PDMP, at a concentration that inhibits both GlcCer and SM synthases, causes a redistribution of IBV M to the ER and a slowing of anterograde traffic in BHK-21 cells. abstract: The M glycoprotein from the avian coronavirus, infectious bronchitis virus (IBV), contains information for localization to the cis-Golgi network in its first transmembrane domain. We hypothesize that localization to the Golgi complex may depend in part on specific interactions between protein transmembrane domains and membrane lipids. Because the site of sphingolipid synthesis overlaps the localization of IBV M, we asked whether perturbation of sphingolipids affected localization of IBV M. Short-term treatment with two inhibitors of sphingolipid synthesis had no effect on localization of IBV M or other Golgi markers. Thus, ongoing synthesis of these lipids was not required for proper localization. Surprisingly, a third inhibitor, d,l-threo-1-phenyl-2-decanoylamino-3-morpholino- 1-propanol (PDMP), shifted the steady-state distribution of IBV M from the Golgi complex to the ER. This effect was rapid and reversible and was also observed for ERGIC-53 but not for Golgi stack proteins. At the concentration of PDMP used, conversion of ceramide into both glucosylceramide and sphingomyelin was inhibited. Pretreatment with upstream inhibitors partially reversed the effects of PDMP, suggesting that ceramide accumulation mediates the PDMP-induced alterations. Indeed, an increase in cellular ceramide was measured in PDMP-treated cells. We propose that IBV M is at least in part localized by retrieval mechanisms. Further, ceramide accumulation reveals this cycle by upsetting the balance of anterograde and retrograde traffic and/ or disrupting retention by altering bilayer dynamics. url: https://www.ncbi.nlm.nih.gov/pubmed/9396747/ doi: nan id: cord-260799-kx6hfpu0 author: Mahmood, Zana H. title: Isolation and molecular characterization of Sul/01/09 avian infectious bronchitis virus, indicates the emergence of a new genotype in the Middle East date: 2011-05-12 words: 3504.0 sentences: 176.0 pages: flesch: 54.0 cache: ./cache/cord-260799-kx6hfpu0.txt txt: ./txt/cord-260799-kx6hfpu0.txt summary: title: Isolation and molecular characterization of Sul/01/09 avian infectious bronchitis virus, indicates the emergence of a new genotype in the Middle East Infectious bronchitis virus (IBV) was isolated from trachea and kidney tissues of eight broiler farms in Kurdistan region of North Iraq from 2008 to 2010. Veterinary Microbiology 150 (2011) 21-27 Infectious bronchitis virus (IBV) was isolated from trachea and kidney tissues of eight broiler farms in Kurdistan region of North Iraq from 2008 to 2010. In order to investigate IBV genotypes in Iraq, where the disease is endemic and widely spread in vaccinated and unvaccinated poultry farms mainly associated with kidney damage and urolethiasis, identification and molecular characterization of IBV (Sul/01/09) isolated from eight infected broiler farms was conducted and the deduced amino acid sequence of the S1 subunit of the virus was compared with geographically related isolates. abstract: Infectious bronchitis virus (IBV) was isolated from trachea and kidney tissues of eight broiler farms in Kurdistan region of North Iraq from 2008 to 2010. The birds were suffering from respiratory and nephropathological symptoms and lesions. A 1116 bp hyper mutable spike glycoprotein (S1) gene was amplified and sequenced using conventional RT-PCR. Sequence analysis and BLAST homology search in GenBank data base indicate that two of the farms were infected with the 4/91 strain, one with an unidentified IBV and five were infected with Sul/01/09. The birds in the latter five farms were suffering from nephropathogenic lesions, however, the virus was isolated from kidney but not from trachea in these cases. The birds were vaccinated regularly with 4/91 or MA5 vaccine. The deduced amino acid sequence of the isolated and amplified S1 subunit (372 aa) of Sul/01/09 was differed in 27–28% from that of all three vaccine strains (4/91, MA5, and H120) used in the region. This dissimilarity is most likely the cause of poor efficacy of vaccines used in the region, at least in five of these farms. Amino acid sequence comparison and phylogenetic tree analysis with other published IBV genotypes indicate that this newly isolated virus together with other regionally related and recently published isolates from Israel (IS/720/99, IS/885) and Egypt (egypt/Benisuef/01) belong to a new genotype. This is the first report of identification and genotyping of IBV isolate in Iraq, which indicate the circulation of 4/91 along with a new variant (Sul/01/09) of IBV in vaccinated broiler farms. url: https://www.sciencedirect.com/science/article/pii/S0378113510005882 doi: 10.1016/j.vetmic.2010.12.015 id: cord-001083-vy1nxax2 author: Malagnac, Fabienne title: Rab-GDI Complex Dissociation Factor Expressed through Translational Frameshifting in Filamentous Ascomycetes date: 2013-09-19 words: 6815.0 sentences: 339.0 pages: flesch: 55.0 cache: ./cache/cord-001083-vy1nxax2.txt txt: ./txt/cord-001083-vy1nxax2.txt summary: In the model fungus Podospora anserina, the PaYIP3 gene encoding the orthologue of the Saccharomyces cerevisiae YIP3 Rab-GDI complex dissociation factor expresses two polypeptides, one of which, the long form, is produced through a programmed translation frameshift. To construct a C-terminal GFP fusion of the frameshifted protein, the 535 bp 39-end fragment of the 39 ORF of the PaYIP3 gene was PCR-amplified using the orf39w-bgl2 (59-GAA-GATCTGGCTCTAGTGCATCCAGGACAC-39) and orf39c-sma1 (59-TTTCCCGGGTCGCTTTCCTTCTAGCAGTACC-39) oligonucleotides, containing, respectively, the BglII and SmaI sites (underlined in the sequence). The PaYIP3 c corrected allele was created by inserting a C in codon nu168, which is just upstream of the frameshift site, and produced the 61.6 kDa polypeptide resulting from the fusion of the proteins produced by the 39 and 59 ORFs. Introduction of PaYIP3 c did not result in the restoration of a wildtype phenotype: ring and ascospore production on wood shaving medium was identical to that observed with the PaYIP3 D mutant (Fig. 5) . abstract: In the model fungus Podospora anserina, the PaYIP3 gene encoding the orthologue of the Saccharomyces cerevisiae YIP3 Rab-GDI complex dissociation factor expresses two polypeptides, one of which, the long form, is produced through a programmed translation frameshift. Inactivation of PaYIP3 results in slightly delayed growth associated with modification in repartition of fruiting body on the thallus, along with reduced ascospore production on wood. Long and short forms of PaYIP3 are expressed in the mycelium, while only the short form appears expressed in the maturing fruiting body (perithecium). The frameshift has been conserved over the evolution of the Pezizomycotina, lasting for over 400 million years, suggesting that it has an important role in the wild. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3777964/ doi: 10.1371/journal.pone.0073772 id: cord-296167-np0b9a7o author: Mardani, Karim title: Naturally occurring recombination between distant strains of infectious bronchitis virus date: 2010-06-24 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: New variants of infectious bronchitis virus (IBV) have emerged in Australia despite its geographical isolation and intensive vaccination programs. In the present study, the 3′ terminal 7.2 kb of the genome of a recently isolated variant of IBV (N1/03) was sequenced and compared with the sequences of classical and novel strains of IBV, the two main groups of these viruses in Australia. The comparison revealed that recombination between classical and novel IBVs was responsible for the emergence of the new variant. It was concluded that novel IBVs, which have not been detected since 1993, and which are phylogenically more distant from classical IBVs than turkey coronaviruses, might still be circulating and contributing to the evolution of IBV in Australia. url: https://doi.org/10.1007/s00705-010-0731-z doi: 10.1007/s00705-010-0731-z id: cord-346629-770qyee8 author: Mase, M. title: Phylogenetic analysis of avian infectious bronchitis virus strains isolated in Japan date: 2004-07-15 words: 2367.0 sentences: 137.0 pages: flesch: 50.0 cache: ./cache/cord-346629-770qyee8.txt txt: ./txt/cord-346629-770qyee8.txt summary: title: Phylogenetic analysis of avian infectious bronchitis virus strains isolated in Japan To define the origin and evolution of recent avian infectious bronchitis virus (IBV) in Japan, a genetic analysis was performed. By phylogenetic analysis based on the S1 gene including the sequence of the hypervariable regions, IBV isolates in Japan were classified into five genetic groups, which included two already-known groups (Mass and Gray). In this study, to define the origin and evolution of recent IBV in Japan, we determined the nucleotide sequences of IBV isolated in Japan using the reverse transcriptase-polymerase chain reaction (RT-PCR) method coupled with direct sequencing, and analyzed the sequences phylogenetically with viruses isolated in other countries. By phylogenetic analysis, the IBV isolates in Japan used in this study were divided into five genetic groups (Fig. 1 ). Typing of field isolates of infectious bronchitis virus based on the sequence of the hypervariable region in the S1 gene abstract: To define the origin and evolution of recent avian infectious bronchitis virus (IBV) in Japan, a genetic analysis was performed. By phylogenetic analysis based on the S1 gene including the sequence of the hypervariable regions, IBV isolates in Japan were classified into five genetic groups, which included two already-known groups (Mass and Gray). Among them, three major genetic groups were associated with the recent outbreaks of IB in Japan. One group is indigenous to Japan and could not be placed within the known existing groups in other countries. The remaining two groups, which have emerged recently, are related to isolates in China and Taiwan. url: https://www.ncbi.nlm.nih.gov/pubmed/15290359/ doi: 10.1007/s00705-004-0369-9 id: cord-296831-wdpatr2z author: Matoo, Javaid Jeelani title: Resiquimod enhances mucosal and systemic immunity against avian infectious bronchitis virus vaccine in the chicken date: 2018-04-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Adjuvant enhancing mucosal immune response is preferred in controlling many pathogens at the portal of entry. Earlier, we reported that a toll-like-receptor 7 (TLR7) agonist, resiquimod (R-848), stimulated the systemic immunity when adjuvanted with the inactivated Newcastle disease virus vaccine in the chicken. Here, we report the effect of R-848 when adjuvanted with live or inactivated avian infectious bronchitis virus (IBV) vaccines with special emphasis on mucosal immunity. Specific pathogen free (SPF) chicks (n = 60) were equally divided into six groups at two weeks of age and immunized with either inactivated or live IBV vaccine adjuvanted with or without R-848. Groups that received either PBS or R-848 served as control. A booster was given on 14 days post-immunization (dpi). R-848 enhanced the antigen specific humoral and cellular immune responses when co-administered with the vaccines as evidenced by an increase in the antibody titre in ELISA and stimulation index in lymphocyte transformation test (LTT) till 35 dpi and increased proportion of CD4(+) and CD8(+) T cells on 21 dpi in the flow cytometry. Interestingly, it potentiated the IgA responses in the tear and intestinal secretions when used with both live and inactivated IBV vaccines. The combination of IBV vaccine with R-848 significantly up-regulated the transforming growth factor beta 4 (TGFβ4) transcripts in the peripheral blood mononuclear cells (PBMCs) than that of the respective vaccine per se. An enhanced secretory IgA response is likely due to the up-regulation of TGFβ4, which is responsible for class switching to IgA. In conclusion, co-administration of R-848 with inactivated or live IBV vaccine enhanced the systemic as well as mucosal immune responses in the chicken. url: https://api.elsevier.com/content/article/pii/S0882401018302948 doi: 10.1016/j.micpath.2018.04.012 id: cord-252048-ftbjsoup author: McKinley, Enid T. title: Attenuated live vaccine usage affects accurate measures of virus diversity and mutation rates in avian coronavirus infectious bronchitis virus date: 2011-04-22 words: 6380.0 sentences: 309.0 pages: flesch: 55.0 cache: ./cache/cord-252048-ftbjsoup.txt txt: ./txt/cord-252048-ftbjsoup.txt summary: The full-length genomes of 11 infectious bronchitis virus (IBV) field isolates from three different types of the virus; Massachusetts (Mass), Connecticut (Conn) and California (CAL) isolated over a 41, 25 and 8 year period respectively, were sequenced and analyzed to determine the mutation rates and level of polymorphisms across the genome. The genetic data also identified a recombinant IBV isolate with 7 breakpoints distributed across the entire genome suggesting that viruses within the same serotype can have a high degree of genetic variability outside of the spike gene. The objective of this study was to determine the levels of polymorphism across the entire genome of IBV isolates with similar spike genes and to examine the mutation rates for viruses with and without vaccine selection pressure. abstract: The full-length genomes of 11 infectious bronchitis virus (IBV) field isolates from three different types of the virus; Massachusetts (Mass), Connecticut (Conn) and California (CAL) isolated over a 41, 25 and 8 year period respectively, were sequenced and analyzed to determine the mutation rates and level of polymorphisms across the genome. Positive selection was not detected and mutation rates ranged from 10(−4) to 10(−6) substitutions/site/year for Mass and Conn IBV types where attenuated live vaccines are routinely used to control the disease. In contrast, for CAL type viruses, for which no vaccine exists, positive selection was detected and mutation rates were 10 fold higher ranging from 10(−2) to 10(−3) substitutions/site/year. Lower levels of genetic diversity among the Mass and Conn viruses as well as sequence similarities with vaccine virus genomes suggest that the origin of the Mass and all but one of the Conn viruses was likely vaccine virus that had been circulating in the field for an unknown but apparently short period of time. The genetic data also identified a recombinant IBV isolate with 7 breakpoints distributed across the entire genome suggesting that viruses within the same serotype can have a high degree of genetic variability outside of the spike gene. These data are important because inaccurate measures of genetic diversity and mutation rates could lead to underestimates of the ability of IBV to change and potentially emerge to cause disease. url: https://doi.org/10.1016/j.virusres.2011.04.006 doi: 10.1016/j.virusres.2011.04.006 id: cord-308950-bl83r4v3 author: Miguel, B. title: The role of feline aminopeptidase N as a receptor for infectious bronchitis virus : Brief Review date: 2002 words: 2543.0 sentences: 157.0 pages: flesch: 56.0 cache: ./cache/cord-308950-bl83r4v3.txt txt: ./txt/cord-308950-bl83r4v3.txt summary: Our objective was to determine if fAPN can serve as a receptor for infectious bronchitis virus (IBV). Feline kidney cells that express fAPN and hamster kidney fibroblasts that do not express fAPN were inoculated with IBV and monitored for replication by indirect fluorescent assay and confocal microscopy and in chicken embryonated eggs. To evaluate the permissiveness of cells to IBV, monolayers of transfected (pBK-fAPN and pBK-CMV) BHK-21, non-transfected BHK-21 and FEK on coverslips were infected with a 10 3.2 EID 50 of Ark/IBV virus. To test the hypothesis that the feline APN had a role in permissiveness of FEK cells to Ark/IBV, BHK-21 cells were transfected with pBK-CMV plasmid or pBK-fAPN. The BHK-21 cells transfected with pBK-fAPN were shown to express the fAPN receptor on the cell surface (Fig. 3) , and were permissive to Ark/IBV (Figs. abstract: Feline aminopeptidase N (fAPN) has been shown to serve as a receptor for feline, canine, porcine and human coronaviruses. Our objective was to determine if fAPN can serve as a receptor for infectious bronchitis virus (IBV). Feline kidney cells that express fAPN and hamster kidney fibroblasts that do not express fAPN were inoculated with IBV and monitored for replication by indirect fluorescent assay and confocal microscopy and in chicken embryonated eggs. The results showed that the feline cells were permissive to IBV but the hamster cells were not. The hamster cells became permissive to IBV after transfection with a fAPN cDNA suggesting that the feline APN molecule plays a role in IBV entry. url: https://www.ncbi.nlm.nih.gov/pubmed/12417943/ doi: 10.1007/s00705-002-0888-1 id: cord-329429-ur8g68vp author: Miłek, Justyna title: Coronaviruses in Avian Species – Review with Focus on Epidemiology and Diagnosis in Wild Birds date: 2018-12-10 words: 3809.0 sentences: 187.0 pages: flesch: 50.0 cache: ./cache/cord-329429-ur8g68vp.txt txt: ./txt/cord-329429-ur8g68vp.txt summary: Within the gamma-CoVs the main representative is avian coronavirus, a taxonomic name which includes the highly contagious infectious bronchitis viruses (IBVs) in chickens and similar viruses infecting other domestic birds such as turkeys, guinea fowls, or quails. The methods adopted in monitoring studies of CoVs in different avian species are mainly based on detection of conservative regions within the viral replicase, nucleocapsid genes, and 3''UTR or 5''UTR. The purpose of this review is to summarise recent discoveries in the areas of epidemiology and diagnosis of CoVs in avian species and to understand the role of wild birds in the virus distribution. This taxonomic name includes IBV which causes a highly contagious disease of chickens, and genetically similar viruses isolated from other domestic galliformes: turkey coronavirus (TCoV), responsible for turkey enteritis, and the more recently detected guinea fowl coronavirus (GfCoV), the aetiological factor of fulminating disease in this species (2, 6, 27) . abstract: Coronaviruses (CoVs) are a large group of enveloped viruses with a single-strand RNA genome, which continuously circulate in mammals and birds and pose a threat to livestock, companion animals, and humans. CoVs harboured by avian species are classified to the genera gamma- and deltacoronaviruses. Within the gamma-CoVs the main representative is avian coronavirus, a taxonomic name which includes the highly contagious infectious bronchitis viruses (IBVs) in chickens and similar viruses infecting other domestic birds such as turkeys, guinea fowls, or quails. Additionally, IBVs have been detected in healthy wild birds, demonstrating that they may act as the vector between domestic and free-living birds. Moreover, CoVs other than IBVs, are identified in wild birds, which suggests that wild birds play a key role in the epidemiology of other gammaCoVs and deltaCoVs. Development of molecular techniques has significantly improved knowledge of the prevalence of CoVs in avian species. The methods adopted in monitoring studies of CoVs in different avian species are mainly based on detection of conservative regions within the viral replicase, nucleocapsid genes, and 3’UTR or 5’UTR. The purpose of this review is to summarise recent discoveries in the areas of epidemiology and diagnosis of CoVs in avian species and to understand the role of wild birds in the virus distribution. url: https://www.ncbi.nlm.nih.gov/pubmed/30584600/ doi: 10.2478/jvetres-2018-0035 id: cord-273661-egpyvqrw author: Mo, Mei-Lan title: Molecular Characterization of Major Structural Protein Genes of Avian Coronavirus Infectious Bronchitis Virus Isolates in Southern China date: 2013-12-04 words: 4705.0 sentences: 215.0 pages: flesch: 51.0 cache: ./cache/cord-273661-egpyvqrw.txt txt: ./txt/cord-273661-egpyvqrw.txt summary: To gain comprehensive genetic information of circulating avian coronavirus infectious bronchitis virus (IBV) isolates in China, analysis of the phylogenetic tree, entropy of the amino acid sequences, and the positive selection as well as computational recombinations of S1, M and N genes of 23 IBV isolates was conducted in the present study. Therefore, in the present study we performed the analysis of the phylogenetic tree, of the entropy of the amino acid sequences, of positive selection as well as of computational recombination based on the sequencing results of the viral structural protein genes S1, M and N in order to provide molecular epidemiology information of IBV and to lay a good foundation for the control of IB in the field. abstract: To gain comprehensive genetic information of circulating avian coronavirus infectious bronchitis virus (IBV) isolates in China, analysis of the phylogenetic tree, entropy of the amino acid sequences, and the positive selection as well as computational recombinations of S1, M and N genes of 23 IBV isolates was conducted in the present study. The phylogenetic trees based on the S1, M and N genes exhibited considerably different topology and the CK/CH/LSC/99I-type isolates were the predominant IBVs based on the phylogenetic analysis of S1 gene. Results of entropy of amino acid sequences revealed that the S1 gene had the largest variation; the M gene had less variation than the N gene. Positive selections were detected in not only S1 but also M and N gene proteins. In addition, five S1 gene recombinants between vaccine strain 4/91 and CK/CH/LSC/99I-type field isolate were confirmed. In conclusion, multiple IBV genotypes co-circulated; genetic diversity and positive selections existed in S1, M and N genes; 4/91 vaccine recombinants emerged in China. Our results show that field IBVs in China are continuing to evolve and vaccine strains may have an important role in the appearance of new IBV strains via recombination. In addition, the present study indicates that IBV evolution is driven by both generations of genetic diversity and selection. url: https://doi.org/10.3390/v5123007 doi: 10.3390/v5123007 id: cord-007648-tm0hn0hz author: Mockett, A.P.Adrian title: Envelope proteins of avian infectious bronchitis virus: Purification and biological properties date: 2002-12-20 words: 2217.0 sentences: 140.0 pages: flesch: 56.0 cache: ./cache/cord-007648-tm0hn0hz.txt txt: ./txt/cord-007648-tm0hn0hz.txt summary: Immunoadsorbents, made with monoclonal antibodies, were used to purify the spike and membrane proteins of infectious bronchitis virus (IBV). A second inoculation of virus at 42 days induced an anamnestic antibody response to the spike and membrane proteins and also for the neutralizing antibodies. The objectives of this work were to produce immunoadsorbents using monoclonal antibodies which have been prepared previously (Mockett et al., 1984) and to purify the virus-coded proteins of the viral envelope in a single step in relatively large amounts. In addition the sequential humoral antibody response of chickens after IBV infection has been studied using the purified viral proteins and whole virus in ELISAs and compared to the results using the neutralization test. Thc chicken, about 10 days after an IBV infection, has antibodies to both the spike and membrane proteins in its serum but only very low concentrations of neutralizing antibodies. abstract: Immunoadsorbents, made with monoclonal antibodies, were used to purify the spike and membrane proteins of infectious bronchitis virus (IBV). The purified proteins were inoculated into rabbits to produce antisera. The rabbit anti-spike sera neutralized the infectivity of the virus whereas the anti-membrane sera did not. IBV-infected chickens produced antibodies to both the spike and membrane proteins. Both these antibodies were at their highest concentration about 9–11 days after inoculation, whereas neutralizing antibodies were present only at very low concentrations at that time. Neutralizing antibodies were at their highest concentration 21 days after inoculation. A second inoculation of virus at 42 days induced an anamnestic antibody response to the spike and membrane proteins and also for the neutralizing antibodies. The neutralizing, anti-spike and anti-membrane antibodies all reached highest concentrations 7–11 days after this inoculation. The advantages of purifying viral proteins using affinity chromatography with monoclonal antibodies are discussed. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7119818/ doi: 10.1016/0166-0934(85)90138-7 id: cord-285330-td4vr0zv author: Mohammadi, Ali title: Viral quantity and pathological changes in broilers experimentally infected by IRFIBV32 isolate of infectious bronchitis virus date: 2015-11-12 words: 3157.0 sentences: 180.0 pages: flesch: 56.0 cache: ./cache/cord-285330-td4vr0zv.txt txt: ./txt/cord-285330-td4vr0zv.txt summary: title: Viral quantity and pathological changes in broilers experimentally infected by IRFIBV32 isolate of infectious bronchitis virus An Iranian isolate of avian infectious bronchitis virus IRFIBV32 was quantified in experimentally infected broilers using real-time reverse transcriptase polymerase chain reaction and histopathological changes was investigated. In this study, we identified IBV load in different tissues of experimentally infected broilers to clarify the replication strength of IRFIBV32 Isolate at intervals post challenge. Gross lesions were recorded and their trachea, lungs, kidneys, caecal tonsils, testes and ovaries were aseptically collected separately for the virus detection, titration and histopathological evaluations. We detected the viral RNA in the caecal tonsils of infected chicken from 1 to 20 dpi and the maximal loads of the virus were on 5 dpi. Pathogenesis and tissue distribution of avian infectious bronchitis virus isolate IRFIBV32 (793/b serotype) in experimentally infected broiler chickens Development and evaluation of a real-time Taqman RT-PCR assay for the detection of infectious bronchitis virus from infected chickens abstract: An Iranian isolate of avian infectious bronchitis virus IRFIBV32 was quantified in experimentally infected broilers using real-time reverse transcriptase polymerase chain reaction and histopathological changes was investigated. Thirty-six 3-week-old commercial broilers were inoculated by 10(5) ELD50/0.1 ml of the virus. On the various days post inoculation (dpi) different tissues were collected. The virus strongly started the replication in trachea at 1 dpi and reached to the maximum titer at 3 dpi. The highest IBV RNA level was shown in this organ. In lung, the virus was replicated with the titer lower than that of the trachea, but it rose up more at 5 dpi. The kidneys were the tissues with the least viral genome copy number, although the duration of the virus presence was considerable. The virus replicated in testes sooner than ovaries also disappeared sooner but the maximum viral yield in the ovaries was more. The virus titer in the studied tissues had an interesting fluctuation especially in caecal tonsils. Testes and ovaries were the organs that the virus could reactivate without using any chemical. The most severe lesions were observed in tracheae but they appeared in the lungs later. Lymphocyte infiltration in the kidneys was noted from 5 dpi even sooner than the lungs. There were no lesions in the caecal tonsils, testes and ovaries in spite of the virus replication in a high titer. url: https://www.ncbi.nlm.nih.gov/pubmed/26645044/ doi: 10.1007/s13337-015-0286-4 id: cord-299428-gon6bzat author: Mondal, Shankar title: Sequence analysis of infectious bronchitis virus isolates from the 1960s in the United States date: 2012-10-11 words: 3262.0 sentences: 152.0 pages: flesch: 56.0 cache: ./cache/cord-299428-gon6bzat.txt txt: ./txt/cord-299428-gon6bzat.txt summary: To better understand the molecular epidemiology of infectious bronchitis virus (IBV) in the United States following the introduction of commercial IBV vaccines, we sequenced the S1 and N structural protein genes of thirteen IBV field isolates collected in the 1960s. Analysis of the S1 sequence showed that seven isolates were of the Massachusetts (Mass) genotype, five were SE17, and one was of the Connecticut (Conn) genotype, suggesting that these three IBVs were circulating in commercial poultry raised in different regions in the United States during the 1960s. In addition, the Mass-type isolates had high levels of sequence identity in the S1 gene compared with widely used modified live vaccines (Mass41, Ma5 and H120) and modern field strains from the USA and other countries, suggesting a common ancestor. abstract: To better understand the molecular epidemiology of infectious bronchitis virus (IBV) in the United States following the introduction of commercial IBV vaccines, we sequenced the S1 and N structural protein genes of thirteen IBV field isolates collected in the 1960s. Analysis of the S1 sequence showed that seven isolates were of the Massachusetts (Mass) genotype, five were SE17, and one was of the Connecticut (Conn) genotype, suggesting that these three IBVs were circulating in commercial poultry raised in different regions in the United States during the 1960s. The S1 genes of Mass-type isolates had high levels of sequence variation, representing 81.3-81.9 % nucleotide (nt) and 77.3-78.7 % amino acid (aa) identity when compared to those of the SE17-type isolates. In contrast, the N genes from the same isolates were less variable (>92 % nt and >93 % aa identity) when compared to those of the SE17-type isolates. Phylogenetic analysis based on the S1 gene indicated that one isolate (L748) was more closely related to the Mass type. In contrast, phylogenetic analysis based on the N gene showed that L748 was more closely related to the SE17 type, indicating that there had been exchange of S1 genetic materials between Mass- and SE17-like viruses. In addition, the Mass-type isolates had high levels of sequence identity in the S1 gene compared with widely used modified live vaccines (Mass41, Ma5 and H120) and modern field strains from the USA and other countries, suggesting a common ancestor. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00705-012-1500-y) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s00705-012-1500-y doi: 10.1007/s00705-012-1500-y id: cord-322410-k23engcx author: Naguib, Mahmoud M. title: New real time and conventional RT-PCRs for updated molecular diagnosis of infectious bronchitis virus infection (IBV) in chickens in Egypt associated with frequent co-infections with avian influenza and Newcastle Disease viruses date: 2017-03-21 words: 5012.0 sentences: 259.0 pages: flesch: 52.0 cache: ./cache/cord-322410-k23engcx.txt txt: ./txt/cord-322410-k23engcx.txt summary: title: New real time and conventional RT-PCRs for updated molecular diagnosis of infectious bronchitis virus infection (IBV) in chickens in Egypt associated with frequent co-infections with avian influenza and Newcastle Disease viruses Conventional RT-PCRs amplifying hypervariable regions (HVRs 1–2 and 3) of the IBV S1 gene were developed and amplificates used for nucleotide sequence-based typing of IBV field strains in Egyptian chickens directly from clinical samples. The specificity of RT-qPCR primer set was evaluated by examining different avian respiratory viruses circulating in poultry in Egypt including AIV H5N1, H9N2 and NDV as well as different coronaviruses including a panel of IBV reference strains as listed in the materials section. Within HVR 1, 2 sequences, however, the existence of two distinct Table 3 RT-qPCRs reveal frequent co-infections in Egyptian poultry samples with avian influenza (AIV), Newcastle Disease (NDV) and infectious bronchitis viruses (IBV). abstract: In Egypt, currently two geographically restricted genotypes of the infectious bronchitis coronavirus (IBV) are circulating with detrimental effects for poultry industry. A sensitive real-time RT-PCR assay targeting the IBV nucleocapsid gene (N) was developed to screen clinical samples for presence of IBV. Conventional RT-PCRs amplifying hypervariable regions (HVRs 1–2 and 3) of the IBV S1 gene were developed and amplificates used for nucleotide sequence-based typing of IBV field strains in Egyptian chickens directly from clinical samples. url: https://www.ncbi.nlm.nih.gov/pubmed/28336367/ doi: 10.1016/j.jviromet.2017.02.018 id: cord-339259-4oi7slk9 author: Naguib, Mahmoud M. title: Full genome sequence analysis of a newly emerged QX-like infectious bronchitis virus from Sudan reveals distinct spots of recombination date: 2016-10-26 words: 4017.0 sentences: 238.0 pages: flesch: 52.0 cache: ./cache/cord-339259-4oi7slk9.txt txt: ./txt/cord-339259-4oi7slk9.txt summary: title: Full genome sequence analysis of a newly emerged QX-like infectious bronchitis virus from Sudan reveals distinct spots of recombination By phylogenetic analysis based on the whole S1-gene according to (Valastro et al., 2016) it appeared that the IBV/Ck/Sudan/AR251-15/2014 is closely related to ITA/90254/ 2005 and the previously reported recombinant strains detected in South Africa (Ck/ZA/3665/11) and Sweden (Ck/SWE/0658946/10) which are clustered together within GI-19 lineage (Fig. 3) . The results showed that the Sudanese isolate was a recombinant virus which probably emerged from at least three different genotypes, including the 4/91 genotype as a major parent and the H120 vaccine strain as well as Italy/90254/2005-like viruses as minor parents (Fig. 4) . Characterization and analysis of the full-length genome of a strain of the european qx-like genotype of infectious bronchitis virus Complete genomic sequence analysis of infectious bronchitis virus ark dpi strain and its evolution by recombination abstract: Infectious bronchitis virus (IBV) infection continues to cause economically important diseases in poultry while different geno- and serotypes continue to circulate globally. Two infectious bronchitis viruses (IBV) were isolated from chickens with respiratory disease in Sudan. Sequence analysis of the hypervariable regions of the S1 gene revealed a close relation to the QX-like genotype which has not been detected in Sudan before. Whole genome analysis of IBV/Ck/Sudan/AR251–15/2014 isolate by next generation sequencing revealed a genome size of 27,646 nucleotides harbouring 13 open reading frames: 5′-1a-1b-S-3a-3b-E-M-4b-4c-5a-5b-N-6b-3′. Highest nucleotide sequence identity of 93% for the whole genome was found with the Chinese IBV strain Ck/CH/LHLJ/140906, the Italian IBV isolate ITA/90254/2005 and the 4/91 vaccine strain. Phylogenetic analysis of the S1 gene revealed that the IBV/Ck/Sudan/AR251–15/2014 isolate clustered together with viruses of the GI-19 lineage. Recombination analysis gave evidence for distinct patterns of origin of RNA in the Sudanese isolate in multiple genes. Several sites of recombination were scattered throughout the genome suggesting that the Sudan-QX-like strain emerged as a unique recombinant from multiple recombination events of parental viruses from 4/91, H120 and ITA/90254/2005 genotypes. The Sudanese QX-like isolate is plausibly genetically different from IBV strains previously reported in Africa and elsewhere. url: https://doi.org/10.1016/j.meegid.2016.10.017 doi: 10.1016/j.meegid.2016.10.017 id: cord-002407-25cawzi0 author: Nogales, Aitor title: Reverse Genetics Approaches for the Development of Influenza Vaccines date: 2016-12-22 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Influenza viruses cause annual seasonal epidemics and occasional pandemics of human respiratory disease. Influenza virus infections represent a serious public health and economic problem, which are most effectively prevented through vaccination. However, influenza viruses undergo continual antigenic variation, which requires either the annual reformulation of seasonal influenza vaccines or the rapid generation of vaccines against potential pandemic virus strains. The segmented nature of influenza virus allows for the reassortment between two or more viruses within a co-infected cell, and this characteristic has also been harnessed in the laboratory to generate reassortant viruses for their use as either inactivated or live-attenuated influenza vaccines. With the implementation of plasmid-based reverse genetics techniques, it is now possible to engineer recombinant influenza viruses entirely from full-length complementary DNA copies of the viral genome by transfection of susceptible cells. These reverse genetics systems have provided investigators with novel and powerful approaches to answer important questions about the biology of influenza viruses, including the function of viral proteins, their interaction with cellular host factors and the mechanisms of influenza virus transmission and pathogenesis. In addition, reverse genetics techniques have allowed the generation of recombinant influenza viruses, providing a powerful technology to develop both inactivated and live-attenuated influenza vaccines. In this review, we will summarize the current knowledge of state-of-the-art, plasmid-based, influenza reverse genetics approaches and their implementation to provide rapid, convenient, safe and more effective influenza inactivated or live-attenuated vaccines. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5297655/ doi: 10.3390/ijms18010020 id: cord-319253-8bssrn9o author: OKINO, Cintia Hiromi title: Rapid detection and differentiation of avian infectious bronchitis virus: an application of Mass genotype by melting temperature analysis in RT-qPCR using SYBR Green I date: 2018-02-27 words: 2502.0 sentences: 114.0 pages: flesch: 42.0 cache: ./cache/cord-319253-8bssrn9o.txt txt: ./txt/cord-319253-8bssrn9o.txt summary: title: Rapid detection and differentiation of avian infectious bronchitis virus: an application of Mass genotype by melting temperature analysis in RT-qPCR using SYBR Green I A method based on Melting Temperature analysis of Hypervariable regions (HVR) of S1 gene within a RT-qPCR was developed to detect different genotypes of avian infectious bronchitis virus (IBV) and identify the Mass genotype. Finally, considering that HVR I and HVR II of S1 gene were thought to be closely associated with major neutralization epitopes and consequently a reliable target for genotyping method, we developed a diagnostic method using Melting Temperature analysis based on these regions aiming to rapid detect and differentiate Mass and non-Mass IBV strains in samples previously isolated and directly in clinical samples. A Real-Time Reverse-Transcription Polymerase Chain Reaction for Differentiation of Massachusetts Vaccine and Brazilian Field Genotypes of Avian Infectious Bronchitis Virus abstract: A method based on Melting Temperature analysis of Hypervariable regions (HVR) of S1 gene within a RT-qPCR was developed to detect different genotypes of avian infectious bronchitis virus (IBV) and identify the Mass genotype. The method was able to rapidly identify the Mass genotype among IBV field isolates, vaccine attenuated strains and reference M41 strain in allantoic liquid and also directly in tissues. The RT-qPCR developed detected the virus in both tracheal and pulmonary samples from M41-infected or H120-infected birds, in a larger post-infection period compared to detection by standard method of virus isolation. RT-qPCR method tested provided a sensitivity and rapid approach for screening on IBV detection and Mass genotyping from IBV isolates. url: https://www.ncbi.nlm.nih.gov/pubmed/29491226/ doi: 10.1292/jvms.17-0566 id: cord-329468-vjsurl60 author: Okino, Cintia Hiromi title: Early immune responses and development of pathogenesis of avian infectious bronchitis viruses with different virulence profiles date: 2017-02-15 words: 5853.0 sentences: 261.0 pages: flesch: 48.0 cache: ./cache/cord-329468-vjsurl60.txt txt: ./txt/cord-329468-vjsurl60.txt summary: This study compared the expression profile of genes related to immune responses in tracheal samples after challenge with two Brazilian field isolates (A and B) of IBV from the same genotype, associating these responses with viral replication and with pathological changes in trachea and kidney. Cell-mediated immune (CMI) related genes presented also lower levels of expression in tracheal samples from birds challenged with B isolate at 1dpi. This differential pattern of early immune responses developed after challenge with IBV B isolate, related to the downregulation of TLR7, leading to insufficient pro-inflammatory response and lower CMI responses, seem to have an association with a most severe renal lesion and an enhanced capability of replication of this isolate in chicken. In this study, we found a suppressive effect on expression of some early innate and adaptive cell-mediated immune genes in the primary site of virus replication (trachea) from chickens infected with one of the tested IBV isolates (B). abstract: Avian infectious bronchitis virus (IBV) primarily replicates in epithelial cells of the upper respiratory tract of chickens, inducing both morphological and immune modulatory changes. However, the association between the local immune responses induced by IBV and the mechanisms of pathogenesis has not yet been completely elucidated. This study compared the expression profile of genes related to immune responses in tracheal samples after challenge with two Brazilian field isolates (A and B) of IBV from the same genotype, associating these responses with viral replication and with pathological changes in trachea and kidney. We detected a suppressive effect on the early activation of TLR7 pathway, followed by lower expression levels of inflammatory related genes induced by challenge with the IBV B isolate when compared to the challenge with to the IBV A isolate. Cell-mediated immune (CMI) related genes presented also lower levels of expression in tracheal samples from birds challenged with B isolate at 1dpi. Increased viral load and a higher percentage of birds with relevant lesions were observed in both tracheal and renal samples from chickens exposed to challenge with IBV B isolate. This differential pattern of early immune responses developed after challenge with IBV B isolate, related to the downregulation of TLR7, leading to insufficient pro-inflammatory response and lower CMI responses, seem to have an association with a most severe renal lesion and an enhanced capability of replication of this isolate in chicken. url: https://www.ncbi.nlm.nih.gov/pubmed/28199419/ doi: 10.1371/journal.pone.0172275 id: cord-272693-432ixb7g author: Phillips, J. E. title: Changes in nonstructural protein 3 are associated with attenuation in avian coronavirus infectious bronchitis virus date: 2011-09-10 words: 6255.0 sentences: 290.0 pages: flesch: 56.0 cache: ./cache/cord-272693-432ixb7g.txt txt: ./txt/cord-272693-432ixb7g.txt summary: Full-length genome sequencing of pathogenic and attenuated (for chickens) avian coronavirus infectious bronchitis virus (IBV) strains of the same serotype was conducted to identify genetic differences between the pathotypes. Analysis of the consensus full-length genome for three different IBV serotypes (Ark, GA98, and Mass41) showed that passage in embryonated eggs, to attenuate the viruses for chickens, resulted in 34.75–43.66% of all the amino acid changes occurring in nsp 3 within a virus type, whereas changes in the spike glycoprotein, thought to be the most variable protein in IBV, ranged from 5.8 to 13.4% of all changes. In this study, we analyzed the consensus full-length genome for the pathogenic and attenuated viruses of three different IBV types and showed that within a virus type, 34.75 to 43.66% of all the amino acid changes between the pathotypes occurred in nsp 3, whereas changes in spike ranged from 5.8 to 13.4% of all changes. abstract: Full-length genome sequencing of pathogenic and attenuated (for chickens) avian coronavirus infectious bronchitis virus (IBV) strains of the same serotype was conducted to identify genetic differences between the pathotypes. Analysis of the consensus full-length genome for three different IBV serotypes (Ark, GA98, and Mass41) showed that passage in embryonated eggs, to attenuate the viruses for chickens, resulted in 34.75–43.66% of all the amino acid changes occurring in nsp 3 within a virus type, whereas changes in the spike glycoprotein, thought to be the most variable protein in IBV, ranged from 5.8 to 13.4% of all changes. The attenuated viruses did not cause any clinical signs of disease and had lower replication rates than the pathogenic viruses of the same serotype in chickens. However, both attenuated and pathogenic viruses of the same serotype replicated similarly in embryonated eggs, suggesting that mutations in nsp 3, which is involved in replication of the virus, might play an important role in the reduced replication observed in chickens leading to the attenuated phenotype. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11262-011-0668-7) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/21909766/ doi: 10.1007/s11262-011-0668-7 id: cord-321545-3gzj09mr author: Pohuang, Tawatchai title: Detection and molecular characterization of infectious bronchitis virus isolated from recent outbreaks in broiler flocks in Thailand date: 2009-09-07 words: 2537.0 sentences: 138.0 pages: flesch: 55.0 cache: ./cache/cord-321545-3gzj09mr.txt txt: ./txt/cord-321545-3gzj09mr.txt summary: title: Detection and molecular characterization of infectious bronchitis virus isolated from recent outbreaks in broiler flocks in Thailand The isolates in group II showed a close relationship with Chinese IBVs. They had nucleotide sequence identities of 97-98% and amino acid sequence identities 96-98% in common with Chinese IBVs (strain A2, SH and QXIBV). Viral RNA was extracted by using Viral Nucleic Acid Extraction Kit (Real Biotech, Taiwan) following the manufacturer''s instructions directly from the supernatants of 10% w/v sample suspensions and from the allantoic fluid of embryonated chicken eggs used for virus isolation. For virus isolation, the supernatants of IBV-positive samples determined by RT-PCR were inoculated into 10-day-old embryonated chicken eggs. The results from both S1 gene comparison and phylogenetic analysis showed that IBV isolates in group I had a distant relation to vaccine strains used in Thailand including Ma5, H120, M41, and Connecticut. Typing of field isolates of infectious bronchitis virus based on the sequence of the hypervariable region in the S1 gene abstract: Thirteen field isolates of infectious bronchitis virus (IBV) were isolated from broiler flocks in Thailand between January and June 2008. The 878-bp of the S1 gene covering a hypervariable region was amplified and sequenced. Phylogenetic analysis based on that region revealed that these viruses were separated into two groups (I and II). IBV isolates in group I were not related to other IBV strains published in the GenBank database. Group 1 nucleotide sequence identities were less than 85% and amino acid sequence identities less than 84% in common with IBVs published in the GenBank database. This group likely represents the strains indigenous to Thailand. The isolates in group II showed a close relationship with Chinese IBVs. They had nucleotide sequence identities of 97-98% and amino acid sequence identities 96-98% in common with Chinese IBVs (strain A2, SH and QXIBV). This finding indicated that the recent Thai IBVs evolved separately and at least two groups of viruses are circulating in Thailand. url: https://www.ncbi.nlm.nih.gov/pubmed/19687622/ doi: 10.4142/jvs.2009.10.3.219 id: cord-304322-k9egxskw author: Promkuntod, N. title: Analysis of the S1 gene of the avian infectious bronchitis virus (IBV) reveals changes in the IBV genetic groups circulating in southern Thailand date: 2015-06-30 words: 2249.0 sentences: 132.0 pages: flesch: 50.0 cache: ./cache/cord-304322-k9egxskw.txt txt: ./txt/cord-304322-k9egxskw.txt summary: title: Analysis of the S1 gene of the avian infectious bronchitis virus (IBV) reveals changes in the IBV genetic groups circulating in southern Thailand Abstract The new variants of the avian infectious bronchitis virus (IBV) produce a range of symptoms and cause global economic losses to the poultry industry. We investigated the S1 glycoprotein of 24 recent IBV isolates from chickens and demonstrated that two predominant genetic groups were circulating in southern Thailand between 2008 and 2013. In this study we investigated the situation and distribution of IBV strains in southern Thailand by collecting isolates from different bird species, with confirmed infections, from different regions between 2008 and 2013. Finally, we determined the phylogenetic relationships of the local isolates both with vaccine strains commercially used in Thailand and with the IBV sequences available in GenBank from other geographical origins. S1 glycoprotein gene analysis of avian infectious bronchitis virus strains isolated in southern Thailand abstract: Abstract The new variants of the avian infectious bronchitis virus (IBV) produce a range of symptoms and cause global economic losses to the poultry industry. We investigated the S1 glycoprotein of 24 recent IBV isolates from chickens and demonstrated that two predominant genetic groups were circulating in southern Thailand between 2008 and 2013. Seven IBV variants, isolated from 2008 to 2009, were clustered in the Thailand THA001 group I while 15 IBV variants, isolated from 2009 to 2013, were classified into the QX-like group II. Moreover, a single isolate from a broiler was categorized into the Massachusetts-type, and an isolate from a layer belonged to the 4/91 type virus. Interestingly, both the IBV groups I and II were isolated from native chickens (62.5%) and caused a range of symptoms. Our results indicate that the QX-like viruses were predominant after 2009, replacing the THA001 type viruses. Furthermore, native chickens may contribute to the epidemiology of IB. url: https://api.elsevier.com/content/article/pii/S003452881500123X doi: 10.1016/j.rvsc.2015.05.002 id: cord-329497-3jow4xbn author: Promkuntod, Naruepol title: Dynamics of avian coronavirus circulation in commercial and non-commercial birds in Asia – a review date: 2015-12-28 words: 8003.0 sentences: 432.0 pages: flesch: 52.0 cache: ./cache/cord-329497-3jow4xbn.txt txt: ./txt/cord-329497-3jow4xbn.txt summary: It is essential to understand the latest situation regarding avian coronaviruses (ACoVs), commonly referred to as the well-known avian infectious bronchitis virus (IBV), given that new and diverse types of IBV are continually being identified worldwide, particularly ones that are isolated from commercial poultry and associated with a wide range of disease conditions. Vaccines against IBVs are generally effective, but new strains continue to emerge causing clinical diseases and production problems in vaccinated flocks, eventually having an economic impact on the global poultry industry Liu et al. In addition, the production of a new generation of vaccines, genetically related to the circulating IBV local strains, is economically beneficial for control of infectious bronchitis (IB) in global geographic regions. Isolation and genetic analysis revealed no predominant new strains of avian infectious bronchitis virus circulating in south China during abstract: It is essential to understand the latest situation regarding avian coronaviruses (ACoVs), commonly referred to as the well-known avian infectious bronchitis virus (IBV), given that new and diverse types of IBV are continually being identified worldwide, particularly ones that are isolated from commercial poultry and associated with a wide range of disease conditions. The existing IBVs continue to evolve in various geographic areas in Asia, which results in the recombination and co-circulation between IBV types. This makes it increasingly difficult to prevent and control IBV infections, despite routine vaccination. Some ACoVs have also been identified in other avian species and they may pose a threat of cross-transmission to commercial sectors. The present review provides an overview of IBV circulation and the dynamic emergence of new variants found throughout Asia via the recombination of IBV strains. In addition to commercial poultry, backyard poultry and free-ranging birds may serve as a ‘hub’ for ACoV transmission within a particular area. These birds may be capable of spreading viruses, either to areas of close proximity, or to remote places via migration and trade. url: https://doi.org/10.1080/01652176.2015.1126868 doi: 10.1080/01652176.2015.1126868 id: cord-353310-19kzb6ag author: Quinteros, José A. title: Analysis of the complete genomic sequences of two virus subpopulations of the Australian infectious bronchitis virus vaccine VicS date: 2015-04-01 words: 5201.0 sentences: 250.0 pages: flesch: 56.0 cache: ./cache/cord-353310-19kzb6ag.txt txt: ./txt/cord-353310-19kzb6ag.txt summary: Compared with VicS-v, the more attenuated VicS-del strain had two non-synonymous changes in the non-structural protein 6 (nsp6), a transmembrane (TM) domain that may participate in autocatalytic release of the 3-chymotrypsin-like protease, a polymorphic difference at the end of the S2 gene, which coincided with the body transcription-regulating sequence (B-TRS) of mRNA 3 and a truncated open reading frame for a peptide encoded by gene 4 (4b). Phylogenetic analysis of the whole genome showed that VicS-v and VicS-del did not cluster with strains from other countries, supporting the hypothesis that Australian IBV strains have been evolving independently for some time, and analyses of individual polymerase peptide and S glycoprotein genes suggested a distant common ancestor with no recent recombination. For VicSdel, the readings were mapped to the genome of VicS-v and the previously determined sequence of the structural protein gene region of VicS-del (GAN JN983807). abstract: Although sequencing of the 3′ end of the genome of Australian infectious bronchitis viruses (IBVs) has shown that their structural genes are distinct from those of IBVs found in other countries, their replicase genes have not been analysed. To examine this, the complete genomic sequences of the two subpopulations of the VicS vaccine, VicS-v and VicS-del, were determined. Compared with VicS-v, the more attenuated VicS-del strain had two non-synonymous changes in the non-structural protein 6 (nsp6), a transmembrane (TM) domain that may participate in autocatalytic release of the 3-chymotrypsin-like protease, a polymorphic difference at the end of the S2 gene, which coincided with the body transcription-regulating sequence (B-TRS) of mRNA 3 and a truncated open reading frame for a peptide encoded by gene 4 (4b). These genetic differences could be responsible for the differences between these variants in pathogenicity in vivo, and replication in vitro. Phylogenetic analysis of the whole genome showed that VicS-v and VicS-del did not cluster with strains from other countries, supporting the hypothesis that Australian IBV strains have been evolving independently for some time, and analyses of individual polymerase peptide and S glycoprotein genes suggested a distant common ancestor with no recent recombination. This study suggests the potential role of the TM domain in nsp6, the integrity of the S2 protein and the B-TRS 3, and the putative accessory protein 4b, as well as the 3′ untranslated region, in the virulence and replication of IBV and has provided a better understanding of relationships between the Australian vaccine strain of IBV and those used elsewhere. url: https://doi.org/10.1080/03079457.2015.1022857 doi: 10.1080/03079457.2015.1022857 id: cord-304278-0qy1nngs author: Raj, G. Dhinakar title: Infectious bronchitis virus: immunopathogenesis of infection in the chicken date: 2007-11-12 words: 12530.0 sentences: 665.0 pages: flesch: 45.0 cache: ./cache/cord-304278-0qy1nngs.txt txt: ./txt/cord-304278-0qy1nngs.txt summary: While infectious bronchitis (IB) is considered primarily a disease of the respiratory system, different IBV strains may show variable tissue tropisms and also affect the oviduct and the kidneys, with serious consequences. Nevertheless, the lack of correlation between antibodies and resistance, discrepancies between in vitro strain differentiation by VN tests and in vivo cross-protection results (Darbyshire, 1985) and re-excretion of virus in the presence of high titres of circulating antibodies (Jones & Ambali, 1987) all suggest that while humoral antibodies play a role in recovery from IBV infection, other immunological mechanisms are involved. Comparison of the susceptibility of chicks of different ages to infection with nephrosis-nephritis causing strain of infectious bronchitis virus Challenge experiments to evaluate cross-protection induced at the trachea and kidney level by vaccine strains and Belgian nephropathogenic isolates of avian infectious bronchitis virus Effects of avian infectious bronchitis virus (Arkansas strain) on vaccinated laying chickens abstract: The immunopathogenesis of infectious bronchitis virus (IBV) infection in the chicken is reviewed. While infectious bronchitis (IB) is considered primarily a disease of the respiratory system, different IBV strains may show variable tissue tropisms and also affect the oviduct and the kidneys, with serious consequences. Some strains replicate in the intestine but apparently without pathological changes. Pectoral myopathy has been associated with an important recent variant. Several factors can influence the course of infection with IBV, including the age, breed and nutrition of the chicken, the environment and intercurrent infection with other infectious agents. Immunogenic components of the virus include the S (spike) proteins and the N nucleoprotein. The humoral, local and cellular responses of the chicken to IBV are reviewed, together with genetic resistance of the chicken. In long-term persistence of IBV, the caecal tonsil or kidney have been proposed as the sites of persistence. Antigenic variation among IBV strains is related to relatively small differences in amino acid sequences in the S1 spike protein. However, antigenic studies alone do not adequately define immunological relationships between strains and cross-immunisation studies have been used to classify IBV isolates into ‘protectotypes’. It has been speculated that changes in the S1 protein may be related to differences in tissue tropisms shown by different strains. Perhaps in the future, new strains of IBV may arise which affect organs or systems not normally associated with IB. url: https://www.ncbi.nlm.nih.gov/pubmed/18483939/ doi: 10.1080/03079459708419246 id: cord-268454-w4qca90s author: Rim, Aouini title: Viral interference between H9N2-low pathogenic avian influenza virus and avian infectious bronchitis virus vaccine strain H120 in vivo date: 2019-06-17 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The interaction between a low pathogenic avian influenza virus (A/CK/TUN/145/2012), a H9N2 Tunisian isolate, and a vaccine strain (H120) of avian infectious bronchitis, administered simultaneously or sequentially three days apart to chicks during 20 days, was evaluated using ELISA antibody levels, quantitative reverse transcription–polymerase chain reaction (qRT-PCR) analyses and histopathology examination. First, the in vivo replication interference of avian influenza virus (AIV) and infectious bronchitis virus (IBV) was evaluated using qRT-PCR to detect accurately either AIV or IBV genomes or viral copy numbers during dual infections. Second, we have determined the amount of specific antibodies in sera of chick’s infected with AIV alone, IBV alone, mixed AIV + IBV, IBV then AIV or AIV IBV 3 days later using an ELISA test. Finally, histopathological analyses of internal organs from inoculated chicks were realized. Quantitative results of AIV and IBV co-infection showed that interferences between the two viruses yielded decreased viral growth. However, in the case of super-infection, the second virus, either AIV or IBV, induced a decrease in the growth of the first inoculated virus. According to our results, vaccine application was safe and do not interfere with AIV H9N2 infection, and does not enhance such infection. In conclusion, co-infection of chicks with AIV and IBV, simultaneously or sequentially, affected the clinical signs, the virus replication dynamics as well as the internal organ integrity. The results proposed that infection with heterologous virus may result in temporary competition for cell receptors or competent cells for replication, most likely interferon-mediated. url: https://www.sciencedirect.com/science/article/pii/S0147957119301109 doi: 10.1016/j.cimid.2019.06.004 id: cord-301720-majpfxqn author: Saadat, Yousef title: Molecular characterization of infectious bronchitis viruses isolated from broiler flocks in Bushehr province, Iran: 2014 - 2015 date: 2017-09-15 words: 2836.0 sentences: 192.0 pages: flesch: 53.0 cache: ./cache/cord-301720-majpfxqn.txt txt: ./txt/cord-301720-majpfxqn.txt summary: title: Molecular characterization of infectious bronchitis viruses isolated from broiler flocks in Bushehr province, Iran: 2014 2015 The aim of this study was to provide information on the molecular characteristic and the phylogenic relationship of infectious bronchitis viruses (IBV) strains in Bushehr province in comparison to other strains reported in the Middle East. [27] [28] [29] The aim of this study was to provide information on the molecular characteristic and the phylogenetic relationship of prevalent IBV genotypes circulating in chicken flocks in Bushehr province, Iran. Some Iraqi researchers studied circulating viruses in Broiler farm and showed that these strains belong to variant 2 (IS/1494-lik) that had high nucleotide sequence identity with IBV isolates from Iran, Israel, Egypt, Turkey, and Kurdistan. Detection and molecular characterization of infectious bronchitis virus isolated from recent outbreaks in broiler flocks in Thailand Molecular characterization of infectious bronchitis viruses isolated from broiler chicken farms in Iran abstract: The aim of this study was to provide information on the molecular characteristic and the phylogenic relationship of infectious bronchitis viruses (IBV) strains in Bushehr province in comparison to other strains reported in the Middle East. Samples were collected from broiler flocks in Bushehr province during 2014 - 2015. These flocks had respiratory problems such as gasping, sneezing and bronchial rales. A number of 135 tracheal swabs were taken from fifteen flocks (nine swabs per flock). Each three swabs collected from each flock were pooled in one tube (finally, we had three tubes for each flock). The samples were subjected to reverse transcription polymerase chain reaction (RT-PCR). The PCR products of positive samples were analyzed by sequencing of a (392 bp) segment of the spike gene and the related results were compared with the other IBV sequences in GenBank database. Samples from twelve farms (80.0%) were found to be positive. The viruses from seven farms (46.6%) were identified as field viruses closely related to variant 2. The viruses from three farms (20.0%) were characterized as Mass type and were related to vaccine strains. Two different IB viruses (variant 2 and Mass) were detected in samples from two farms (13.3%). The variant 2 genotype detected in Bushehr had high similarity to variant 2 reported from the Middle East. These variants displayed homologies ranging from 72.9% to 76.5%, and 78.8% to 80.0% with H120 and 4/91, respectively. It is necessary to design vaccination program of poultry farms using IBV strains circulating in the region. url: https://www.ncbi.nlm.nih.gov/pubmed/29085606/ doi: nan id: cord-271359-dpa8zzc3 author: Sapats, S. I. title: Novel Variation in the N Protein of Avian Infectious Bronchitis Virus date: 1996-12-15 words: 2317.0 sentences: 141.0 pages: flesch: 66.0 cache: ./cache/cord-271359-dpa8zzc3.txt txt: ./txt/cord-271359-dpa8zzc3.txt summary: Despite the considerable variation observed between the two virus groups, all N proteins contained a high proportion of basic residues, 80% of which were conserved in position. The N protein of all coronaviruses virus lacks a sequence of 184-196 nucleotides that has is overall very basic and in IBV contains 409 amino acids been detected in five other IBV strains. located downstream of the HVR (315 nucleotides ending The N protein of 27 strains of IBV isolated over a period at the poly(A) tail) is highly conserved in strains of IBV, of 60 years from diverse locations such as the U.S.A., the probably indicative of its role in the synthesis of negative-UK, Holland, Saudi Arabia, and Japan has been shown to strand RNA. For each virus two or more for the N proteins of IBV also contain a region of complete independent cDNA clones were sequenced using the conservation between positions 242 and 296 (4). abstract: Abstract The nucleocapsid protein of coronaviruses has been considered highly conserved, showing greater than 94% conservation within strains of a given species. We determined the nucleotide sequence of the N gene and the 3′ untranslated region (UTR) of eight naturally occurring strains of IBV which differed in pathogenicity and tissue tropism. In pairwise comparisons, the deduced amino acid sequences of N of five strains Vic S, N1/62, N9/74, N2/75, and V5/90 (group I) shared 92.3–98.8% identity. The three strains N1/88, Q3/88, and V18/91 (group II) shared 85.8–89.2% identity with each other, but only 60.0–63.3% identity with viruses of group I. Amino acid substitutions, deletions, and insertions occurred throughout the N protein and involved regions previously identified as being conserved. Despite the considerable variation observed between the two virus groups, all N proteins contained a high proportion of basic residues, 80% of which were conserved in position. In addition, all strains contained approximately 30 serine residues of which 10 were conserved, the majority occurring between positions 168 and 194. As for all other coronaviruses, the region between positions 92 and 103 was highly conserved. Hence, a large number of amino acid changes can be tolerated within the N protein without affecting its integrity or functioning. The 3′ UTR immediately downstream from the N gene was highly heterogeneous with extensive deletions occurring in the group II strains. url: https://www.sciencedirect.com/science/article/pii/S0042682296906704 doi: 10.1006/viro.1996.0670 id: cord-334090-66d8c75g author: Seger, Waleed title: Genotyping of infectious bronchitis viruses from broiler farms in Iraq during 2014-2015 date: 2016-02-18 words: 3613.0 sentences: 178.0 pages: flesch: 54.0 cache: ./cache/cord-334090-66d8c75g.txt txt: ./txt/cord-334090-66d8c75g.txt summary: Thus, the spread of viral respiratory diseases has become the most commonly reported condition in commercial broiler flocks in Iraq; however, there have been no studies on the detection and genotyping of these viruses using molecular techniques and sequencing. Phylogenetic analysis of the 32 strains (Fig. 2) revealed that Iraqi IBV strains could be classified into four genetic groups or genotypes: group I, variant 2 IS/1494-like viruses, including 15 field isolates (46.87 %); group II, 793/Blike viruses, including 13 field strains (40.62 %); group III, QX-like viruses, including three field strains (9.37); and caused by bacteria and mycoplasmas have already been detected on broiler farms located in the central and southern parts of Iraq. Our result were in line with those of Mahmood et al., who conducted the first study of identification and genotyping of IBV isolates and indicated that the 4/91-like virus is circulating on vaccinated broiler farms of the Kurdistan region of Iraq [21] . abstract: Infectious bronchitis virus (IBV) is one of the most critical pathogens in the poultry industry, causing serious economic losses in all countries including Iraq. IBV has many genotypes that do not confer any cross-protection. This virus has been genotyped by sequence analysis of the S1 glycoprotein gene. A total of 100 tracheal and kidney tissue specimens from different commercial broiler flocks in the middle and south of Iraq were collected from September 2013 to September 2014. Thirty-two IBV-positive samples were selected from among the total and were further characterized by nested PCR. Phylogenetic analysis revealed that isolates belong to four groups (group I, variant 2 [IS/1494-like]; group II, 793/B-like; group III, QX-like; group IV, DY12-2-like). Sequence analysis revealed nucleotide sequence identities within groups I, II, and III of 99.68 %-100 %, 99.36 %-100 %, and 96.42 %-100 %, respectively. Group I (variant 2) was the dominant IBV genotype. One Chinese-like recombinant virus (DY12-2-like) that had not been reported in the Middle East was detected. In addition, the presence of QX on broiler chicken farms in the area studied was confirmed. This is the first comprehensive study on the genotyping of IBV in Iraq with useful information regarding the molecular epidemiology of IBV. The phylogenetic relationship of the strains with respect to different time sequences and geographical regions displayed complexity and diversity. Further studies are needed and should include the isolation and full-length molecular characterization of IBV in this region. url: https://www.ncbi.nlm.nih.gov/pubmed/26887967/ doi: 10.1007/s00705-016-2790-2 id: cord-344745-sgkq1l93 author: Selim, Karim title: Molecular characterization of infectious bronchitis viruses isolated from broiler and layer chicken farms in Egypt during 2012 date: 2013-11-18 words: 2757.0 sentences: 172.0 pages: flesch: 56.0 cache: ./cache/cord-344745-sgkq1l93.txt txt: ./txt/cord-344745-sgkq1l93.txt summary: title: Molecular characterization of infectious bronchitis viruses isolated from broiler and layer chicken farms in Egypt during 2012 The aim of this study aimed to survey the Egyptian chicken field for infectious bronchitis virus and study the genomic differentiation between isolated field samples seeking the new variant strain emerged in the Egyptian field. For virus isolation, the supernatants of IBV-positive selected 13 samples determined by RT-PCR were inoculated into five specific pathogen free embryonated chicken eggs (KoumOshiem SPF chicken farm, Fayoum, Egypt) 10-day-old for each sample. The genetic analysis of 100 amino acids sequence from position 263-362 of SP1 gene for the selected 13 Egyptian viruses was done and the hypervariable region of SP1 gene showed multiple mutations as shown in Table 4 in comparison with variant-2 strain. S1 gene sequence analysis of a nephro-pathogenic strain of avian infectious bronchitis virus in Egypt abstract: One of the major problems of avian infectious bronchitis virus (IBV) is the frequent emergence of new variants. In the present study 205 tracheal swabs and organs were collected from broilers and layers chicken farms during January to August 2012 from 19 governorates all over Egypt. The chickens demonstrated respiratory signs and mortality. Out of the examined samples, 130 of which (about 64%) of suspected farms were positive for IBV with real time RT-PCR. 13 IBV-positive samples were selected for further isolation and characterization. Isolation in specific pathogen free (SPF) embryos was carried out after studies three blind successive passages and the hypervariable region of spike protein1 (SP1) was amplified by RT-PCR and sequenced to study the genetic diversity between the isolated viruses. Phylogenetic analysis of the obtained sequences of 13 isolates compared with other IBV strains from the Middle East and worldwide reveled that 11 out of the 13 isolates had close relationship the Israeli variants (IS/885 and IS/1494/06) with nucleotide homology reached up to 89.9% and 82.3%, respectively. Only two isolates had close relationship with CR/88121 and 4/91 viruses with identities of 95% and 96%, respectively. This study indicates existence of two variant groups of IBV circulating in Egypt during 2012. Group I was similar but distinguishable from Israeli variant IS/885 and group II was related to 4/91 and CR/88121 vaccine strains. There was no geographical link between the 2 groups as they were distributed all over the country. These findings necessitate the need to revise the vaccination programs and control measures for IBV. url: https://www.ncbi.nlm.nih.gov/pubmed/32289036/ doi: 10.1016/j.ijvsm.2013.10.002 id: cord-263178-lvxxdvas author: Shan, Dan title: Effects of hypervariable regions in spike protein on pathogenicity, tropism, and serotypes of infectious bronchitis virus date: 2018-05-02 words: 6872.0 sentences: 378.0 pages: flesch: 55.0 cache: ./cache/cord-263178-lvxxdvas.txt txt: ./txt/cord-263178-lvxxdvas.txt summary: To study the roles of hypervariable regions (HVRs) in receptor-binding subunit S1 of the spike protein, we manipulated the genome of the IBV Beaudette strain using a reverse genetics system to construct seven recombinant strains by separately or simultaneously replacing the three HVRs of the Beaudette strain with the corresponding fragments from a QX-like nephropathogenic isolate ck/CH/LDL/091022 from China. We could not detect the replication with ck/CH/ LDL/091022 in Vero cells, so the neutralization tests were performed in 9-day-old SPF embryonated eggs to confirm whether the serotypes of the recombinant IBVs belonged to ck/CH/LDL/091022. Viral antigen was observed in Vero cells infected with the Beaudette strain and the seven recombinant IBVs (Fig. 1b) . S1 gene sequencing results confirmed that the heterogenous HVRs were stably maintained in the recombinant IBVs (Sup Fig. 1) , and no additional mutations were detected in the S protein after three passages in cells or eggs. abstract: To study the roles of hypervariable regions (HVRs) in receptor-binding subunit S1 of the spike protein, we manipulated the genome of the IBV Beaudette strain using a reverse genetics system to construct seven recombinant strains by separately or simultaneously replacing the three HVRs of the Beaudette strain with the corresponding fragments from a QX-like nephropathogenic isolate ck/CH/LDL/091022 from China. We characterized the growth properties of these recombinant IBVs in Vero cells and embryonated eggs, and their pathogenicity, tropism, and serotypes in specific pathogen-free (SPF) chickens. All seven recombinant IBVs proliferated in Vero cells, but the heterogenous HVRs could reduce their capacity for adsorption during in vitro infection. The recombinant IBVs did not significantly increase the pathogenicity compared with the Beaudette strain in SPF chickens, and they still shared the same serotype as the Beaudette strain, but the antigenic relatedness values between the recombinant strain and Beaudette strain generally decreased with the increase in the number of the HVRs exchanged. The results of this study demonstrate the functions of HVRs and they may help to develop a vaccine candidate, as well as providing insights into the prevention and control of IBV. url: https://www.sciencedirect.com/science/article/pii/S0168170217309103 doi: 10.1016/j.virusres.2018.04.013 id: cord-323568-s0wmll4q author: Shang, Jian title: Cryo-EM structure of infectious bronchitis coronavirus spike protein reveals structural and functional evolution of coronavirus spike proteins date: 2018-04-23 words: 7464.0 sentences: 452.0 pages: flesch: 60.0 cache: ./cache/cord-323568-s0wmll4q.txt txt: ./txt/cord-323568-s0wmll4q.txt summary: Specifically, among different genera, the two domains of S1, the N-terminal domain (S1-NTD) and C-terminal domain (S1-CTD), diverge from simpler tertiary structures and quaternary packing to more complex ones, leading to different functions of the spikes in receptor usage and membrane fusion. The initial model of IBV spike ectodomain was obtained by fitting the seven parts (S1-NTD, S1-CTD, two parts of SD1, two parts of SD2, and S2) of the porcine delta coronavirus spike structure (PDB ID: 6B7N) individually into the cryo-EM density map of IBV spike using UCSF Chimera [41] and Coot [42] . Based on the structural similarity between the S1-NTDs from different coronavirus genera, the sugar-binding site in IBV S1-NTD might also be located in the pocket formed between the core structure and the partial ceiling (Figs 2B and 3C) . The putative RBMs of IBV S1-CTD and the partial ceiling Structure, function, and evolution of IBV spike protein of IBV S1-NTD are both involved in the cross-subunit packing. abstract: As cell-invading molecular machinery, coronavirus spike proteins pose an evolutionary conundrum due to their high divergence. In this study, we determined the cryo-EM structure of avian infectious bronchitis coronavirus (IBV) spike protein from the γ-genus. The trimeric IBV spike ectodomain contains three receptor-binding S1 heads and a trimeric membrane-fusion S2 stalk. While IBV S2 is structurally similar to those from the other genera, IBV S1 possesses structural features that are unique to different other genera, thereby bridging these diverse spikes into an evolutionary spectrum. Specifically, among different genera, the two domains of S1, the N-terminal domain (S1-NTD) and C-terminal domain (S1-CTD), diverge from simpler tertiary structures and quaternary packing to more complex ones, leading to different functions of the spikes in receptor usage and membrane fusion. Based on the above structural and functional comparisons, we propose that the evolutionary spectrum of coronavirus spikes follows the order of α-, δ-, γ-, and β-genus. This study has provided insight into the evolutionary relationships among coronavirus spikes and deepened our understanding of their structural and functional diversity. url: https://doi.org/10.1371/journal.ppat.1007009 doi: 10.1371/journal.ppat.1007009 id: cord-345088-krb1eidw author: Shen, S title: A single amino acid mutation in the spike protein of coronavirus infectious bronchitis virus hampers its maturation and incorporation into virions at the nonpermissive temperature date: 2004-09-01 words: 6949.0 sentences: 316.0 pages: flesch: 56.0 cache: ./cache/cord-345088-krb1eidw.txt txt: ./txt/cord-345088-krb1eidw.txt summary: title: A single amino acid mutation in the spike protein of coronavirus infectious bronchitis virus hampers its maturation and incorporation into virions at the nonpermissive temperature Here, we report the emergence and isolation of two temperature sensitive (ts) mutants and a revertant in the process of cold-adaptation of coronavirus infectious bronchitis virus (IBV) to a monkey kidney cell line. Evidence presented demonstrated that the Q(294)-to-L(294) mutation, located at a highly conserved domain of the S1 subunit, might hamper processing of the S protein to a matured 180-kDa, endo-glycosidase H-resistant glycoprotein and the translocation of the protein to the cell surface. In virus-infected cells, the Endo-H sensitive, 155-kDa form of ts291602 was abundant at the nonpermissive temperature, clearly indicating that the mutant S protein was trimmed in the ER and cis-Golgi but was not transported to the trans-Golgi. abstract: The spike (S) glycoprotein of coronavirus is responsible for receptor binding and membrane fusion. A number of variants with deletions and mutations in the S protein have been isolated from naturally and persistently infected animals and tissue cultures. Here, we report the emergence and isolation of two temperature sensitive (ts) mutants and a revertant in the process of cold-adaptation of coronavirus infectious bronchitis virus (IBV) to a monkey kidney cell line. The complete sequences of wild type (wt) virus, two ts mutants, and the revertant were compared and variations linked to phenotypes were mapped. A single amino acid reversion (L(294)-to-Q) in the S protein is sufficient to abrogate the ts phenotype. Interestingly, unlike wt virus, the revertant grows well at and below 32 °C, the permissive temperature, as it carries other mutations in multiple genes that might be associated with the cold-adaptation phenotype. If the two ts mutants were allowed to enter cells at 32 °C, the S protein was synthesized, core-glycosylated and at least partially modified at 40 °C. However, compared with wt virus and the revertant, no infectious particles of these ts mutants were assembled and released from the ts mutant-infected cells at 40 °C. Evidence presented demonstrated that the Q(294)-to-L(294) mutation, located at a highly conserved domain of the S1 subunit, might hamper processing of the S protein to a matured 180-kDa, endo-glycosidase H-resistant glycoprotein and the translocation of the protein to the cell surface. Consequently, some essential functions of the S protein, including mediation of cell-to-cell fusion and its incorporation into virions, were completely abolished. url: https://api.elsevier.com/content/article/pii/S0042682204003988 doi: 10.1016/j.virol.2004.06.016 id: cord-003148-o7y3wygc author: Shirvani, Edris title: A Recombinant Newcastle Disease Virus (NDV) Expressing S Protein of Infectious Bronchitis Virus (IBV) Protects Chickens against IBV and NDV date: 2018-08-10 words: 8668.0 sentences: 423.0 pages: flesch: 55.0 cache: ./cache/cord-003148-o7y3wygc.txt txt: ./txt/cord-003148-o7y3wygc.txt summary: However, the results of the inoculation of the tracheal swab samples into 10-day-old embrynated chicken eggs showed that 14 out of 15 (93.3%) chickens vaccinated with rNDV expressing codon optimized S protein of IBV and 0 out of 5 (0%) of non-infected chickens were shedding virus in trachea, respectively, whereas 15 out of 15 (100%) of chickens of all other groups were shedding virus in the trachea (data not shown). To evaluate the effect of the route of inoculation of virulent IB challenge virus on the outcomes of the protective efficacy of rNDV expressing codon optimized S protein of IBV, SPF chicks were immunized at 1-day-old age. The protective efficacy of rNDV expressing codon optimized S gene of IBV was determined by challenging the immunized chickens with 10 4 EID 50 virulent IBV strain Mass-41 by the intraocular route at 3 week post-immunization. abstract: Infectious bronchitis virus (IBV) causes a highly contagious respiratory, reproductive and urogenital tract disease in chickens worldwide, resulting in substantial economic losses for the poultry industry. Currently, live-attenuated IBV vaccines are used to control the disease. However, safety, attenuation and immunization outcomes of current vaccines are not guaranteed. Several studies indicate that attenuated IBV vaccine strains contribute to the emergence of variant viruses in the field due to mutations and recombination. Therefore, there is a need to develop a stable and safe IBV vaccine that will not create variant viruses. In this study, we generated recombinant Newcastle disease viruses (rNDVs) expressing the S1, S2 and S proteins of IBV using reverse genetics technology. Our results showed that the rNDV expressing the S protein of IBV provided better protection than the rNDV expressing S1 or S2 protein of IBV, indicating that the S protein is the best protective antigen of IBV. Immunization of 4-week-old SPF chickens with the rNDV expressing S protein elicited IBV-specific neutralizing antibodies and provided complete protection against virulent IBV and virulent NDV challenges. These results suggest that the rNDV expressing the S protein of IBV is a safe and effective bivalent vaccine candidate for both IBV and NDV. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6086832/ doi: 10.1038/s41598-018-30356-2 id: cord-344297-qqohijqi author: Smith, Jacqueline title: The early immune response to infection of chickens with Infectious Bronchitis Virus (IBV) in susceptible and resistant birds date: 2015-10-09 words: 5076.0 sentences: 284.0 pages: flesch: 52.0 cache: ./cache/cord-344297-qqohijqi.txt txt: ./txt/cord-344297-qqohijqi.txt summary: title: The early immune response to infection of chickens with Infectious Bronchitis Virus (IBV) in susceptible and resistant birds RESULTS: Genes and biological pathways involved in the early host response to IBV infection were determined andgene expression differences between susceptible and resistant birds were identified. [18] we used Affymetrix wholegenome chicken microarrays to examine the tracheal gene expression profiles of a line of birds known to be susceptible to IBV infection (line 15I) and a line known to show resistance (line N). Gene expression differences found in the susceptible 15I line between infected and control birds over days 2, 3 and 4 post infection were analysed, with a view to examining the innate host response to infection by IBV. Gene expression seen during the host response to IBV infection in the trachea of susceptible birds. Genes found to be differentially expressed between susceptible and resistant lines in response to IBV infection in the trachea. abstract: BACKGROUND: Infectious Bronchitis is a highly contagious respiratory disease which causes tracheal lesions and also affects the reproductive tract and is responsible for large economic losses to the poultry industry every year. This is due to both mortality (either directly provoked by IBV itself or due to subsequent bacterial infection) and lost egg production. The virus is difficult to control by vaccination, so new methods to curb the impact of the disease need to be sought. Here, we seek to identify genes conferring resistance to this coronavirus, which could help in selective breeding programs to rear chickens which do not succumb to the effects of this disease. METHODS: Whole genome gene expression microarrays were used to analyse the gene expression differences, which occur upon infection of birds with Infectious Bronchitis Virus (IBV). Tracheal tissue was examined from control and infected birds at 2, 3 and 4 days post-infection in birds known to be either susceptible or resistant to the virus. The host innate immune response was evaluated over these 3 days and differences between the susceptible and resistant lines examined. RESULTS: Genes and biological pathways involved in the early host response to IBV infection were determined andgene expression differences between susceptible and resistant birds were identified. Potential candidate genes for resistance to IBV are highlighted. CONCLUSIONS: The early host response to IBV is analysed and potential candidate genes for disease resistance are identified. These putative resistance genes can be used as targets for future genetic and functional studies to prove a causative link with resistance to IBV. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12917-015-0575-6) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1186/s12917-015-0575-6 doi: 10.1186/s12917-015-0575-6 id: cord-338307-vfutmwxq author: Sturman, Lawrence S. title: The Molecular Biology of Coronaviruses date: 1983-12-31 words: 21959.0 sentences: 1287.0 pages: flesch: 52.0 cache: ./cache/cord-338307-vfutmwxq.txt txt: ./txt/cord-338307-vfutmwxq.txt summary: The pattern of three major structural proteins and their organization in the virion as shown for MHV-A59 in Fig. 3 is generally applicable to most other species of coronaviruses (reviewed in detail by Siddell et al., 1982) . (1981b) , using a cDNA probe prepared against the mRNA of MHV-A59 which coded for the nucleocapsid protein, obtained evidence of 7 0 4 0 % homology by analysis of hybridization kinetics of viral RNA from cells infected with MHV-1, -3, -S, and -JHM. t 1980) demonstrated that different size classes of poly(A)containing intracellular MHV-JHM RNAs fractionated on sucroseformamide gradients directed the synthesis of different structural proteins in cell-free translation systems. The studies showed that, like avian coronaviruses, for the murine coronavirus MHV-A59, the oligonucleotides of each of the subgenomic RNAs were included within the next larger species, starting from the 3'' end of the genome. abstract: Publisher Summary Coronaviruses have recently emerged as an important group of animal and human pathogens that share a distinctive replicative cycle. Some of the unique characteristics in the replication of coronaviruses include generation of a 3' coterminal-nested set of five or six subgenomic mRNAs, each of which appears to direct the synthesis of one protein. Two virus-specific RNA polymerase activities have been identified. Many of the distinctive features of coronavirus infection and coronavirus-induced diseases may result from the properties of the two coronavirus glycoproteins. The intracellular budding site, which may be important in the establishment and maintenance of persistent infections, appears to be due to the restricted intracytoplasmic migration of the E1 glycoprotein, which acts as a matrix-like transmembrane glycoprotein. E1 also exhibits distinctive behavior by self-aggregating on heating at 100°C in sodium dodecyl sulfate (SDS) and by its interaction with RNA in the viral nucleocapsid. The E1 of mouse hepatitis virus (MHV) is an O-linked glycoprotein, unlike most other viral glycoproteins. Thus, the coronavirus system may be a useful model for the study of synthesis, glycosylation, and transport of O-linked cellular glycoproteins. url: https://www.ncbi.nlm.nih.gov/pubmed/6362367/ doi: 10.1016/s0065-3527(08)60721-6 id: cord-316234-vtjsfi2c author: Sultankulova, Kulyaisan T. title: New oligonucleotide microarray for rapid diagnosis of avian viral diseases date: 2017-04-05 words: 4693.0 sentences: 228.0 pages: flesch: 45.0 cache: ./cache/cord-316234-vtjsfi2c.txt txt: ./txt/cord-316234-vtjsfi2c.txt summary: BACKGROUND: We developed a new oligonucleotide microarray comprising 16 identical subarrays for simultaneous rapid detection of avian viruses: avian influenza virus (AIV), Newcastle disease virus (NDV), infection bronchitis virus (IBV), and infectious bursal disease virus (IBDV) in singleand mixed-virus infections. METHODS AND RESULTS: The paper describes the technique for rapid and simultaneous diagnosis of avian diseases such as avian influenza, Newcastle disease, infectious bronchitis and infectious bursal disease with use of oligonucleotide microarray, conditions for hybridization of fluorescent-labelled viral cDNA on the microarray and its specificity tested with use of AIV, NDV, IBV, IBDV strains as well as biomaterials from poultry. The paper describes the technique for rapid and simultaneous diagnosis of avian diseases such as avian influenza, Newcastle disease, infectious bronchitis and infectious bursal disease with use of oligonucleotide microarray, conditions for hybridization of fluorescentlabelled viral cDNA on the microarray and its specificity tested with use of AIV, NDV, IBV, IBDV strains as well as biomaterials from poultry. abstract: BACKGROUND: We developed a new oligonucleotide microarray comprising 16 identical subarrays for simultaneous rapid detection of avian viruses: avian influenza virus (AIV), Newcastle disease virus (NDV), infection bronchitis virus (IBV), and infectious bursal disease virus (IBDV) in single- and mixed-virus infections. The objective of the study was to develop an oligonucleotide microarray for rapid diagnosis of avian diseases that would be used in the course of mass analysis for routine epidemiological surveillance owing to its ability to test one specimen for several infections. METHODS AND RESULTS: The paper describes the technique for rapid and simultaneous diagnosis of avian diseases such as avian influenza, Newcastle disease, infectious bronchitis and infectious bursal disease with use of oligonucleotide microarray, conditions for hybridization of fluorescent-labelled viral cDNA on the microarray and its specificity tested with use of AIV, NDV, IBV, IBDV strains as well as biomaterials from poultry. Sensitivity and specificity of the developed microarray was evaluated with use of 122 specimens of biological material: 44 cloacal swabs from sick birds and 78 tissue specimens from dead wild and domestic birds, as well as with use of 15 AIV, NDV, IBV and IBDV strains, different in their origin, epidemiological and biological characteristics (RIBSP Microbial Collection). This microarray demonstrates high diagnostic sensitivity (99.16% within 95% CI limits 97.36–100%) and specificity (100%). Specificity of the developed technique was confirmed by direct sequencing of NP and M (AIV), VP2 (IBDV), S1 (IBV), NP (NDV) gene fragments. CONCLUSION: Diagnostic effectiveness of the developed DNA microarray is 99.18% and therefore it can be used in mass survey for specific detection of AIV, NDV, IBV and IBDV circulating in the region in the course of epidemiological surveillance. Rather simple method for rapid diagnosis of avian viral diseases that several times shortens duration of assay versus classical diagnostic methods is proposed. url: https://doi.org/10.1186/s12985-017-0738-0 doi: 10.1186/s12985-017-0738-0 id: cord-269150-d1sgnxc0 author: Tan, Yong Wah title: Binding of the 5′-untranslated region of coronavirus RNA to zinc finger CCHC-type and RNA-binding motif 1 enhances viral replication and transcription date: 2012-02-22 words: 6977.0 sentences: 346.0 pages: flesch: 53.0 cache: ./cache/cord-269150-d1sgnxc0.txt txt: ./txt/cord-269150-d1sgnxc0.txt summary: In a screen based on a yeast three-hybrid system using the 5′-untranslated region (5′-UTR) of SARS coronavirus (SARS-CoV) RNA as bait against a human cDNA library derived from HeLa cells, we found a positive candidate cellular protein, zinc finger CCHC-type and RNA-binding motif 1 (MADP1), to be able to interact with this region of the SARS-CoV genome. In this study, we describe the interaction of a cellular protein, MADP1 (zinc finger CCHC-type and RNA binding motif 1) with the 5 0 -UTR of IBV and SARS-CoV, using yeast-based three hybrid screen (34) and RNA-binding assays. Using indirect immunofluorescence, we confirmed that MADP1, despite being reported as a nuclear protein (35) , was detected in the cytoplasm of virus-infected cells and partially co-localized with the RTCs. Upon silencing of MADP1 using siRNA, viral RNA synthesis on general has been affected, resulting in a lower replication efficiency and infectivity. abstract: Coronaviruses RNA synthesis occurs in the cytoplasm and is regulated by host cell proteins. In a screen based on a yeast three-hybrid system using the 5′-untranslated region (5′-UTR) of SARS coronavirus (SARS-CoV) RNA as bait against a human cDNA library derived from HeLa cells, we found a positive candidate cellular protein, zinc finger CCHC-type and RNA-binding motif 1 (MADP1), to be able to interact with this region of the SARS-CoV genome. This interaction was subsequently confirmed in coronavirus infectious bronchitis virus (IBV). The specificity of the interaction between MADP1 and the 5′-UTR of IBV was investigated and confirmed by using an RNA pull-down assay. The RNA-binding domain was mapped to the N-terminal region of MADP1 and the protein binding sequence to stem–loop I of IBV 5′-UTR. MADP1 was found to be translocated to the cytoplasm and partially co-localized with the viral replicase/transcriptase complexes (RTCs) in IBV-infected cells, deviating from its usual nuclear localization in a normal cell using indirect immunofluorescence. Using small interfering RNA (siRNA) against MADP1, defective viral RNA synthesis was observed in the knockdown cells, therefore indicating the importance of the protein in coronaviral RNA synthesis. url: https://doi.org/10.1093/nar/gks165 doi: 10.1093/nar/gks165 id: cord-259738-yuqc6dk0 author: Tang, Mengjun title: Enhancement of the immunogenicity of an infectious bronchitis virus DNA vaccine by a bicistronic plasmid encoding nucleocapsid protein and interleukin-2 date: 2008-03-07 words: 3841.0 sentences: 209.0 pages: flesch: 49.0 cache: ./cache/cord-259738-yuqc6dk0.txt txt: ./txt/cord-259738-yuqc6dk0.txt summary: title: Enhancement of the immunogenicity of an infectious bronchitis virus DNA vaccine by a bicistronic plasmid encoding nucleocapsid protein and interleukin-2 A DNA vaccine against infectious bronchitis virus (IBV) can induce specific humoral and cell-mediated immunity. When chickens were challenged with a virulent strain of IBV, the protective efficacy could be enhanced significantly after immunization with bicistronic DNA vaccine. In the present study, a bicistronic plasmid encoding the nucleocapsid protein and immune-stimulatory interleukin-2 has been constructed and its immunogenicity and protective effect in chickens has been evaluated. These recombinant plasmids were inoculated in chickens and tested in a protection-challenge experiment, demonstrating that vaccination with the co-expression plasmid pIRES-N/IL2 can induce stronger immune response than vaccination with pIRES-N. These results suggested that vaccination with the co-expression plasmid of N protein gene and IL-2 may have increased the protection rate against challenge. Partial protection against infectious bursal disease virus through DNA-mediated vaccination with the VP2 capsid protein and chicken IL-2 genes abstract: A DNA vaccine against infectious bronchitis virus (IBV) can induce specific humoral and cell-mediated immunity. However, compared to conventional vaccines, DNA vaccines usually induce poor antibody responses. To develop a more potent IBV DNA vaccine formulations, a monocistronic vector encoding the nucleocapsid protein of IBV and a bicistronic vector separately encoding the nucleocapsid protein and immune-stimulatory interleukin-2 were constructed. When the DNA vaccines were administered to the quadriceps muscle of chickens, the induced humoral and cellular responses were evaluated. There was a significant difference in ELISA antibody levels elicited by either monocistronic or bicistronic DNA vaccines. The percentage of CD3(+), CD3(+)CD8(+) and CD3(+)CD4(+) subgroups of peripheral blood T-lymphocytes in chickens immunized with bicistronic DNA vaccine were higher than those in chickens immunized with monocistronic DNA vaccine. When chickens were challenged with a virulent strain of IBV, the protective efficacy could be enhanced significantly after immunization with bicistronic DNA vaccine. These results demonstrated that bicistronic DNA vaccine is an effective approach to increase IBV DNA vaccine immunogenicity. url: https://www.ncbi.nlm.nih.gov/pubmed/18329109/ doi: 10.1016/j.jviromet.2008.01.017 id: cord-308591-cs8os2f5 author: Tawakol, Maram M. title: Evaluation of bacteriophage efficacy in reducing the impact of single and mixed infections with Escherichia coli and infectious bronchitis in chickens date: 2019-11-29 words: 4183.0 sentences: 223.0 pages: flesch: 45.0 cache: ./cache/cord-308591-cs8os2f5.txt txt: ./txt/cord-308591-cs8os2f5.txt summary: title: Evaluation of bacteriophage efficacy in reducing the impact of single and mixed infections with Escherichia coli and infectious bronchitis in chickens Bacteriophage treatment delayed the onset and reduced the severity of clinical signs, and prevented the mortality associated with single and mixed infection with IBV and E. In vivo study was conducted to evaluate the efficacy of bacteriophages in reducing the pathogenicity of single and mixed infections with APEC and IBV. In the present study samples were collected from birds with respiratory manifestations from a total of forty farms, and subjected to characterization based on currently circulating IBV and APEC strains. In addition, the efficacy of bacteriophage treatment in reducing APEC replication in the avian respiratory tract was studied in vivo, as well as their effect in reducing IBV pathogenicity after mixed APEC and IBV infections. abstract: Infectious bronchitis virus (IBV) represents a major threat to poultry production worldwide particularly when complicated with bacterial infection. In the present study samples were collected from forty broiler farms with respiratory manifestations to characterize IBV and E. coli. Bacteriophages were isolated and enriched from sampled farms to study its efficacy to control single and mixed infections with E. coli and IBV in vivo. Twelve out of forty farms were positive for IBV. Phylogenetic analysis of partial spike protein revealed that all positive cases clustered within the GI-23 genotype. Eight out of forty farms were positive for E. coli serogroups O26, O78, O86, O114, O119, with O125 found on three farms. Bacteriophage treatment delayed the onset and reduced the severity of clinical signs, and prevented the mortality associated with single and mixed infection with IBV and E. coli. Furthermore, in mixed infections, bacteriophage treatment significantly reduced E. coli as well as IBV shedding. Groups treated with bacteriophages showed a significant reduction of E. coli shedding that gradually decreased over time, in contrast to higher and gradually increasing shedding without bacteriophage treatment. In conclusion, bacteriophage treatment significantly reduced the pathogenicity and shedding of IBVand E. coli in mixed infections. url: https://doi.org/10.1080/20008686.2019.1686822 doi: 10.1080/20008686.2019.1686822 id: cord-268788-jcu3pasy author: Thor, Sharmi W. title: Recombination in Avian Gamma-Coronavirus Infectious Bronchitis Virus date: 2011-09-23 words: 4426.0 sentences: 219.0 pages: flesch: 49.0 cache: ./cache/cord-268788-jcu3pasy.txt txt: ./txt/cord-268788-jcu3pasy.txt summary: In this study, the full-length genomes of eight avian gamma-coronavirus infectious bronchitis virus (IBV) isolates were sequenced and along with other full-length IBV genomes available from GenBank were analyzed for recombination. In this study we sequenced and analyzed the entire genome of eight IBV strains that represent different serotypes that have not been previously sequenced, and we compared these sequences with other gamma-coronavirus full-length genome sequences available in GenBank for evidence of recombination [16] . A phylogenetic compatibility matrix constructed at the 70% bootstrap level for 250 bp sequence fragments at 100 bp intervals also showed that recombination breakpoints were distributed throughout the IBV genomes (data not shown). Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus Complete genome sequence and recombination analysis of infectious bronchitis virus attenuated vaccine strain H120 abstract: Recombination in the family Coronaviridae has been well documented and is thought to be a contributing factor in the emergence and evolution of different coronaviral genotypes as well as different species of coronavirus. However, there are limited data available on the frequency and extent of recombination in coronaviruses in nature and particularly for the avian gamma-coronaviruses where only recently the emergence of a turkey coronavirus has been attributed solely to recombination. In this study, the full-length genomes of eight avian gamma-coronavirus infectious bronchitis virus (IBV) isolates were sequenced and along with other full-length IBV genomes available from GenBank were analyzed for recombination. Evidence of recombination was found in every sequence analyzed and was distributed throughout the entire genome. Areas that have the highest occurrence of recombination are located in regions of the genome that code for nonstructural proteins 2, 3 and 16, and the structural spike glycoprotein. The extent of the recombination observed, suggests that this may be one of the principal mechanisms for generating genetic and antigenic diversity within IBV. These data indicate that reticulate evolutionary change due to recombination in IBV, likely plays a major role in the origin and adaptation of the virus leading to new genetic types and strains of the virus. url: https://doi.org/10.3390/v3091777 doi: 10.3390/v3091777 id: cord-261388-d56ci0hl author: Tibbles, K.W title: Activity of a purified His-tagged 3C-like proteinase from the coronavirus infectious bronchitis virus date: 1999-05-28 words: 3906.0 sentences: 173.0 pages: flesch: 51.0 cache: ./cache/cord-261388-d56ci0hl.txt txt: ./txt/cord-261388-d56ci0hl.txt summary: Previous studies in vitro of the processing of cloned polyprotein fragments from the coronavirus infectious bronchitis virus (IBV) large open reading frame (ORF1), confirmed the activity of a predicted 3C-like proteinase (3CLP) domain and suggested that the proteinase is released autocatalytically from the polyprotein in the form of a 35 kDa protein, 3CLpro, capable of further cleavages in trans. The bacterial expression system described utilises the minimum processing unit identified in our previous studies which established that, in addition to the 3CLP domain, MP2 protein sequence between the Q/S 4 cleavage target and a point delimited by an NcoI restriction site (ntd position 10118) was that minimally required for processing. Identification of a 24-kDa polypeptide processed from the coronavirus infectious bronchitis virus 1a polyprotein by the 3C-like proteinase and determination of its cleavage sites abstract: Previous studies in vitro of the processing of cloned polyprotein fragments from the coronavirus infectious bronchitis virus (IBV) large open reading frame (ORF1), confirmed the activity of a predicted 3C-like proteinase (3CLP) domain and suggested that the proteinase is released autocatalytically from the polyprotein in the form of a 35 kDa protein, 3CLpro, capable of further cleavages in trans. In order to identify such cleavages within the ORF1 polyprotein mediated by 3CLpro, the proteinase was expressed in bacteria, purified and used in trans cleavage assays with polyprotein fragments lacking the 3CLP domain as targets. The proteinase was expressed as a polyprotein fragment which was able to process during expression in bacterial cells, releasing mature 3CLpro. A histidine (His(6)) tag was introduced close to the C-terminus of the proteinase to aid purification. Processing demonstrated by the tagged proteinase was indistinguishable from that of the wild-type enzyme indicating that the site chosen for the tag was permissive. From these studies we were able to demonstrate trans cleavages consistent with the use of most of the previously predicted or identified sites within the open reading frame of gene 1. This tentatively completes the processing map for the ORF1 region with respect to 3CLpro. url: https://www.sciencedirect.com/science/article/pii/S0168170299000118 doi: 10.1016/s0168-1702(99)00011-8 id: cord-278324-eqqvwwh6 author: Wang, Huanan title: Development of a sensitive and specific xMAP assay for detection of antibodies against infectious laryngotracheitis and bronchitis viruses date: 2018-09-21 words: 3512.0 sentences: 191.0 pages: flesch: 48.0 cache: ./cache/cord-278324-eqqvwwh6.txt txt: ./txt/cord-278324-eqqvwwh6.txt summary: BACKGROUND: A serological method to simultaneously detect antibodies against infectious laryngotracheitis virus (ILTV) and infectious bronchitis virus (IBV) is imperative for the differential diagnosis and evaluation of antibodies titers after vaccination. Therefore, it is important to establish a method to simultaneously detect ILTV and IBV antibodies for the differential diagnosis and immune response evaluation after vaccination. In this study, a method employing Luminex xMAP technology to simultaneously detect ILTV and IBV antibodies in serum was established, optimized and used for the differential diagnosis of IBV and ILTV. 2 and 3 demonstrated that xMAP duplex assay for ILTV and IBV has a high specificity since there were no cross-reactions with serum positive for other avian diseases, such as avian influenza virus To compare duplex xMAP assay with ELISA for ILTV/IBV detection, 90 chicken serum samples from a chicken farm in Huizhou, China were used and the results are shown in Table 7 . abstract: BACKGROUND: A serological method to simultaneously detect antibodies against infectious laryngotracheitis virus (ILTV) and infectious bronchitis virus (IBV) is imperative for the differential diagnosis and evaluation of antibodies titers after vaccination. METHOD: The microspheres coated with purified recombinant glycoprotein D (gD) of ILTV or nucleocapsid (N) protein of IBV were incubated with serum samples. The simultaneous quantification of ILTV and IBV antibodies were achieved through the interrogation of microspheres by Luminex 200 detection system. . RESULTS: This xMAP detection demonstrated no nonspecific reactions with avian influenza virus (AIV), avian leukosis virus (ALV), newcastle disease virus (NDV), and Marek’s disease virus (MDV). The results also demonstrated that the xMAP assay was four times more sensitive than the enzyme-linked immunosorbent assay (ELISA) for ILTV detection and two times more sensitive for IBV detection. A total of 90 chicken serum samples from a chicken farm were tested by xMAP and ELISA assays. The results showed that the coincidence rates were 84.44 and 100% for ILTV and IBV detection, respectively. CONCLUSION: This study exhibited an opportunity for the differential diagnosis through simultaneous detection of multiplex antibodies in serum and can be used for the multiplex antibodies evaluation after vaccination. url: https://doi.org/10.1186/s12985-018-1048-x doi: 10.1186/s12985-018-1048-x id: cord-354547-eomm1sl5 author: Wang, Jibin title: Interaction of the Coronavirus Infectious Bronchitis Virus Membrane Protein with β-Actin and Its Implication in Virion Assembly and Budding date: 2009-03-16 words: 6319.0 sentences: 295.0 pages: flesch: 51.0 cache: ./cache/cord-354547-eomm1sl5.txt txt: ./txt/cord-354547-eomm1sl5.txt summary: title: Interaction of the Coronavirus Infectious Bronchitis Virus Membrane Protein with β-Actin and Its Implication in Virion Assembly and Budding In this study, we report that interaction between coronavirus membrane protein (M) and actin with functional implication in facilitating virion assembly and budding. Similarly, analysis of cells expressing the M protein either on its own or together with the Myc-tagged actin by Western blot with anti-M polyclonal antibodies showed the detection of the full-length glycosylated (two upper bands) and unglycosylated (25 kDa) forms of the M protein (Fig. 2, lanes 5 and 6) . In cells transfected with both wild type and MD5 constructs with or without IBV infection, detection of similar amounts of M protein was observed (Fig. 5b, top two panels, lanes 1 and 2) , suggesting that both constructs were expressed at similar efficiencies. abstract: Coronavirus M protein is an essential component of virion and plays pivotal roles in virion assembly, budding and maturation. The M protein is integrated into the viral envelope with three transmembrane domains flanked by a short amino-terminal ectodomain and a large carboxy-terminal endodomain. In this study, we showed co-purification of the M protein from coronavirus infectious bronchitis virus (IBV) with actin. To understand the cellular factors that may be involved in virion assembly, budding and maturation processes, IBV M was used as the bait in a yeast two-hybrid screen, resulting in the identification of β-actin as a potentially interacting partner. This interaction was subsequently confirmed by coimmunoprecipitation and immunofluorescence microscopy in mammalian cells, and mutation of amino acids A159 and K160 on the M protein abolished the interaction. Introduction of the A159-K160 mutation into an infectious IBV clone system blocks the infectivity of the clone, although viral RNA replication and subgenomic mRNA transcription were actively detected. Disruption of actin filaments with cell-permeable agent cytochalasin D at early stages of the infection cycle led to the detection of viral protein synthesis in infected cells but not release of virus particles to the cultured media. However, the same treatment at late stages of the infection cycle did not affect the release of virus particles to the media, suggesting that disruption of the actin filaments might block virion assembly and budding, but not release of the virus particles. This study reveals an essential function of actin in the replication cycle of coronavirus. url: https://doi.org/10.1371/journal.pone.0004908 doi: 10.1371/journal.pone.0004908 id: cord-294679-7pklrmz5 author: Wei, Lei title: Purification, crystallization and preliminary crystallographic analysis of avian infectious bronchitis virus nsp3 ADRP domain date: 2008-08-09 words: 1069.0 sentences: 73.0 pages: flesch: 61.0 cache: ./cache/cord-294679-7pklrmz5.txt txt: ./txt/cord-294679-7pklrmz5.txt summary: title: Purification, crystallization and preliminary crystallographic analysis of avian infectious bronchitis virus nsp3 ADRP domain Avian infectious bronchitis virus (IBV) encodes 15 nonstructural proteins (nsps) which play crucial roles in RNA transcription and genome replication. One of them, nsp3, contains an ADRP (adenosine diphosphate-ribose-1′-phosphatase) domain which was revealed in recent studies to have ADP-ribose-1′-monophos­phatase (Appr-1′-pase) activity. The gene segment encoding the IBV nsp3 ADRP domain has been cloned and expressed in Escherichia coli. Considering that the genomes encoding the nonstructural proteins (nsps) are conserved among SARS-Cov, IBV, human-Cov 229E etc., the study of IBV will facilitate the thorough understanding of coronaviruses. Initial crystals were obtained from Index Screen condition No. 84 containing 0.2 M magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5, 25%(w/v) polyethylene glycol 3350. A typical diffraction pattern of an IBV nsp3 ADRP domain crystal collected on a Rigaku R-AXIS IV ++ image-plate detector. Avian infectious bronchitis virus nsp3 abstract: Avian infectious bronchitis virus (IBV) encodes 15 nonstructural proteins (nsps) which play crucial roles in RNA transcription and genome replication. One of them, nsp3, contains an ADRP (adenosine diphosphate-ribose-1′-phosphatase) domain which was revealed in recent studies to have ADP-ribose-1′-monophos­phatase (Appr-1′-pase) activity. Appr-1′-pase catalyzes the conversion of ADP-ribose-1′-monophosphate (Appr-1′-p) to ADP-ribose in the tRNA-splicing pathway. The gene segment encoding the IBV nsp3 ADRP domain has been cloned and expressed in Escherichia coli. The protein has been crystallized and the crystals diffracted to 1.8 Å resolution. They belonged to space group P1, with unit-cell parameters a = 41.1, b = 43.2, c = 48.9 Å, α = 78.0, β = 80.0, γ = 73.6°. Each asymmetric unit contains two molecules. url: https://doi.org/10.1107/s1744309108024391 doi: 10.1107/s1744309108024391 id: cord-253695-tjdw2uta author: Winter, Christine title: Infection of the tracheal epithelium by infectious bronchitis virus is sialic acid dependent date: 2007-12-28 words: 3679.0 sentences: 208.0 pages: flesch: 52.0 cache: ./cache/cord-253695-tjdw2uta.txt txt: ./txt/cord-253695-tjdw2uta.txt summary: Avian Infectious bronchitis virus (IBV) is a coronavirus that infects chickens via the respiratory epithelium as primary target cells. Here we analyze the importance of the sialic acid binding activity for the infection of tracheal organ cultures (TOCs) by different IBV strains. Desialylation induced by neuraminidase treatment of tracheal organ cultures prior to infection by IBV delayed the ciliostatic effect or resulted in partial loss of ciliary activity. After having shown recently that sialic acid serves as a receptor determinant for IBV on cultured cells, we were interested to find out whether this type of sugar is also important for an infection in vivo. From this result we conclude that a2,3-linked sialic acid serves as a receptor determinant for the infection of avian tracheal epithelial cells by the Beaudette strain of IBV. Sialic acid is a receptor determinant for infection of cells by avian Infectious bronchitis virus abstract: Avian Infectious bronchitis virus (IBV) is a coronavirus that infects chickens via the respiratory epithelium as primary target cells. The binding of coronaviruses to the cell surface is mediated by the viral surface protein S. Recently we demonstrated that α2,3-linked sialic acid serves as a receptor determinant for IBV on Vero cells and primary chicken embryo kidney cells. Here we analyze the importance of the sialic acid binding activity for the infection of tracheal organ cultures (TOCs) by different IBV strains. Our results show that α2,3-linked sialic acid also serves as a receptor determinant on chicken TOCs. Infection of TOCs by IBV results in ciliostasis. Desialylation induced by neuraminidase treatment of tracheal organ cultures prior to infection by IBV delayed the ciliostatic effect or resulted in partial loss of ciliary activity. This effect was observed with both respiratory and nephropathogenic strains. Inhibition of ciliostasis was also observed when TOCs were pretreated with an α2,3-specific neuraminidase. Analysis of the tracheal epithelium for reactivity with lectins revealed that the susceptible cells in the epithelium abundantly express α2,3-linked sialic acid. These results indicate that α2,3-linked sialic acid plays an important role for infection of the respiratory epithelium by IBV. url: https://www.ncbi.nlm.nih.gov/pubmed/18396435/ doi: 10.1016/j.micinf.2007.12.009 id: cord-280442-jtvez46y author: Wu, Xuan title: Simultaneous and visual detection of infectious bronchitis virus and Newcastle disease virus by multiple LAMP and lateral flow dipstick date: 2019-11-01 words: 5308.0 sentences: 271.0 pages: flesch: 55.0 cache: ./cache/cord-280442-jtvez46y.txt txt: ./txt/cord-280442-jtvez46y.txt summary: To evaluate this novel detection method, PCR assays (including conventional RT-PCR, qRT-PCR and nRT-PCR) and reverse-transcription LAMP (RT-LAMP) monitored by electrophoresis were also conducted and the specificity and sensitivity of the assays were compared with those of the mRT-LAMP-LFD assay. A total of 13 IBV strains, 7 NDV strains, and the PCR and LAMP target sequences of 6 NDV and 1 turkey coronavirus strains (TCoV) synthesized by Sangon Biotech (Shanghai, China) Co, as well as 6 other avian virus strains, were used for the determination of the specificities of RT-PCR and RT-LAMP assays. Statistical significance difference studies showed that the mean detection rates of mRT-LAMP-LFD were significantly higher than that of conventional RT-PCR assays when detecting IBV or NDV alone (P < 0.05). The mean IBV and NDV detection rates of different samples, detected by mRT-LAMP-LFD, were both 95%, and were significantly higher than those detected by conventional RT-PCR and qRT-PCR (P < 0.05, Figure 6B) . abstract: ABSTRACT Infectious bronchitis virus (IBV) and Newcastle disease virus (NDV) are both important viruses seriously affecting poultry industry worldwide. In this study, reverse-transcription LAMP (RT-LAMP) was combined with lateral flow dipstick (LFD) forming a novel detection tool which could simultaneously detect IBV and NDV visually. Primers targeted the 5′-untranslated region (5′-UTR) of IBV genome and the conserved region of NDV large polymerase gene (LP). The specificity and sensitivity of this multiple reverse transcription-LAMP-LFD (mRT-LAMP-LFD) assay were compared with those of conventional RT-PCR, nested RT-PCR (nRT-PCR), quantification RT-PCR (qRT-PCR), and RT-LAMP monitored by electrophoresis. No non-specific amplifications were observed when the assays were tested with unrelated viruses. According to the sensitivity study, when detecting IBV or NDV alone, the lowest detection limits of mRT-LAMP-LFD were 100.8 IBV RNA copies/reaction and 100.7 NDV RNA copies/reaction. Furthermore, when detecting IBV and NDV simultaneously, the lowest detection limit was the same as that of the single detection assays. In the clinical sample study, mRT-LAMP-LFD performed the best among these assays. When tested with IBV or NDV single infected samples, the mean detection rates were 98.65% and 97.25%, respectively. In the IBV and NDV co-infected sample study, the mean detection rates of IBV and NDV were both 95%. This study showed that mRT-LAMP-LFD was a promising qualitative detection tool suitable for field single or multiple IBV and NDV detection. url: https://www.ncbi.nlm.nih.gov/pubmed/31265112/ doi: 10.3382/ps/pez372 id: cord-263476-ju7xqwa7 author: Xia, Jing title: Phylogenetic and antigenic analysis of avian infectious bronchitis virus in southwestern China, 2012–2016 date: 2016-08-13 words: 5699.0 sentences: 276.0 pages: flesch: 55.0 cache: ./cache/cord-263476-ju7xqwa7.txt txt: ./txt/cord-263476-ju7xqwa7.txt summary: The aim of this study was to decipher the molecular epidemiological and antigenic characteristics of infectious bronchitis virus strains (IBVs) isolated in recent years in southwestern China. The antigenicity of ten IBVs, including seven field strains and commonly used vaccine strains, were assayed with a viral cross-neutralization assay in chicken embryonated kidney cells (CEK). To determine the antigenic relatedness between the field IBV isolates and the vaccine viral strains, double-direction viral cross-neutralization (VN) tests were performed in chicken embryo kidney (CEK) cells using constant viral titers and diluted serum. The tested strains came from six different genotypes and included seven IBV field isolates (Sczy3, cK/CH/SCDY/141030, cK/CH/SCLS/140104, cK/CH/CQKX/ 150203, cK/CH/SCYB/140913, cK/CH/SCMY/10I, cK/CH/SCYB/141102) and the three most commonly used vaccine viral strains (H120, M41, and 4/91). Ten IBVs, including seven field strains from different genotype backgrounds and three commonly used vaccine strains (H120, 4/91, and M41), were analyzed and grouped into four serotypes: Massachusetts (Mass hereafter), 793B, Sczy3, and SCYB. abstract: The aim of this study was to decipher the molecular epidemiological and antigenic characteristics of infectious bronchitis virus strains (IBVs) isolated in recent years in southwestern China. A total of 24 field strains were isolated from diseased chickens between 2012 and 2016. Phylogenetic analysis based on S1 nucleotide sequences showed that 16 of the 24 isolates were clustered into four distinct genotypes: QX (37.5%), TW (16.7%, TWI and TWII), Mass (8.3%), and J2 (4.2%). The QX genotype was still the prevalent genotype in southwestern China. Recombination analysis of the S1 subunit gene showed that eight of the 24 field strains were recombinant variants that originated from field strains and vaccine strains. A new potential recombination hotspot [ATTTT(T/A)] was identified, implying that recombination events may become more and more common. The antigenicity of ten IBVs, including seven field strains and commonly used vaccine strains, were assayed with a viral cross-neutralization assay in chicken embryonated kidney cells (CEK). The results showed that the ten IBVs could be divided into four serotypes (Massachusetts, 793B, Sczy3, and SCYB). Sczy3 and 793B were the predominant serotypes. Six of the seven field isolates (all except for cK/CH/SCYB/140913) cross-reacted well with anti-sera against other field strains. In conclusion, the genetic and antigenic features of IBVs from southwestern China in recent years have changed when compared to the previous reports. The results could provide a reference for vaccine development and the prevention of infectious bronchitis in southwestern China. url: https://www.ncbi.nlm.nih.gov/pubmed/27530216/ doi: 10.1016/j.meegid.2016.08.011 id: cord-328046-5us4se5o author: Xu, H. Y. title: Further Identification and Characterization of Novel Intermediate and Mature Cleavage Products Released from the ORF 1b Region of the Avian Coronavirus Infectious Bronchitis Virus 1a/1b Polyprotein date: 2001-09-30 words: 5643.0 sentences: 279.0 pages: flesch: 51.0 cache: ./cache/cord-328046-5us4se5o.txt txt: ./txt/cord-328046-5us4se5o.txt summary: In cells infected with avian coronavirus infectious bronchitis virus (IBV), three proteins of 100, 39, and 35 kDa, respectively, were previously identified as mature cleavage products released from the 1b region of the 1a/1b polyprotein by the 3C-like proteinase. Immunofluorescent staining of IBV-infected cells and cells expressing individual cleavage products showed that the 100-, 68-, and 58-kDa proteins were associated with the membranes of the endoplasmic reticulum, and the 39and 35-kDa proteins displayed diffuse distribution patterns. Taken together with the Q 3928 -S 2929 dipeptide bond (encoded by nucleotides 12310-12315) identified as the N-terminal cleavage site of the 100-kDa protein, cleavage at these positions would result in the release of five mature products with molecular masses of approximately 100, 68, 58, 39, and 35 kDa. Among them, the 100-, 39-, and 35-kDa proteins were specifically identified in IBV-infected cells (Liu et al., 1994 . abstract: Abstract The coronavirus 3C-like proteinase is one of the viral proteinases responsible for processing of the 1a and 1a/1b polyproteins to multiple mature products. In cells infected with avian coronavirus infectious bronchitis virus (IBV), three proteins of 100, 39, and 35 kDa, respectively, were previously identified as mature cleavage products released from the 1b region of the 1a/1b polyprotein by the 3C-like proteinase. In this report, we show the identification of two more cleavage products of 68 and 58 kDa released from the same region of the polyprotein. In addition, two stable intermediate cleavage products with molecular masses of 160 and 132 kDa, respectively, were identified in IBV-infected cells. The 160-kDa protein was shown to be an intermediate cleavage product covering the 100- and 68-kDa proteins, and the 132-kDa protein to be an intermediate cleavage product covering the 58-, 39-, and 35-kDa proteins. Immunofluorescent staining of IBV-infected cells and cells expressing individual cleavage products showed that the 100-, 68-, and 58-kDa proteins were associated with the membranes of the endoplasmic reticulum, and the 39- and 35-kDa proteins displayed diffuse distribution patterns. url: https://api.elsevier.com/content/article/pii/S0042682201910980 doi: 10.1006/viro.2001.1098 id: cord-352511-gkm7i62s author: Yamada, Yoshiyuki title: Acquisition of Cell–Cell Fusion Activity by Amino Acid Substitutions in Spike Protein Determines the Infectivity of a Coronavirus in Cultured Cells date: 2009-07-02 words: 5731.0 sentences: 317.0 pages: flesch: 55.0 cache: ./cache/cord-352511-gkm7i62s.txt txt: ./txt/cord-352511-gkm7i62s.txt summary: title: Acquisition of Cell–Cell Fusion Activity by Amino Acid Substitutions in Spike Protein Determines the Infectivity of a Coronavirus in Cultured Cells Here we report that acquisition of the cell–cell fusion activity by amino acid mutations in the S protein determines the infectivity of IBV in cultured cells. This study demonstrates that acquisition of the cell–cell fusion activity in S protein determines the selection and/or adaptation of a coronavirus from chicken embryo to cultured cells of human and animal origins. In this study, we report that acquisition of the cell-cell fusion activity by point mutations in the spike (S) protein of avian coronavirus infectious bronchitis virus (IBV) plays a critical role in adaptation and/or selection of a variant that infects cultured cells. Sequence comparison of two S protein constructs, S(EP3) and S(CK), cloned from EP3 and CK-adapted IBV strains, respectively, showed amino acid substitutions at 31 positions (Fig. 1a) . abstract: Coronavirus host and cell specificities are determined by specific interactions between the viral spike (S) protein and host cell receptor(s). Avian coronavirus infectious bronchitis (IBV) has been adapted to embryonated chicken eggs, primary chicken kidney (CK) cells, monkey kidney cell line Vero, and other human and animal cells. Here we report that acquisition of the cell–cell fusion activity by amino acid mutations in the S protein determines the infectivity of IBV in cultured cells. Expression of S protein derived from Vero- and CK-adapted strains showed efficient induction of membrane fusion. However, expression of S protein cloned from the third passage of IBV in chicken embryo (EP3) did not show apparent syncytia formation. By construction of chimeric S constructs and site-directed mutagenesis, a point mutation (L857-F) at amino acid position 857 in the heptad repeat 1 region of S protein was shown to be responsible for its acquisition of the cell–cell fusion activity. Furthermore, a G405-D point mutation in the S1 domain, which was acquired during further propagation of Vero-adapted IBV in Vero cells, could enhance the cell–cell fusion activity of the protein. Re-introduction of L857 back to the S gene of Vero-adapted IBV allowed recovery of variants that contain the introduced L857. However, compensatory mutations in S1 and some distant regions of S2 were required for restoration of the cell–cell fusion activity of S protein carrying L857 and for the infectivity of the recovered variants in cultured cells. This study demonstrates that acquisition of the cell–cell fusion activity in S protein determines the selection and/or adaptation of a coronavirus from chicken embryo to cultured cells of human and animal origins. url: https://www.ncbi.nlm.nih.gov/pubmed/19572016/ doi: 10.1371/journal.pone.0006130 id: cord-000924-wwuqxx1r author: Yan, Fang title: Protection of chickens against infectious bronchitis virus with a multivalent DNA vaccine and boosting with an inactivated vaccine date: 2013-03-24 words: 3775.0 sentences: 198.0 pages: flesch: 51.0 cache: ./cache/cord-000924-wwuqxx1r.txt txt: ./txt/cord-000924-wwuqxx1r.txt summary: title: Protection of chickens against infectious bronchitis virus with a multivalent DNA vaccine and boosting with an inactivated vaccine The protective efficacy of DNA plasmids encoding avian infectious bronchitis virus (IBV) S1, N, or M protein was investigated in chickens. The serum antibody titers in the prime-boost birds were significantly higher than those of the multivalent DNA vaccine group (p < 0.01) but not significantly different compared to the inactivated vaccine group at 49 days of age. Additionally, the prime-boost group also showed the highest level of IBV-specific cellular proliferation compared to the monovalent groups (p < 0.01) but no significant difference was found compared to the multivalent DNA vaccine group, and the prime-boost group completely protected from followed viral challenge. These results indicate that immunization with a combination of the three-gene DNA vaccine and an inactivated vaccine not only elicited the strongest antibody response, but also induced the highest IBV-specific cellular proliferation rates in the chickens. abstract: The protective efficacy of DNA plasmids encoding avian infectious bronchitis virus (IBV) S1, N, or M protein was investigated in chickens. Chickens were inoculated monovalently (with plasmid pVAX1-16S1, pVAX1-16M, or pVAX1-16N alone) or multivalently (combination of the three different plasmids, pVAX1-16S1/M/N). A prime-boost immunization protocol against IBV was developed. Chickens were immunized with the multivalent DNA vaccine twice and then boosted with an inactivated vaccine once. Antibody titers of the chickens immunized with pVAX1-16S1/M/N were much higher than those of the monovalent groups (p < 0.01). A protective rate up to 90% was observed in the pVAX1-16S1/M/N group. The serum antibody titers in the prime-boost birds were significantly higher than those of the multivalent DNA vaccine group (p < 0.01) but not significantly different compared to the inactivated vaccine group at 49 days of age. Additionally, the prime-boost group also showed the highest level of IBV-specific cellular proliferation compared to the monovalent groups (p < 0.01) but no significant difference was found compared to the multivalent DNA vaccine group, and the prime-boost group completely protected from followed viral challenge. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3615232/ doi: 10.4142/jvs.2013.14.1.53 id: cord-003208-lwirkob3 author: Yan, Liping title: Novel protein chip for the detection of antibodies against infectious bronchitis virus date: 2018-09-17 words: 3973.0 sentences: 220.0 pages: flesch: 52.0 cache: ./cache/cord-003208-lwirkob3.txt txt: ./txt/cord-003208-lwirkob3.txt summary: RESULTS: We have developed two indirect microarray methods to detect antibodies against IBV: a chemiluminescent immunoassay test (CIT) and a rapid diagnostic test (RDT). Compared with these methods, enzyme-linked immunosorbent assay (ELISA) has been widely used for testing IBV early infection and continuous infection, and this technique can be used for both antigenic and antibody detection. The data showed that 130 serum samples were positive for antibodies against IBV, and 14 samples were negative, similar to the results of the IDEXX IBV Ab Test kit with the nsp5 concentration of 0.2 mg/mL (Table 4 ). The specific experiments of the RDT showed that no cross-reaction Fig. 4 a Distribution of the SNRs of the IDEXX-positive (n = 142) and IDEXX-negative (n = 42) serum samples of the clinical sera obtained from the IBV protein microarray. abstract: BACKGROUND: Infectious bronchitis (IB) caused by the IB virus (IBV) can cause acute damage to chickens around the world. Therefore, rapid diagnosis and immune status determination are critical for controlling IBV outbreaks. Enzyme-linked immunosorbent assays (ELISAs) have been widely used in the detection of IBV antibodies in the early infection and continuous infection of IB because they are more sensitive and quicker than other diagnostic methods. RESULTS: We have developed two indirect microarray methods to detect antibodies against IBV: a chemiluminescent immunoassay test (CIT) and a rapid diagnostic test (RDT). IBV nonstructural protein 5 (nsp5) was expressed, purified from Escherichia coli, and used to spot the initiator integrated poly(dimethylsiloxane), which can provide a near “zero” background for serological assays. Compared with the IDEXX IBV Ab Test kit, CIT and RDT have a sensitivity and specificity of at least 98.88% and 91.67%, respectively. No cross-reaction was detected with antibodies against avian influenza virus subtypes (H5, H7, and H9), Newcastle disease virus, Marek’s disease virus, infectious bursal disease virus, and chicken anemia virus. The coefficients of variation of the reproducibility of the intra- and inter-assays for CIT ranged from 0.8 to 18.63%. The reproducibility of RDT was consistent with the original results. The application of the IBV nsp5 protein microarray showed that the positive rate of the CIT was 96.77%, that of the nsp5 ELISA was 91.40%, and that of the RDT was 90.32%. Furthermore, the RDT, which was visible to the naked eye, could be completed within 15 min. Our results indicated that compared with nsp5 ELISA, the CIT was more sensitive, and the RDT had similar positive rates but was faster. Furthermore, the two proposed methods were specific and stable. CONCLUSIONS: Two microarray assays, which were rapid, specific, sensitive, and relatively simple, were developed for the detection of an antibody against IBV. These methods can be of great value for the surveillance of pathogens and monitoring the efficiency of vaccination. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6142349/ doi: 10.1186/s12917-018-1586-x id: cord-291174-rym84kni author: Yang, Yazhi title: A label-free electrochemical assay for coronavirus IBV H120 strain quantification based on equivalent substitution effect and AuNPs-assisted signal amplification date: 2020-10-23 words: 3577.0 sentences: 234.0 pages: flesch: 51.0 cache: ./cache/cord-291174-rym84kni.txt txt: ./txt/cord-291174-rym84kni.txt summary: title: A label-free electrochemical assay for coronavirus IBV H120 strain quantification based on equivalent substitution effect and AuNPs-assisted signal amplification According to the differences of S1 protein in various infectious bronchitis virus (IBV) strains, a target DNA sequence that can specifically recognize H120 RNA forming a DNA-RNA hybridized double-strand structure has been designed. Therefore, developing a rapid and sensitive method for identification and quantification of different IBV strains based on hypervariable region of S1 gene can effectively solve the problem, which plays important roles in IB early diagnosis and control, especially for vaccine production. Herein, a label-free electrochemical assay based on equivalent substitution effect and AuNPs-assisted signal amplification is developed for identification and quantification detection of IBV H120 strain. In this work, we designed the sequence of the target DNA based on the hypervariable region in the S1 gene between different IBV strains, then, constructed the standard plasmid containing characteristic sequence of S1 gene in H120 strain, Fig. 2 Real-time fluorescence quantitative PCR plot. abstract: A label-free electrochemical strategy is proposed combining equivalent substitution effect with AuNPs-assisted signal amplification. According to the differences of S1 protein in various infectious bronchitis virus (IBV) strains, a target DNA sequence that can specifically recognize H120 RNA forming a DNA-RNA hybridized double-strand structure has been designed. Then, the residual single-stranded target DNA is hydrolyzed by S1 nuclease. Therefore, the content of target DNA becomes equal to the content of virus RNA. After equivalent coronavirus, the target DNA is separated from DNA-RNA hybridized double strand by heating, which can partly hybridize with probe 2 modified on the electrode surface and probe 1 on AuNPs’ surface. Thus, AuNPs are pulled to the surface of the electrode and the abundant DNA on AuNPs’ surface could adsorb a large amount of hexaammineruthenium (III) chloride (RuHex) molecules, which produce a remarkably amplified electrochemical response. The voltammetric signal of RuHex with a peak near − 0.28 V vs. Ag/AgCl is used as the signal output. The proposed method shows a detection range of 1.56e(−9) to 1.56e(−6) μM with the detection limit of 2.96e(−10) μM for IBV H120 strain selective quantification detection, exhibiting good accuracy, stability, and simplicity, which shows a great potential for IBV detection in vaccine research and avian infectious bronchitis diagnosis. [Figure: see text] ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00604-020-04582-3) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s00604-020-04582-3 doi: 10.1007/s00604-020-04582-3 id: cord-348660-qnbgywgy author: Yilmaz, Huseyin title: Production of Recombinant N Protein of Infectious Bronchitis Virus Using the Baculovirus Expression System and Its Assessment as a Diagnostic Antigen date: 2018-07-09 words: 3921.0 sentences: 183.0 pages: flesch: 43.0 cache: ./cache/cord-348660-qnbgywgy.txt txt: ./txt/cord-348660-qnbgywgy.txt summary: Following optimization of the ELISA protocol, 18 test sera were obtained from broiler chickens exposed to natural wild-type IBV infection, 18 test sera from broiler chickens vaccinated with a live-attenuated commercial IBV vaccine, and sera obtained at different time-points from chicks immunized with recombinant IBV N protein (described above) were analyzed to detect IBV N-specific antibodies. To assess the reliability of the performance of our in-house indirect IBV N ELISA, a panel of sera was obtained from chickens naturally infected with local wild-type IBV strains, chickens vaccinated with live-attenuated commercial IBV vaccine, and chickens immunized with recombinant IBV N protein (expressed in a baculovirus expression system). This represents the first study in Turkey that expressed recombinant IBV N protein in baculovirus and examined its reactivity against antisera obtained from Turkish chickens for potential use as antigen Fig. 5 Detection of IBV N specific antibodies in sera obtained from naturally infected chicken (a) and vaccinated chickens (b) using an in-house IBV-N ELISA and a commercial ELISA. abstract: The avian coronavirus-infectious bronchitis virus (AvCoV-IBV) is recognized as an important avian pathogen, and new viral variants are a continuous threat to the poultry industry worldwide. Sensitive diagnostics and efficacious vaccines are necessary to combat IBV infections in chickens. The aim of this study was to produce recombinant N protein of IBV in the baculovirus system to use in ELISA diagnostic tests in order to enable the assessment of the sero-prevalence and risk of IBV infections in chickens in Turkey. For this, the gene encoding the N protein of the Beaudette strain of IBV was expressed using a recombinant baculovirus expression system. The recombinant N protein was purified using Ni-NTA affinity chromatography. An estimated 50-kDa recombinant protein corresponding to the expected molecular weight of IBV N including the 6xHis tag was detected using an anti-His monoclonal antibody. Specific immunoreactivity of the recombinant protein was confirmed by Western blot using antiserum obtained from vaccinated and naturally infected chicken from Turkey as well as using a monoclonal antibody raised against the N protein of the IBV Massachusetts strain. The results obtained with the in-house ELISA had high agreement with a commercial ELISA. Immunoreactivity analysis using antisera in Western blotting and the in-house ELISA suggests that the recombinant IBV N protein could be broadly cross-reactive with antisera produced against different IBV strains. We conclude that the recombinant baculovirus expressed IBV N protein could serve as a useful diagnostic antigen for detection of IBV infections in chickens by ELISA. url: https://www.ncbi.nlm.nih.gov/pubmed/29987628/ doi: 10.1007/s12010-018-2815-2 id: cord-281526-7t9e4lgn author: Yin, Lijuan title: Immunogenicity and protective efficacy of recombinant fusion proteins containing spike protein of infectious bronchitis virus and hemagglutinin of H3N2 influenza virus in chickens date: 2016-09-02 words: 4464.0 sentences: 234.0 pages: flesch: 47.0 cache: ./cache/cord-281526-7t9e4lgn.txt txt: ./txt/cord-281526-7t9e4lgn.txt summary: title: Immunogenicity and protective efficacy of recombinant fusion proteins containing spike protein of infectious bronchitis virus and hemagglutinin of H3N2 influenza virus in chickens To investigate whether the recombinant proteins could induce better immune response against IBV infection, we detected IBVspecific antibody in the sera of vaccinated chicken using indirect ELISA. Two weeks after booster vaccination (day 28), the levels of anti-IBV antibodies increased further in chickens immunized with inactivated M41 virus, rS1, rS1-H3(TM) and rS1-HA2. After challenged with virulent IBV M41 strain, our results demonstrated that fusion proteins performed better protection compared with inactivated M41 vaccine and recombinant rS1 protein alone, while the latter groups presented similar protection ratio. The S1 glycoprotein but not the N or M proteins of avian infectious bronchitis virus induces protection in vaccinated chickens Induction of protective immunity in chickens vaccinated with infectious bronchitis virus S1 glycoprotein expressed by a recombinant baculovirus abstract: Infectious bronchitis (IB) is an acute and highly contagious viral respiratory disease of chickens and vaccination is the main method for disease control. The S1 protein, which contains several virus neutralization epitopes, is considered to be a target site of vaccine development. However, although protective immune responses could be induced by recombinant S1 protein, the protection rate in chickens was still low (<50%). Here, we generated fused S1 proteins with HA2 protein (rS1-HA2) or transmembrane domain and cytoplasmic tail (rS1-H3(TM)) from hemagglutinin of H3N2 influenza virus. After immunization, animals vaccinated with fusion proteins rS1-HA2 and rS1-H3(TM) demonstrated stronger robust humoral and cellular immune responses than that of rS1 and inactivated M41 vaccine. The protection rates of groups immunized with rS1-HA2 (87%) were significantly higher than the groups inoculated with rS1 (47%) and inactivated M41 vaccine (53%). And chickens injected with rS1-H3(TM) had similar level of protection (73%) comparing to chickens vaccinated with rS1 (47%) (P = 0.07). Our data suggest that S1 protein fused to the HA2 or TM proteins from hemagglutinin of H3N2 influenza virus may provide a new strategy for high efficacy recombinant vaccine development against IBV. url: https://api.elsevier.com/content/article/pii/S016817021630274X doi: 10.1016/j.virusres.2016.07.010 id: cord-337441-c5bxthwn author: You, Jae-Hwan title: Three-Dimensional Reconstruction of the Nucleolus Using Meta-Confocal Microscopy in Cells Expressing the Coronavirus Nucleoprotein date: 2006 words: 1752.0 sentences: 100.0 pages: flesch: 52.0 cache: ./cache/cord-337441-c5bxthwn.txt txt: ./txt/cord-337441-c5bxthwn.txt summary: We investigated the three-dimensional structure of the nucleolus and sub-nuclear bodies within cells expressing IBV and severe acute respiratory syndrome coronavirus (SARS-CoV) N protein. Live cell imaging data indicated that both EGFP and ECFP, when expressed as individual proteins, had no distinct distribution pattern and were present in both the cytoplasm and nucleus but not nucleolus (Fig. 1A) . In contrast to EGFP-tagged IBV N protein, ECFP-tagged SARS-CoV N protein localized to the cytoplasm and, in a minority of cells, to what appeared to be a nuclear body (arrowed). To investigate whether IBV N protein localized to a specific part of the nucleolus, Cos-7 cells were transfected with pEGFP-IBV-N, fixed 24 hr post-transfection, stained with PI to visualize the nucleus and nucleolus, then sectioned by confocal microscopy (Fig. 2) . META-confocal analysis and three-dimensional reconstructions of cells expressing IBV N protein revealed that N protein does not localize throughout the nucleolus and may be confined to the DFC. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/17037551/ doi: 10.1007/978-0-387-33012-9_55 id: cord-296364-7rp60d2m author: Youn, Soonjeon title: In vitro assembled, recombinant infectious bronchitis viruses demonstrate that the 5a open reading frame is not essential for replication date: 2005-02-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Molecular clones of infectious bronchitis virus (IBV), derived from the Vero cell adapted Beaudette strain, were constructed, using an in vitro assembly method. In vitro transcribed RNA from a cDNA template that had been constructed from seven cDNA fragments, encompassing the entire genome of IBV, was electroporated into BHK-21 cells. The cells were overlaid onto the susceptible Vero cells and viable virus was recovered from the molecular clone. The molecularly cloned IBV (MIBV) demonstrated growth kinetics, and plaque size and morphology that resembled the parental Beaudette strain IBV. The recombinant virus was further manipulated to express enhanced green fluorescent protein (EGFP) by replacing an open reading frame (ORF) of the group-specific gene, ORF 5a, with the EGFP ORF. The rescued recombinant virus, expressing EGFP (GIBV), replicated to lower viral titers and formed smaller plaques compared to the parental virus and the MIBV. After six passages of GIBV, a minority of plaques were observed that had reverted to the larger plaque size and virus from these plaques no longer expressed EGFP. Direct sequencing of RT-PCR products derived from cells infected with the plaque-purified virus, which had lost expression of EGFP, confirmed loss of the EGFP ORF. The loss of EGFP expression (Δ5a IBV) was also accompanied by reversion to growth kinetics resembling the standard virus and intact recombinant virus. This study demonstrates that the 5a ORF is not essential for viral multiplication in Vero cells. url: https://www.sciencedirect.com/science/article/pii/S0042682204007421 doi: 10.1016/j.virol.2004.10.045 id: cord-291718-cz1bi0ym author: Yu, Liping title: The papain-like protease of avian infectious bronchitis virus has deubiquitinating activity date: 2017-03-18 words: 3426.0 sentences: 180.0 pages: flesch: 54.0 cache: ./cache/cord-291718-cz1bi0ym.txt txt: ./txt/cord-291718-cz1bi0ym.txt summary: Furthermore, the IBV replicase-encoded PLP, including the downstream transmembrane (TM) domain, is a DUB enzyme and dramatically reduced the level of Ub-conjugated proteins, while processing both K48and K63-linked polyubiquitin chains. Overall, these results demonstrate that the IBV-encoded PLP-TM functions as a DUB enzyme and suggest that IBV may interfere with the activation of host antiviral signaling pathway by degrading polyubiquitin-associated proteins. Further experiments indicated that the proteinase PLP-TM plays an important role in IBV DUB activity and can process both K48-and K63-linked polyubiquitin chains. Overall, the results of our study show that IBV has DUB activity and confirm that PLP-TM is not only a classic papain-like protease encoded by IBV but is also a multifunctional protein that plays important roles in the regulation of interactions between IBV and host antiviral innate immune response proteins. IBV PLP-TM may prevent the activation of host antiviral signaling pathways by degrading polyubiquitin chains associated with ubiquitin proteins. abstract: Coronavirus papain-like proteases (PLPs) can act as proteases that process virus-encoded large replicase polyproteins and also as deubiquitinating (DUB) enzymes. Like the PLPs of other coronaviruses (CoVs), the avian infectious bronchitis virus (IBV) PLP catalyzes proteolysis of Gly-Gly dipeptide bonds to release mature cleavage products. However, the other functions of the IBV PLP are not well understood. In this study, we found that IBV exhibits strong global DUB activity with significant reductions of the levels of ubiquitin (Ub)-, K48-, and K63-conjugated proteins. The DUB activity exhibited a clear time dependence, with stronger DUB activity in the early stage of viral infection. Furthermore, the IBV replicase-encoded PLP, including the downstream transmembrane (TM) domain, is a DUB enzyme and dramatically reduced the level of Ub-conjugated proteins, while processing both K48- and K63-linked polyubiquitin chains. By contrast, PLP did not cause any reduction of haemagglutinin (HA)-Ub-conjugated proteins. In addition, mutations of the catalytic residues of PLP-TM, Cys1274Ser and His1437Lys, reduced DUB activity against Ub-, K48- and K63- conjugated proteins, indicating that the DUB activity of the PLP-TM wild-type protein is not completely dependent on its catalytic activity. Overall, these results demonstrate that the IBV-encoded PLP-TM functions as a DUB enzyme and suggest that IBV may interfere with the activation of host antiviral signaling pathway by degrading polyubiquitin-associated proteins. url: https://doi.org/10.1007/s00705-017-3328-y doi: 10.1007/s00705-017-3328-y id: cord-326319-3538jmqd author: Yuan, Yuan title: Protection against Virulent Infectious Bronchitis Virus Challenge Conferred by a Recombinant Baculovirus Co-Expressing S1 and N Proteins date: 2018-06-27 words: 7470.0 sentences: 370.0 pages: flesch: 54.0 cache: ./cache/cord-326319-3538jmqd.txt txt: ./txt/cord-326319-3538jmqd.txt summary: title: Protection against Virulent Infectious Bronchitis Virus Challenge Conferred by a Recombinant Baculovirus Co-Expressing S1 and N Proteins The levels of immune protection of these subunit vaccines were evaluated by inoculating specific pathogen-free (SPF) chickens at 14 days of age, giving them a booster with the same dose 14 days later and challenging them with a virulent GX-YL5 strain of IBV 14 days post-booster (dpb). At 14 dpv, IBV-specific antibody levels in birds immunized with subunit vaccines rHBM-S1-N, rHBM-S1, rHBM-N and inactivated vaccine strain H120 started to rise (p > 0.05). At 14 dpv, IBV-specific antibody levels in birds immunized with subunit vaccines rHBM-S1-N, rHBM-S1, rHBM-N and inactivated vaccine strain H120 started to rise (p > 0.05). Induction of protective immunity in chickens vaccinated with infectious bronchitis virus S1 glycoprotein expressed by a recombinant baculovirus The S1 glycoprotein but not the N or M proteins of avian infectious bronchitis virus induces protection in vaccinated chickens abstract: Avian infectious bronchitis virus (IBV) is the causative agent of infectious bronchitis, which results in considerable economic losses. It is imperative to develop safe and efficient candidate vaccines to control IBV infection. In the current study, recombinant baculoviruses co-expressing the S1 and N proteins and mono-expressing S1 or N proteins of the GX-YL5 strain of IBV were constructed and prepared into subunit vaccines rHBM-S1-N, rHBM-S1 and rHBM-N. The levels of immune protection of these subunit vaccines were evaluated by inoculating specific pathogen-free (SPF) chickens at 14 days of age, giving them a booster with the same dose 14 days later and challenging them with a virulent GX-YL5 strain of IBV 14 days post-booster (dpb). The commercial vaccine strain H120 was used as a control. The IBV-specific antibody levels, as well as the percentages of CD4+ and CD8+ T lymphocytes, were detected within 28 days post-vaccination (dpv). The morbidity, mortality and re-isolation of the virus from the tracheas and kidneys of challenged birds were evaluated at five days post-challenge (dpc). The results showed that the IBV-specific antibody levels and the percentages of CD4+ and CD8+ T lymphocytes were higher in the rHBM-S1-N vaccinated birds compared to birds vaccinated with the rHBM-S1 and rHBM-N vaccines. At 5 dpc, the mortality, morbidity and virus re-isolation rate of the birds vaccinated with the rHBM-S1-N vaccine were slightly higher than those vaccinated with the H120 control vaccine but were lower than those vaccinated with the rHBM-S1 and rHBM-N vaccines. The present study demonstrated that the protection of the recombinant baculovirus co-expressing S1 and N proteins was better than that of recombinant baculoviruses mono-expressing the S1 or N protein. Thus, the recombinant baculovirus co-expressing S1 and N proteins could serve as a potential IBV vaccine and this demonstrates that the bivalent subunit vaccine including the S1 and N proteins might be a strategy for the development of an IBV subunit vaccine. url: https://doi.org/10.3390/v10070347 doi: 10.3390/v10070347 id: cord-277804-ujabzic4 author: Yuk, Seong-su title: Comparison between dot-immunoblotting assay and clinical sign determination method for quantifying avian infectious bronchitis virus vaccine by titration in embryonated eggs date: 2016-01-21 words: 4146.0 sentences: 202.0 pages: flesch: 53.0 cache: ./cache/cord-277804-ujabzic4.txt txt: ./txt/cord-277804-ujabzic4.txt summary: title: Comparison between dot-immunoblotting assay and clinical sign determination method for quantifying avian infectious bronchitis virus vaccine by titration in embryonated eggs In this study, we used a dot-immunoblotting assay (DIA) to measure the titers of IBV vaccines that originated from different pathogenic strains or attenuation methods in embryonated eggs, and we compared this assay to the currently used method, clinical sign evaluation. The aim of this study was to evaluate and compare the sensitivity and specificity of the DIA to the clinical sign determination method for detecting IBV in inoculated embryonated eggs during titration of IBV vaccines. Propagation of the inoculated virus was determined using real-time RT-PCR, DIA, and the EE index method, and the 50% egg infectious dose (EID 50 ) of the five vaccines was calculated based on the method of Reed and Muench (1938) . abstract: A sensitive and specific method for measuring the vaccine titer of infectious bronchitis virus (IBV) is important to commercial manufacturers for improving vaccine quality. Typically, IBV is titrated in embryonated chicken eggs, and the infectivity of the virus dilutions is determined by assessing clinical signs in the embryos as evidence of viral propagation. In this study, we used a dot-immunoblotting assay (DIA) to measure the titers of IBV vaccines that originated from different pathogenic strains or attenuation methods in embryonated eggs, and we compared this assay to the currently used method, clinical sign evaluation. To compare the two methods, we used real-time reverse transcription-PCR, which had the lowest limit of detection for propagated IBV. As a clinical sign of infection, dwarfism of the embryo was quantified using the embryo: egg (EE) index. The DIA showed 9.41% higher sensitivity and 15.5% higher specificity than the clinical sign determination method. The DIA was particularly useful for measuring the titer of IBV vaccine that did not cause apparent stunting but propagated in embryonated chicken eggs such as a heat-adapted vaccine strain. The results of this study indicate that the DIA is a rapid, sensitive, reliable method for determining IBV vaccine titer in embryonated eggs at a relatively low cost. url: https://doi.org/10.1016/j.jviromet.2016.01.008 doi: 10.1016/j.jviromet.2016.01.008 id: cord-316525-uadfehr6 author: Zhang, X. W. title: Testing the hypothesis of a recombinant origin of the SARS-associated coronavirus date: 2004-10-11 words: 3023.0 sentences: 152.0 pages: flesch: 52.0 cache: ./cache/cord-316525-uadfehr6.txt txt: ./txt/cord-316525-uadfehr6.txt summary: Surprisingly, we found that 7 putative recombination regions, located in Replicase 1ab and Spike protein, exist between SARS-CoV and other 6 coronaviruses: porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), bovine coronavirus (BCoV), human coronavirus 229E (HCoV), murine hepatitis virus (MHV), and avian infectious bronchitis virus (IBV). After potential recombination events were identified by at least 3 methods above, separate neighbor joining trees were constructed for each putative recombination region to better evaluate the evidence for conflicting evolutionary histories of different sequence regions. Two regions (13151-13299 and 16051-16449, position in alignment) are identified as putative recombination regions and all 6 coronaviruses are potential parents with SARS-CoV as potential daughter. In this study, seven recombination detection methods and phylogenetic analyses were performed on SARS-CoV and the six coronaviruses identified by BLAST (IBV, BCoV, HCoV, MHV, PEDV and TGEV). abstract: The origin of severe acute respiratory syndrome-associated corona-virus (SARS-CoV) is still a matter of speculation, although more than one year has passed since the onset of the SARS outbreak. In this study, we implemented a 3-step strategy to test the intriguing hypothesis that SARS-CoV might have been derived from a recombinant virus. First, we blasted the whole SARS-CoV genome against a virus database to search viruses of interest. Second, we employed 7 recombination detection techniques well documented in successfully detecting recombination events to explore the presence of recombination in SARS-CoV genome. Finally, we conducted phylogenetic analyses to further explore whether recombination has indeed occurred in the course of coronaviruses history predating the emergence of SARS-CoV. Surprisingly, we found that 7 putative recombination regions, located in Replicase 1ab and Spike protein, exist between SARS-CoV and other 6 coronaviruses: porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), bovine coronavirus (BCoV), human coronavirus 229E (HCoV), murine hepatitis virus (MHV), and avian infectious bronchitis virus (IBV). Thus, our analyses substantiate the presence of recombination events in history that led to the SARS-CoV genome. Like the other coronaviruses used in the analysis, SARS-CoV is also a mosaic structure. url: https://www.ncbi.nlm.nih.gov/pubmed/15480857/ doi: 10.1007/s00705-004-0413-9 id: cord-263785-0iift8zy author: Zhang, Xiaorong title: Evaluation of the reproductive system development and egg-laying performance of hens infected with TW I-type infectious bronchitis virus date: 2020-07-31 words: 3690.0 sentences: 171.0 pages: flesch: 50.0 cache: ./cache/cord-263785-0iift8zy.txt txt: ./txt/cord-263785-0iift8zy.txt summary: title: Evaluation of the reproductive system development and egg-laying performance of hens infected with TW I-type infectious bronchitis virus Our findings suggest that TW I-type IBV is deadly to chickens and could cause permanent damage to the oviduct, resulting in the poor laying performance of female survivors and decreasing the breeding value and welfare of the infected flock. In this study, the pathogenicity of TW I-type IBV was evaluated by examining clinical symptoms, mortality rates, virus shedding, lesions, and laying performance in terms of egg quantity and quality in infected chickens. The pathogenicity of TW I-type IBV in the early stage post-infection was evaluated via the clinical symptoms, pathological lesions, and virus shedding from trachea and cloaca. Abbreviations IBV: infectious bronchitis virus; SPF: specific-pathogen-free; dpi: days post infection; RT-qPCR: reverse transcription-quantitative polymerase chain reaction. abstract: The prevalence of TW I-type infectious bronchitis virus (IBV) has been increasing rapidly, and it has become the second most common genotype of IBV in China threatening the poultry industry. In this study, 1-day-old specific-pathogen-free (SPF) chickens infected with TW I-type IBV were continuously observed for 200 days. TW I-type IBV affected the respiratory, urinary, and female reproductive systems, resulting in a mortality rate of 10% as well as a decrease in egg quantity and an increase in inferior eggs. During the monitoring period, serious lesions occurred in the female reproductive system, such as yolk peritonitis, a shortened oviduct, and cysts of different sizes with effusion in the degenerated right oviduct. The infective viruses persisted in vivo for a long time, and due to the stress of laying, virus shedding was detected again after the onset of egg production. Our findings suggest that TW I-type IBV is deadly to chickens and could cause permanent damage to the oviduct, resulting in the poor laying performance of female survivors and decreasing the breeding value and welfare of the infected flock. url: https://www.ncbi.nlm.nih.gov/pubmed/32736651/ doi: 10.1186/s13567-020-00819-4 id: cord-351564-nikcd44o author: Zhang, Xiaozhan title: Molecular characterization of variant infectious bronchitis virus in China, 2019: Implications for control programmes date: 2020-01-24 words: 2798.0 sentences: 124.0 pages: flesch: 45.0 cache: ./cache/cord-351564-nikcd44o.txt txt: ./txt/cord-351564-nikcd44o.txt summary: Although the gross pathologic appearance of these two IB outbreaks was different, the newly identified IBV strains were all closely related to the ck/China/I0529/17 strain and grouped into GI‐19 genotype clade based on the sequencing and phylogenetic analysis of the complete S1 genes. In conclusion, this study provided an insight of the recently emerging IBV outbreaks in IBV‐vaccinated commercial poultry farms and identified the genetic characteristics of three virulent GI‐19 IBV strains, which shows the need to carry out proper preventive measures and control strategies. Herein, we reported two IB outbreaks in IBV-vaccinated commercial broiler farms in central China, and the complete S1 genes of the newly identified IBV strains were sequenced, and its genotype, phylogeny and variations were analysed further. abstract: Infectious bronchitis virus (IBV), an ongoing emergence enveloped virus with a single‐stranded positive‐sense RNA genome, belongs to the Gammacoronavirus genus in the Coronaviridae family. IBV‐associated tracheitis, nephritis, salpingitis, proventriculitis and egg drop have caused devastating economic losses to poultry industry worldwide. Since the end of 2018, a remarkably increasing number of commercial broilers and layers, vaccinated or not, were infected with IBV in China. Here, we described two IB outbreaks with severe respiratory system or kidney injury in IBV‐vaccinated commercial poultry farms in central China. Other possible causative viral pathogens, including avian influenza virus (AIV), Newcastle disease virus (NDV) and Kedah fatal kidney syndrome virus (KFKSV), were excluded by reverse transcription‐polymerase chain reaction (RT‐PCR), and three virulent IBV strains, HeN‐1/China/2019, HeN‐2/China/2019 and HeN‐101/China/2019, were identified. Although the gross pathologic appearance of these two IB outbreaks was different, the newly identified IBV strains were all closely related to the ck/China/I0529/17 strain and grouped into GI‐19 genotype clade based on the sequencing and phylogenetic analysis of the complete S1 genes. Moreover, there are still some evolutionary distance between the newly identified IBV strains, HeN‐101/China/2019 in particular, and other GI‐19 strains, suggesting that Chinese IBV strains constantly emerge and evolve towards different directions. In conclusion, this study provided an insight of the recently emerging IBV outbreaks in IBV‐vaccinated commercial poultry farms and identified the genetic characteristics of three virulent GI‐19 IBV strains, which shows the need to carry out proper preventive measures and control strategies. url: https://www.ncbi.nlm.nih.gov/pubmed/31943814/ doi: 10.1111/tbed.13477 id: cord-355703-l9l4ybfn author: Zhao, Fei title: Genomic Characteristics and Changes of Avian Infectious Bronchitis Virus Strain CK/CH/LDL/97I after Serial Passages in Chicken Embryos date: 2014-08-29 words: 5859.0 sentences: 300.0 pages: flesch: 49.0 cache: ./cache/cord-355703-l9l4ybfn.txt txt: ./txt/cord-355703-l9l4ybfn.txt summary: title: Genomic Characteristics and Changes of Avian Infectious Bronchitis Virus Strain CK/CH/LDL/97I after Serial Passages in Chicken Embryos To identify specific sequence changes responsible for adaptation of the field IBV isolate to chicken embryonic tissue and subsequent attenuation, the whole viral genome of the IBV P5 pathogenic parental CK/CH/LDL/97I strain was sequenced and compared with the attenuated, P115 level virus, to provide a better understanding of the relationship between the genomic differences and related characteristics of the pathogenic and attenuated viruses. Limited information is currently available regarding the pathogenicity of CK/CH/ LDL/97I-type IBV strains and embryo-passaged, attenuated P115 in the chicken oviduct. Altered pathogenicity, immunogenicity, tissue tropism and 3 ′ -7 kb region sequence of an avian infectious bronchitis coronavirus strain after serial passage in embryos Sequence changes of infectious bronchitis virus isolates in the 3 ′ -7.3 kb of the genome after attenuating passage in embryonated eggs abstract: BACKGROUND: We previously attenuated the infectious bronchitis virus (IBV) strain CK/CH/LDL/97I and found that it can convey protection against the homologous pathogenic virus. OBJECTIVE: To compare the full-length genome sequences of the Chinese IBV strain CK/CH/LDL/97I and its embryo-passaged, attenuated level to identify sequence substitutions responsible for the attenuation and define markers of attenuation. METHODS: The full-length genomes of CK/CH/LDL/97I P5 and P115 were amplified and sequenced. The sequences were assembled and compared using the MEGALIGN program (DNAStar) and a phylogenetic tree was constructed using MEGA4 software. RESULTS: The CK/CH/LDL/97I virus population contained subpopulations with a mixture of genetic mutants. Changes were observed in nsp4, nsp9, nsp11/12, nsp14, nsp15, nsp16, and ORF3a, but these did not result in amino acid substitutions or did not show functional variations. Amino acid substitutions occurred in the remaining genes between P5 and P115; most were found in the S region, and some of the nucleotide mutations resulted in amino acid substitutions. Among the 9 nsps in the ORF1 region, nsp3 contained the most nucleotide substitutions. CONCLUSIONS: Sequence variations in different genes, especially the S gene and nsp3, in the genomes of CK/CH/LDL/97I viruses might contribute to differences in viral replication, pathogenicity, antigenicity, immunogenicity, and tissue tropism. url: https://www.ncbi.nlm.nih.gov/pubmed/25195733/ doi: 10.1159/000365193 id: cord-272437-gvzfl8c3 author: Zhao, Jing title: Replicase 1a gene plays a critical role in pathogenesis of avian coronavirus infectious bronchitis virus date: 2020-08-20 words: 565.0 sentences: 51.0 pages: flesch: 57.0 cache: ./cache/cord-272437-gvzfl8c3.txt txt: ./txt/cord-272437-gvzfl8c3.txt summary: title: Replicase 1a gene plays a critical role in pathogenesis of avian coronavirus infectious bronchitis virus Avian coronavirus infectious bronchitis virus (IBV) is an important pathogen threatening poultry production worldwide. Our findings demonstrate that the replicase 1a gene of avian coronavirus IBV is a determinant of pathogenicity. In this study, we used an IBV reverse genetics system based on virulent strain Fig. 2. Recombinant live attenuated avian coronavirus 431 vaccines with deletions in the accessory genes 3ab and/or 5ab protect against infectious 432 bronchitis in chickens attenuated Chinese QX-like infectious bronchitis virus strain as a candidate vaccine S gene and 5a accessory gene 455 are responsible for the attenuation of virulent infectious bronchitis coronavirus abstract: Avian coronavirus infectious bronchitis virus (IBV) is an important pathogen threatening poultry production worldwide. Here, two recombinant IBVs (rYN-1a-aYN and rYN-1b-aYN) were generated in which ORF1a or ORF1b of the virulent YN genome were replaced by the corresponding regions from the attenuated strain aYN. The pathogenicity and virulence of rIBVs were evaluated in ovo and in vivo. The results revealed that mutations in the ORF1a gene during passage in embryonated eggs caused the decreased pathogenicity of virulent IBV YN strain, proven by determination of virus replication in ECEs and CEK cells, the observation of clinical signs, gross lesions, microscopic lesions, tracheal ciliary activity and virus distribution in chickens following exposure to rIBVs. However, mutations in ORF1b had no obvious effect on virus replication in both ECEs and CEK cells, or pathogenicity in chickens. Our findings demonstrate that the replicase 1a gene of avian coronavirus IBV is a determinant of pathogenicity. url: https://api.elsevier.com/content/article/pii/S0042682220301628 doi: 10.1016/j.virol.2020.08.009 id: cord-272305-eniovfwy author: Zhao, Ye title: Safety and efficacy of an attenuated Chinese QX-like infectious bronchitis virus strain as a candidate vaccine date: 2015-10-22 words: 5918.0 sentences: 359.0 pages: flesch: 55.0 cache: ./cache/cord-272305-eniovfwy.txt txt: ./txt/cord-272305-eniovfwy.txt summary: Strain YN-inoculated birds had clinical signs of varying severity with 30% mortality, while the attenuated group appeared healthy, with less tissue damage. The resulting attenuated YN strain was shorted as aYN and was titrated by inoculating 10-fold serial dilutions with phosphate-buffered saline (PBS) of the virus stocks into the allantoic sac of 10-day-old SPF embryonated eggs. Gross changes were noted and samples of trachea, kidney, lung, proventriculus, duodenum, and bursa of Fabricius were collected for virus detection via real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) and in 10% neutral formalin for histopathological examination. In terms of the real-time RT-qPCR examination, both strains were detected in respiratory and non-respiratory tissues, including the kidney, trachea, lungs, proventriculus, duodenum, and bursa of Fabricius, indicating viral replication in these organs; however, this was relatively limited in the birds infected with the YN attenuated strain. Efficacy and safety of an attenuated live QX-like infectious bronchitis virus strain as a vaccine for chickens abstract: Infectious bronchitis (IB) is a highly contagious respiratory and urogenital disease of chickens caused by infectious bronchitis virus (IBV). This disease is of considerable economic importance and is primarily controlled through biosecurity and immunization with live attenuated and inactivated IB vaccines of various serotypes. In the present study, we tested the safety and efficacy of an attenuated predominant Chinese QX-like IBV strain. The results revealed that the attenuated strain has a clear decrease in pathogenicity for specific-pathogen-free (SPF) chickens compared with the parent strain. Strain YN-inoculated birds had clinical signs of varying severity with 30% mortality, while the attenuated group appeared healthy, with less tissue damage. The attenuated strain also had relatively low tissue replication rates and higher antibody levels. The superior protective efficacy of the attenuated strain was observed when vaccinated birds were challenged with a homologous or heterologous field IBV strain, indicating the potential of the attenuated YN (aYN) as a vaccine. Producing a vaccine targeting the abundant serotype in China is essential to reducing the economic impact of IB on the poultry industry. url: https://doi.org/10.1016/j.vetmic.2015.07.036 doi: 10.1016/j.vetmic.2015.07.036 id: cord-291754-1zxztadu author: Zhao, Ye title: Successful establishment of a reverse genetic system for QX-type infectious bronchitis virus and technical improvement of the rescue procedure date: 2019-10-15 words: 6848.0 sentences: 344.0 pages: flesch: 54.0 cache: ./cache/cord-291754-1zxztadu.txt txt: ./txt/cord-291754-1zxztadu.txt summary: In this study, a pathogenic avian infectious bronchitis virus (IBV) QX-type strain YN was successfully rescued by vaccinia virus based reverse genetic technology. To compare the in vitro replication of the rescued virus rYN and its parental strain YN on CEK cells, 200 μl PBS containing 10 3.0 TCID 50 of rYN or YN virus were inoculated onto the CEK cells in 24-well plates, and 200 μl supernatants from three wells from each group were harvested at the time points of 6, 12, 24, 36, 48, and 60 hpi for a real-time PCR detection assay for IBV N gene as described above. Collectively, these results demonstrate the successful rescue of the pathogenic IBV strain YN from cloned cDNA by using electroporation of full-length IBV in vitro transcripts into N-protein expressing cells and subsequent virus amplification in the allantoic cavities of ECE. abstract: In this study, a pathogenic avian infectious bronchitis virus (IBV) QX-type strain YN was successfully rescued by vaccinia virus based reverse genetic technology. Ten fragments contiguously spanning the complete IBV genome were amplified and cloned into the vaccinia virus genome by homologous recombination. The full-length genomic cDNA was transcribed in vitro, and its transcript was transfected into BHK-21/N cells that could stably express IBV N protein. At 48 h post transfection, the culture medium was harvested and inoculated into 10-day-old specific-pathogen-free embryonated chicken eggs to replicate the rescued virus. This strategy was chosen to facilitate the rescue procedure and to ensure that the recombinant rYN virus will not require any cell culture adaptations. After only one in ovo passage, the recombinant YN virus (rYN) was successfully recovered and confirmed to possess the introduced silent marker mutation in its genome. Biological characteristics of rYN such as the EID(50), TCID(50), replication in ovo, and replication kinetcs in vitro were tested and all were similar to its parental strain YN. Our findings demonstrate the successful construction of highly-pathogenic QX-type IBV using a modified rescue procedure, allowing for future studies of the molecular biology and pathogenicity of IBV field strains. url: https://www.ncbi.nlm.nih.gov/pubmed/31430502/ doi: 10.1016/j.virusres.2019.197726 id: cord-292428-j3wdlpp6 author: Zhou, J.‐Y. title: Characterization of an Avian Infectious Bronchitis Virus Isolated in China from Chickens with Nephritis date: 2004-06-30 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: One IBV isolate, SC021202, was isolated from the kidneys of the infected young chickens by inoculating embryonated eggs, and its morphology, physiochemical and haemagglutonating properties were detected. Virulence of the isolate SC021202 was determined with specific pathogen‐free (SPF) chicken inoculation. Nucleotide acid sequence of S1 gene of the isolate SC021202 was further sequenced and analysed. The physiochemical and morphological properties of the isolate SC021202 were in accordance to that of typical infectious bronchitis virus (IBV). In a pathogenicity experiment, the clinical signs and related gross lesions resembling those of field outbreak were reproduced and the virus isolate SC021202 was re‐isolated from the kidneys of the infected chicken. Sequence data demonstrated that the full length of the amplified S1 gene of the isolate SC021202 was composed of 1931 nucleotides, coding a polypeptide of 543 amino acid residues. Compared with IBV strains from GenBank, the nucleotide and deduced amino acid sequence of S1 gene of the isolate SC021202 shared 60.0–91.4% and 49.1–88.9% identities, respectively. A nucleotide fragment of ′CTTTTTAATTATACTAACGGA′ was inserted at nucleotide site 208 in the S1 gene of the isolate. These results indicated that IBV isolate SC021202 was a new variant IBV isolate and responsible for field outbreak of nephritis. url: https://www.ncbi.nlm.nih.gov/pubmed/15228547/ doi: 10.1111/j.1439-0450.2004.00744.x id: cord-305079-foifc8ch author: Zhou, Ying Shun title: Establishment of reverse genetics system for infectious bronchitis virus attenuated vaccine strain H120 date: 2013-02-22 words: 4842.0 sentences: 229.0 pages: flesch: 54.0 cache: ./cache/cord-305079-foifc8ch.txt txt: ./txt/cord-305079-foifc8ch.txt summary: The remaining one third of the genome encodes the structural proteins and group-specific ORFs, including spike glycoprotein (S), envelope protein (E), membrane Veterinary Microbiology 162 (2013) Infectious bronchitis virus (IBV) strain H120 was successfully rescued as infectious clone by reverse genetics. In this study, we describe the in vitro assembly and recovery of an infectious clone of IBV-H120, the biological and immune characteristics of the rescued H120 virus (R-H120), and the potential to use R120 as a candidate of vaccine vector in the future vaccine development. The IBV strains, H120 and Mass41, obtained from China Institute of Veterinary Drug Control (IVDC), were propagated in the allantoic cavities of the 10-day-old specific pathogen-free (SPF) embryonated chicken eggs (ECE), and the allantoic fluid was harvested 36 h post inoculation. Three groups of chickens were challenged with the virulent strain Mass41 to test if the rescued virus could protect the immunized animals from IBV infection. abstract: Infectious bronchitis virus (IBV) strain H120 was successfully rescued as infectious clone by reverse genetics. Thirteen 1.5–2.8 kb fragments contiguously spanning the virus genome were amplified and cloned into pMD19-T. Transcription grade complete length cDNA was acquired by a modified “No See’m” ligation strategy, which employed restriction enzyme Bsa I and BsmB I and ligated more than two fragments in one T4 ligase reaction. The full-length genomic cDNA was transcribed and its transcript was transfected by electroporation into BHK-21 together with the transcript of nucleocapsid gene. At 48 h post transfection, the medium to culture the transfected BHK-21 cells was harvested and inoculated into 10-days old SPF embryonated chicken eggs (ECE) to replicate the rescued virus. After passage of the virus in ECE five times, the rescued H120 virus (R-H120) was successfully recovered. R-H120 was subsequently identified to possess the introduced silent mutation site in its genome. Some biological characteristics of R-H120 such as growth curve, EID50 and HA titers, were tested and all of them were very similar to its parent strain H120. In addition, both R-H120 and H120 induced a comparable titer of HA inhibition (HI) antibody in immunized chickens and also provided up to 85% of immune protection to the chickens that were challenged with Mass41 IBV strain. The present study demonstrated that construction of infectious clone from IBV vaccine strain H120 is possible and IBV-H120 can be use as a vaccine vector for the development of novel vaccines through molecular recombination and the modified reverse genetics approach. url: https://www.sciencedirect.com/science/article/pii/S0378113512004646 doi: 10.1016/j.vetmic.2012.08.013 id: cord-263193-paeosfiu author: Zhu, Jinyan title: Infectious bronchitis virus inhibits activation of the TLR7 pathway, but not the TLR3 pathway date: 2020-06-10 words: 2831.0 sentences: 163.0 pages: flesch: 55.0 cache: ./cache/cord-263193-paeosfiu.txt txt: ./txt/cord-263193-paeosfiu.txt summary: Here, primary chicken embryo kidney (CEK) cells and specific-pathogen-free (SPF) chickens were infected with three pathogenic IBV strains, and it was observed that the TLR7-MYD88 pathway was inhibited but the TLR3-TIRF pathway was activated. To investigate the effect of innate immune molecules, agonists of TLR3, TLR7, and MDA5 and inhibitors of key molecules of the TLR3 pathway were added to CEK cells that had grown to 80-90% as instructed by the reagent manufacturer (InvivoGen, CA, USA) as follows: 5 μg of imiquimod (a TLR7 agonist) per mL for 12 h, 10 μg of low-molecular-weight (LMW) polyinosinic-polycytidylic acid (poly(I:C)) (a TLR3 agonist) per mL for 12 h, 0.5 μg of poly (I:C)-LMW/LyoVec (an MDA5 agonist) per mL for 12 h, 10 μM Pepinh-TRIF (a TRIF inhibitor) for 6 h, 5 μM celastrol (an NF-κB inhibitor) for 1 h, 50 μM chloroquine (an inhibitor of endosomal acidification) for 0.5 h, and 5 μM BX795 (a TBK1 inhibitor) for 6 h. abstract: Various strains of infectious bronchitis virus (IBV) cause different forms of infectious bronchitis with different clinical signs. Here, primary chicken embryo kidney (CEK) cells and specific-pathogen-free (SPF) chickens were infected with three pathogenic IBV strains, and it was observed that the TLR7-MYD88 pathway was inhibited but the TLR3-TIRF pathway was activated. After treatment with poly(I:C)-LMW, poly (I:C)-LMW/LyoVec, and Imiquimod, the replication of IBV was significantly suppressed after 24 h. However, treatment with TLR3 pathway inhibitors such as Pepinh-TRIF, celastrol, chloroquine, and BX795 resulted in increased replication of IBV after 36 h. These results also showed that chloroquine and celastrol were most effective inhibitors of the antiviral response at 48 hpi. url: https://www.ncbi.nlm.nih.gov/pubmed/32524263/ doi: 10.1007/s00705-020-04690-8 id: cord-286332-cdg4im5h author: van Beurden, Steven J. title: A reverse genetics system for avian coronavirus infectious bronchitis virus based on targeted RNA recombination date: 2017-06-12 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Avian coronavirus infectious bronchitis virus (IBV) is a respiratory pathogen of chickens that causes severe economic losses in the poultry industry worldwide. Major advances in the study of the molecular biology of IBV have resulted from the development of reverse genetics systems for the highly attenuated, cell culture-adapted, IBV strain Beaudette. However, most IBV strains, amongst them virulent field isolates, can only be propagated in embryonated chicken eggs, and not in continuous cell lines. METHODS: We established a reverse genetics system for the IBV strain H52, based on targeted RNA recombination in a two-step process. First, a genomic and a chimeric synthetic, modified IBV RNA were co-transfected into non-susceptible cells to generate a recombinant chimeric murinized (m) IBV intermediate (mIBV). Herein, the genomic part coding for the spike glycoprotein ectodomain was replaced by that of the coronavirus mouse hepatitis virus (MHV), allowing for the selection and propagation of recombinant mIBV in murine cells. In the second step, mIBV was used as the recipient. To this end a recombination with synthetic RNA comprising the 3′-end of the IBV genome was performed by introducing the complete IBV spike gene, allowing for the rescue and selection of candidate recombinants in embryonated chicken eggs. RESULTS: Targeted RNA recombination allowed for the modification of the 3′-end of the IBV genome, encoding all structural and accessory genes. A wild-type recombinant IBV was constructed, containing several synonymous marker mutations. The in ovo growth kinetics and in vivo characteristics of the recombinant virus were similar to those of the parental IBV strain H52. CONCLUSIONS: Targeted RNA recombination allows for the generation of recombinant IBV strains that are not able to infect and propagate in continuous cell lines. The ability to introduce specific mutations holds promise for the development of rationally designed live-attenuated IBV vaccines and for studies into the biology of IBV in general. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12985-017-0775-8) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/28606144/ doi: 10.1186/s12985-017-0775-8 id: cord-317347-by8albr9 author: van Ginkel, Frederik W. title: Age-dependent immune responses and immune protection after avian coronavirus vaccination date: 2015-05-28 words: 5792.0 sentences: 288.0 pages: flesch: 53.0 cache: ./cache/cord-317347-by8albr9.txt txt: ./txt/cord-317347-by8albr9.txt summary: The delayed and/or lower antibody response combined with lower IgG avidity indices coincided with increased tracheal inflammation and depletion of tracheal epithelia cells and goblet cells upon IBV field strain challenge. Therefore, the ability of SPF chickens of different age to induce an IBV-specific antibody response and protect against challenge with an IBV field strain was measured. In order to measure IgG (IgY), IgA and IgM antibody levels in plasma and tears of chicken, an IBV-specific enzyme-linked immunosorbent assay (ELISA) was developed as previously described [20] . These data are consistent with a delay in the IgA plasma response to IBV in birds vaccinated at a younger age and a non-significant decline in mean IgA titers in the 1-day-old group. This would be consistent with a drop of presumably natural maternal IBV-specific IgM antibodies in these SPF chickens in the day 7 control age group. abstract: Infectious bronchitis virus (IBV) is an endemic disease of chickens and a major contributor to economic losses for the poultry industry despite vaccination. Recent observations indicated that chicks may have an immature immune system immediately after hatching when vaccinated for IBV. Therefore we hypothesized that early IBV vaccination will generate an immature, poorly protective IBV-specific immune response contributing to immune escape and persistence of IBV. To test this hypothesis the IBV-specific immune response and immune protection were measured in chicks vaccinated at different ages. This demonstrated a delayed production of IgG and IgA plasma antibodies in the 1, 7 and 14-day-old vaccination groups and also lower IgA antibody levels were observed in plasma of the 1-day-old group. Similar observations were made for antibodies in tears. In addition, IgG antibodies from the 1-day-old group had lower avidity indices than day 28 vaccinated birds. The delayed and/or lower antibody response combined with lower IgG avidity indices coincided with increased tracheal inflammation and depletion of tracheal epithelia cells and goblet cells upon IBV field strain challenge. The lack of vaccine-mediated protection was most pronounced in the 1-day-old vaccination group and to a lesser extent the 7-day-old group, while the 14-day-old and older chickens were protected. These data strongly support IBV vaccination after day 7 post hatch. url: https://api.elsevier.com/content/article/pii/S0264410X1500479X doi: 10.1016/j.vaccine.2015.04.026 ==== make-pages.sh questions [ERIC WAS HERE] ==== make-pages.sh search /data-disk/reader-compute/reader-cord/bin/make-pages.sh: line 77: /data-disk/reader-compute/reader-cord/tmp/search.htm: No such file or directory Traceback (most recent call last): File "/data-disk/reader-compute/reader-cord/bin/tsv2htm-search.py", line 51, in with open( TEMPLATE, 'r' ) as handle : htm = handle.read() FileNotFoundError: [Errno 2] No such file or directory: '/data-disk/reader-compute/reader-cord/tmp/search.htm' ==== make-pages.sh topic modeling corpus Zipping study carrel