Summary of your 'study carrel' ============================== This is a summary of your Distant Reader 'study carrel'. The Distant Reader harvested & cached your content into a collection/corpus. It then applied sets of natural language processing and text mining against the collection. The results of this process was reduced to a database file -- a 'study carrel'. The study carrel can then be queried, thus bringing light specific characteristics for your collection. These characteristics can help you summarize the collection as well as enumerate things you might want to investigate more closely. This report is a terse narrative report, and when processing is complete you will be linked to a more complete narrative report. Eric Lease Morgan Number of items in the collection; 'How big is my corpus?' ---------------------------------------------------------- 168 Average length of all items measured in words; "More or less, how big is each item?" ------------------------------------------------------------------------------------ 4993 Average readability score of all items (0 = difficult; 100 = easy) ------------------------------------------------------------------ 53 Top 50 statistically significant keywords; "What is my collection about?" ------------------------------------------------------------------------- 168 IBV 20 RNA 17 PCR 16 Fig 12 virus 12 China 8 protein 6 strain 5 cell 5 ORF 5 NDV 5 Mass 5 H120 4 Vero 4 MHV 4 ELISA 3 group 3 figure 3 dna 3 SARS 3 Iraq 3 Egypt 3 CEK 3 AIV 2 bird 2 M41 2 Iran 2 ILTV 2 H9N2 2 EGFP 2 Beaudette 2 ANV 1 western 1 vaccine 1 swedish 1 sc021202 1 response 1 recombinant 1 receptor 1 r-848 1 pseudoknot 1 polish 1 pigeon 1 pathway 1 nanoparticle 1 mitochondrial 1 membrane 1 m41s 1 m41 1 line Top 50 lemmatized nouns; "What is discussed?" --------------------------------------------- 9762 virus 5433 protein 4917 cell 4746 strain 3710 bronchitis 3659 gene 3375 chicken 2992 sequence 2650 vaccine 2589 coronavirus 2432 % 2322 group 2148 infection 1879 study 1635 analysis 1411 genome 1402 antibody 1368 type 1333 region 1308 bird 1296 sample 1225 s1 1155 day 1153 isolate 1139 acid 1097 spike 1081 recombination 1065 disease 1063 result 1049 time 1043 replication 956 egg 933 control 912 site 903 coronaviruse 897 response 872 c 859 serotype 833 expression 826 genotype 816 membrane 773 amino 766 detection 746 vaccination 727 method 727 challenge 720 kidney 720 glycoprotein 717 level 691 protection Top 50 proper nouns; "What are the names of persons or places?" -------------------------------------------------------------- 9645 IBV 4077 al 3597 . 3288 et 2587 RNA 1515 PCR 1395 Fig 1236 S1 1115 S 1035 M 973 RT 932 N 892 China 711 CH 648 MHV 547 H120 538 C 508 IB 497 CK 450 SARS 421 ORF 414 SPF 377 Coronavirus 377 Beaudette 373 USA 353 Mass 351 Table 344 PBS 343 QX 337 E 333 ELISA 331 Vero 321 CoV 311 T 302 NDV 301 S2 296 Cavanagh 269 allantoic 269 M41 259 AIV 258 II 245 ck 242 Massachusetts 230 mRNA 220 Liu 215 TCoV 214 GenBank 205 B 198 Taiwan 196 Golgi Top 50 personal pronouns nouns; "To whom are things referred?" ------------------------------------------------------------- 1526 it 1170 we 444 they 416 i 132 them 36 he 35 us 30 itself 20 p110 14 you 9 ch/ 8 themselves 8 mrnas 5 one 4 irfibv32 3 svlps 3 is/1494 3 him 2 imagej 2 ibv-200 2 ibv-199 1 β2.7 1 αβ 1 utr41 1 und 1 s 1 ribvs 1 ribv 1 r132 1 pkt0-ibvn 1 nsp4 1 is/1201 1 ifit5 1 ifih1 1 ibvsx4 1 ibv_bdtt 1 ibv14931-f 1 ibv-281 1 ibv-212 1 hsp60 1 hku4-covs 1 h120 1 gammacovs 1 fapn 1 de072 1 bhkexp.pcineo 1 ayn Top 50 lemmatized verbs; "What do things do?" --------------------------------------------- 27903 be 3892 use 3764 have 2214 show 1284 isolate 1256 infect 1156 detect 1122 contain 986 induce 897 indicate 847 observe 835 include 825 base 808 follow 781 find 732 compare 729 express 724 identify 700 do 681 cause 655 determine 643 describe 628 suggest 594 associate 581 result 580 perform 578 bind 535 report 501 inoculate 501 demonstrate 496 obtain 483 encode 473 increase 467 provide 459 collect 404 occur 403 strain 402 generate 401 involve 392 confirm 389 accord 387 challenge 379 analyze 375 relate 370 require 370 incubate 368 reveal 365 purify 351 treat 348 see Top 50 lemmatized adjectives and adverbs; "How are things described?" --------------------------------------------------------------------- 4134 infectious 2212 not 2023 viral 1982 avian 1604 - 1434 other 1430 also 1305 different 1122 high 1005 respiratory 988 specific 944 recombinant 857 however 831 positive 776 only 673 new 661 like 638 more 627 most 625 molecular 625 genetic 624 immune 619 well 619 respectively 616 clinical 608 first 571 low 566 then 560 structural 549 nucleotide 541 similar 538 old 537 previously 535 negative 531 infected 531 further 527 same 504 such 485 phylogenetic 453 non 452 anti 447 present 445 significant 439 commercial 437 single 431 highly 427 attenuated 425 several 419 important 415 live Top 50 lemmatized superlative adjectives; "How are things described to the extreme?" ------------------------------------------------------------------------- 232 most 115 high 102 least 50 low 49 Most 48 good 41 large 17 small 15 close 11 early 8 ClustalW 6 vNotI 6 near 6 great 4 long 4 few 4 farth 3 strong 3 outermost 3 late 2 simple 2 safe 2 rIBV 2 fast 2 big 2 P3- 1 ≈200 1 weak 1 vvIBV 1 southernmost 1 short 1 rB 1 poly(U 1 old 1 lympholyte 1 easy 1 eIF2-alpha 1 bad 1 GATTGG-3 1 Conn46/91 1 AuNPs 1 -t 1 -proximal 1 -Pol 1 -JHM 1 -I 1 -CAGATTGCTTACAAC 1 -"52/70 Top 50 lemmatized superlative adverbs; "How do things do to the extreme?" ------------------------------------------------------------------------ 395 most 77 least 15 well 3 highest 2 oldest 1 worst 1 rnaase 1 ribv 1 long 1 fewest 1 clustalw Top 50 Internet domains; "What Webbed places are alluded to in this corpus?" ---------------------------------------------------------------------------- 14 doi.org 11 dx.doi.org 7 www.ncbi.nlm.nih.gov 5 www.megasoftware.net 5 blast.ncbi.nlm.nih.gov 4 www.mdpi.com 3 www.ncbi 3 www.generunner.com 3 www.ebi.ac.uk 3 www 3 tree.bio.ed.ac.uk 3 talk.ictvonline.org 2 www.mbio.ncsu.edu 2 www.intl-pag.org 2 www.ictv.global 2 www.geneious.com 2 www.cbs.dtu.dk 2 www.access.gpo.gov 2 tools.immuneepitope.org 2 podospora.igmors.u-psud.fr 2 orcid.org 2 mafft.cbrc.jp 2 github.com 2 dx 2 creativecommons.org 1 www5.invitrogen.com 1 www2.eur.nl 1 www.who.int 1 www.viprbrc.org 1 www.viprb 1 www.tree-puzzle.de 1 www.pymol.org 1 www.phylogeny.fr 1 www.ncbi.nim.nih.gov 1 www.math.wustl.edu 1 www.lynnon.com 1 www.lrrfinder.com 1 www.kfsh.med.sa 1 www.hiv.lanl.gov 1 www.generunner 1 www.dnastar.com 1 www.ddg-pharmfac.net 1 www.datamonkey.org 1 www.ch.embnet.org 1 www.cbs 1 www.bioss.sari.ac.uk 1 web.uct.ac.za 1 tree.bio.ed.ac 1 sray.med.som.jhmi.edu 1 spades.bioinf Top 50 URLs; "What is hyperlinked from this corpus?" ---------------------------------------------------- 3 http://www.ncbi 3 http://www.generunner.com 3 http://www 3 http://blast.ncbi.nlm.nih.gov/ 2 http://www.ncbi.nlm.nih.gov/BLAST/ 2 http://www.ncbi.nlm.nih.gov/ 2 http://www.megasoftware.net/ 2 http://www.ictv.global 2 http://www.geneious.com/ 2 http://www.ebi.ac.uk/arrayexpress/ 2 http://www.access.gpo.gov/nara/cfr/waisidx 2 http://tools.immuneepitope.org/tools/ 2 http://dx.doi.org/10.1016/j.jviromet.2016.01.008 2 http://dx 2 http://doi.org/10.1016/j.vetmic.2020.108693 2 http://doi.org/10.1016/j.vetmic.2019.01.020 2 http://creativecommons.org/licenses/by/4.0/ 2 http://blast.ncbi.nlm.nih.gov/Blast.cgi 1 http://www5.invitrogen.com/custom-genomic-products/tools/ 1 http://www2.eur.nl/fgg/kgen/primer/Overlapping 1 http://www.who.int/ 1 http://www.viprbrc.org/ 1 http://www.viprb 1 http://www.tree-puzzle.de/ 1 http://www.pymol.org/ 1 http://www.phylogeny.fr/simple_phylogeny.cgi 1 http://www.ncbi.nlm.nih.gov/gorf/gorf.html 1 http://www.ncbi.nlm.nih.gov/BLAST 1 http://www.ncbi.nlm.nih.gov 1 http://www.ncbi.nim.nih.gov/orffinder/ 1 http://www.megasoftware.net/mega41.html 1 http://www.megasoftware.net/index.html 1 http://www.megasoftware.net 1 http://www.mdpi.com/1999-4915/12/5/536/s1 1 http://www.mdpi.com/1999-4915/11/10/898/s1 1 http://www.mdpi.com/1999-4915/10/9/477/s1 1 http://www.mdpi.com/1999-4915/10/7/347/s1 1 http://www.mbio.ncsu.edu/bioedit.htm 1 http://www.mbio.ncsu.edu/bioEdit/bioedit 1 http://www.math.wustl.edu/∼sawyer/geneconv/ 1 http://www.lynnon.com/ 1 http://www.lrrfinder.com/result.php 1 http://www.kfsh.med.sa/KFSH_WebSite/ 1 http://www.intl-pag.org/11/abstracts/P2c 1 http://www.intl-pag.org/ 1 http://www.hiv.lanl.gov/content/ 1 http://www.generunner 1 http://www.ebi.ac.uk/pdbe/prot_ 1 http://www.dnastar.com/ 1 http://www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.html Top 50 email addresses; "Who are you gonna call?" ------------------------------------------------- 1 whongning@163.com 1 mjackwoo@uga.edu 1 chingho@ntu.edu.tw Top 50 positive assertions; "What sentences are in the shape of noun-verb-noun?" ------------------------------------------------------------------------------- 26 cells were then 21 samples were positive 16 virus is not 14 s1 is unable 14 virus induces protection 12 protein was not 11 ibv does not 11 protein was also 11 virus are essential 10 birds had significantly 10 birds were positive 10 cells were cultured 10 cells were mock 10 virus was not 9 cells containing sg 9 ibv was first 9 pcr using primers 9 protein is not 8 chickens were randomly 8 genes are not 8 group were randomly 8 ibv induced sg 8 ibv infected cek 8 virus infecting domestic 8 virus isolate sc021202 7 % were positive 7 ibv is also 7 samples were also 7 vaccines are not 7 virus infected cells 6 coronavirus is more 6 genes were significantly 6 ibv has also 6 ibv infected cells 6 ibv is not 6 protein has not 6 protein is highly 6 rna is not 6 samples were then 6 sequences were available 6 strain infected group 6 strains were also 6 virus isolates foreign 6 virus using tracheal 6 virus using transient 6 virus was also 6 viruses did not 5 birds were not 5 birds were orally 5 cells expressing egfp Top 50 negative assertions; "What sentences are in the shape of noun-verb-no|not-noun?" --------------------------------------------------------------------------------------- 12 virus is not essential 6 genes are not essential 4 groups were not statistically 3 birds were not significantly 3 gene is not essential 2 analysis showed no significant 2 birds did not significantly 2 cells showed no difference 2 infection does not actively 2 pcr is not satisfactory 2 protein is not essential 2 region is not necessary 2 strain was not pathogenic 2 vaccines are not effective 1 . indicated not significant 1 antibodies were no longer 1 birds are not fully 1 birds have not so 1 cells are not naturally 1 cells contained no e2 1 cells induces not only 1 cells showed no fluorescence 1 cells were not exhausted 1 chickens are not fully 1 gene is not usually 1 genes are not well 1 genes did not significantly 1 genome is not available 1 group did not significantly 1 group is not significantly 1 group showed no common 1 group was not quite 1 group were not statistically 1 groups showed no clinical 1 groups was not as 1 groups was not significant 1 ibv are not fully 1 ibv had no effect 1 ibv is not able 1 ibv is not clear 1 ibv is not complete 1 ibv is not easily 1 ibv is not evident 1 ibv is not well 1 ibv were not more 1 infection is not clear 1 infection is not only 1 infection was not able 1 infections are not yet 1 infections were not synergistic A rudimentary bibliography -------------------------- 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 keywords = IBV 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 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 keywords = HRM; IBV; PCR 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. 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 keywords = Egypt; F/03; IBV 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 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 keywords = IBV; M41 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 ). 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 keywords = IBV; ORF 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 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 keywords = IBV; Sweden; isolate; swedish 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 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 keywords = IBV; P20; P60 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. 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 keywords = IBV; Iraq; strain 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. 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 keywords = IBV; SPF 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. 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 keywords = Hasa; IBV 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 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 keywords = IBV; RNA; Vero 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. 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 keywords = IBV; protein; recombinant 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 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 keywords = Beau; IBV; M41-Struct-2; Rep 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. 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 keywords = IBV; ILTV; NDV; WOA 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 ). 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 keywords = CR88; H120; IBV 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 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 keywords = IBV summary = 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 keywords = IBV 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 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 keywords = IBV; SARS; autophagy; pathway summary = 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 keywords = IBV; virus 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 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 keywords = IBV; Iran 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 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 keywords = IBV; RNA 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. 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 keywords = IBV summary = 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 keywords = IBV; m41s 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) . 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 keywords = G3BP1; IBV; RNA 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 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 keywords = IBV; PCR 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. 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 keywords = IBV; RNA 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. 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 keywords = China; IBV; Taiwan 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 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 keywords = Fig; IBV; PBS; nanoparticle; protein 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. 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 keywords = CEK; IBV; cell; figure 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. 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 keywords = CEK; HPE; IBV; IFN; figure 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). 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 keywords = China; IBV; LGX/111119 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) . 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 keywords = CEK; Fig; IBV 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. 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 keywords = GSH; IBV; NDV 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. 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 keywords = IBV; cell; receptor 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] . doi = 10.1186/1743-422x-4-20 id = cord-022378-ovxmy1as author = Cook, Jane K.A. title = Coronaviridae date = 2009-05-15 keywords = IBV; virus 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. 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 keywords = IBV 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) . 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 keywords = CD4; IBV; ODN; USA 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. 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 keywords = ANV; IBV; PCR 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. 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 keywords = China; East; IBV; MERS; RNA; SARS; bat; coronavirus 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. 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 keywords = IBV; Poland; polish; strain summary = 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 keywords = IBV; PCR 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 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 keywords = EGFP; Fig; IBV 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) . 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 keywords = IBV; M41; RNA; membrane summary = 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 keywords = IBV 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. 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 keywords = AMPV; IBV 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 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 keywords = IBV 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 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 keywords = ATR; Fig; IBV 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) . 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 keywords = Fig; IBV; RNA; Vero 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. 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 keywords = IBV; QY16; YX10 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 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 keywords = ELISA; IBV; western 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 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 keywords = Company; IBV; Italy; italian 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. 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 keywords = IBV; pigeon 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. 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 keywords = IBV; PCR 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 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 keywords = China; IBV; strain 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. 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 keywords = IBV; ORF 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. 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 keywords = IBV; RNA 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%. 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 keywords = Beaudette; HD11; IBV; figure 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. 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 keywords = AIV; H9N2; IBV 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. 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 keywords = IBV 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. 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 keywords = IBV 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 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 keywords = IBV; bird; challenge; virus summary = 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 keywords = IBV; PCR; group 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. 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 keywords = China; IBV 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 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 keywords = IBV 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 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 keywords = I1101/16; IBV; LJL/140901 summary = 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 keywords = China; IBV; strain summary = 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 keywords = IBV; PCR 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. 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 keywords = H120; IBV; indian 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. 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 keywords = IBV; RNA; dna; mitochondrial 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. 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 keywords = IBV; virus 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 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 keywords = IBV; L10H; MBL; l10l 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 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 keywords = HSP90; IBV; host; protein; virus 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. 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 keywords = ANV; IBV; PCR 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. 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 keywords = Fig; IBV; RNA 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) . 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 keywords = IBV 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 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 keywords = IBV 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 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 keywords = ANXA2; IBV; RNA; pseudoknot summary = 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 keywords = BCV; IBV; MHV; ORF; RNA; TGEV 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. 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 keywords = Gene; IBV 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 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 keywords = IBV; MHV; ORF; RNA 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 ). 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 keywords = IBV; PCR; korean 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. 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 keywords = IBV; protein 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. 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 keywords = DEV; IBV 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). 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 keywords = IBV 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. 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 keywords = IBV 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 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 keywords = IBV 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. 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 keywords = IBV 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. 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 keywords = IBV; arg 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. 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 keywords = China; IBV 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. 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 keywords = IBV; LLN/98I 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) . 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 keywords = IBV; P70 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] . 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 keywords = IBV; LHLJ/07VII; strain 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 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 keywords = IBV; PCR 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 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 keywords = Algeria; IBV 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 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 keywords = Fig; H120; IBV; SCS1 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). 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 keywords = Bronchitis; IBV; Infectious; Virus; chicken 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] . 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 keywords = China; I0636/16; IBV; strain summary = 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 keywords = Golgi; IBV; PDMP 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. 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 keywords = IBV; Iraq 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. 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 keywords = Fig; IBV; PaYIP3 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) . 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 keywords = Australia; IBV summary = 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 keywords = IBV; Japan 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 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 keywords = IBV; TGF; r-848; vaccine summary = 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 keywords = Conn; IBV; Mass; virus 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. 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 keywords = IBV; cell 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. 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 keywords = IBV; RNA; bird; virus 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) . 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 keywords = IBV 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. 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 keywords = IBV; protein 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. 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 keywords = IBV; RNA; virus 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 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 keywords = IBV; Mass 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. 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 keywords = Egypt; IBV; RNA 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). 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 keywords = IBV; Sudan 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 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 keywords = IAV; IBV; influenza; virus summary = 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 keywords = IBV; PCR 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 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 keywords = Fig; IBV; group 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). 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 keywords = Ark; GA98; IBV; Mass 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. 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 keywords = IBV 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 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 keywords = IBV; Thailand 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 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 keywords = China; IBV; Mass 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 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 keywords = IBV; VicS 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). 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 keywords = IBV; Jones; Raj; bronchitis; infectious; virus 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 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 keywords = AIV; H9N2; IBV summary = 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 keywords = IBV; Iran; PCR 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 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 keywords = IBV 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). 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 keywords = IBV; Iraq; PCR 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] . 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 keywords = Acc; IBV; PCR 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 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 keywords = Beaudette; IBV; Vero 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. 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 keywords = Fig; IBV; S1-CTD 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. 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 keywords = IBV; cell; protein 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. 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 keywords = IBV; NDV 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. 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 keywords = IBV; gene; infection; line; response 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. 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 keywords = A59; Fig; Holmes; IBV; MHV; RNA 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. 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 keywords = AIV; IBDV; IBV; NDV 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. 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 keywords = -utr; IBV; MADP1; RNA 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. 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 keywords = IBV; dna 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 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 keywords = APEC; Egypt; IBV 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. 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 keywords = IBV; Mass; virus 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 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 keywords = IBV 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 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 keywords = ELISA; IBV; ILTV 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 . 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 keywords = Fig; IBV; protein 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. 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 keywords = ADP; IBV 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 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 keywords = IBV; acid; cell 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 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 keywords = IBV; LAMP; NDV; PCR 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) . 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 keywords = China; IBV 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. 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 keywords = Fig; IBV; protein 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 . 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 keywords = Fig; IBV; Vero 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) . 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 keywords = IBV 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. 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 keywords = ELISA; IBV; RDT 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. 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 keywords = H120; IBV; dna 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. 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 keywords = ELISA; IBV 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. 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 keywords = IBV; m41 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 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 keywords = IBV 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. 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 keywords = EGFP; IBV; ORF; PCR summary = 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 keywords = IBV; PLP; dub 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. 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 keywords = HBM; IBV 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 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 keywords = IBV; PCR 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) . 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 keywords = IBV; SARS 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). 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 keywords = IBV; virus 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. 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 keywords = China; IBV 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. 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 keywords = IBV; LDL/97I 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 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 keywords = IBV 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 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 keywords = China; Fig; IBV 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 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 keywords = BHK-21; IBV; RNA 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. 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 keywords = IBV; sc021202 summary = 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 keywords = H120; IBV 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. 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 keywords = IBV; TLR3 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. 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 keywords = H52; IBV; LR7; MHV; RNA summary = 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 keywords = Fig; IBV; day; group 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. doi = 10.1016/j.vaccine.2015.04.026