# ent

id: cord-003148-o7y3wygc
type: DNA
entity:
  rNDV rNDV S1 rNDV S1 IBV S TM CT rNDV S1 cs NDV F TM CT and rNDV S1 cs NDV F TM CT respectively A 130 kDa band


id: cord-003148-o7y3wygc
type: DNA
entity:
  rNDV rNDV S1 rNDV S1 IBV S TM CT rNDV S1 cs NDV F TM CT rNDV S1 cs NDV F TM CT respectively A 130 kD band


id: cord-003148-o7y3wygc
type: DNA
entity:
  rNDV S1 rNDV S1 IBV S TM CT rNDV S1 cs NDV F TM CT rNDV S1 cs NDV F TM CT rNDV S2 rNDV codon optimized S and rNDV non codon optimized S respectively


id: cord-003148-o7y3wygc
type: DNA
entity:
  N gene 296 forward primer 5 GACCAGCCGCTAACCTGAAT 3 and b N gene 445 reverse primer 5 GTCCTCCGTCTGAAAACCGT 3 amplifying 150 nt


id: cord-003148-o7y3wygc
type: CHEMICAL
entity:
  N gene 296 forward primer 5 GACCAGCCGCTAACCTGAAT 3 and b N gene 445 reverse primer 5 GTCCTCCGTCTGAAAACCGT 3 amplifying 150 nt of N gene of IBV strain Mass 41 PCRs


id: cord-263178-lvxxdvas
type: PROTEIN
entity:
  rHVR I II 7 10 0 10 10 10 6 10 4 10 0 10 0 10 0 10 3 10 5 10 7 10 10 10 7 10 10 10 10 10 10 10 10 10 rHVR I III 7 10 1 10 10 10 7 9 2 9 0 9 0 9 0 10 2 10 4 10 6 10 10 10 6 10 9 9 9 9 9 9 9 9 rHVR II III 8 10 2 10 10 10 6 8 1 8 0 8 0 8 0 10 1 10 3 10 6 10 10 10 7 10 8 8 8 8 8 8 8


id: cord-263178-lvxxdvas
type: PROTEIN
entity:
  rHVR I II III 7 10 0 10 10 10 6 10 5 10 0 10 0 10 0 10 2 10 5 10 7 10 10 10 8 10 10 10 10 10 10 10 10 10 Beaudette 9 10 1 10 10 10 4 9 4 9 1 9 0 9 0 10 2 10 4 10 6 10 10 10 6 10 9 9 9 9 9 9 9 9 ck CH LDL 091022 2 5 c 0 5 5 5 3 5 2 5 0 5 0 5 0 10 5 6 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 PBS 10 10 3 10 10 10 8 9 3 7 0 7 0 7 0 10 0 10 0 10 0 10 0 10 3 10 4 9 5 7 7 7 7 7 a


id: cord-004810-g0y7ied0
type: DNA
entity:
  hypervariable region 1 HVR 1 residues 56 69 and hypervariable region 2 HVR 2 residues 117 131 of IBV 6 20


id: cord-255619-5h3l6nh6
type: CELL_LINE
entity:
  TW T T BJ AAP92682 P V ArkDPI AAX39764 T V TW2296 95 AAT39490 T T CK CH LHB 961 ABC02826 S V Beaudette AAA70242 P T TW2575 98 ABG36794 Strains in gray are recruited for BI and CODEML analyses IBV N protein


id: cord-256859-7ixegm72
type: DNA
entity:
  CK CH LDL 97I IBV 87 S1Oligo3 Arg Arg Thr Gly Arg DQ068701 CK CH LLN 98I S1Oligo5 IBV 212 His Arg Arg Arg Arg DQ167145 CK CH LDL 98I IBV 87 S1Oligo3 Arg Arg Thr Gly Arg DQ167132 CK CH LHLJ 99I S1Oligo5 IBV 212 IBV 87 S1Oligo3 Arg Arg Thr Gly Arg DQ167130 CK CH LXJ 02I S1Oligo5 IBV 212 His Arg Arg Arg Arg


id: cord-256859-7ixegm72
type: PROTEIN
entity:
  CK CH LSD 03I S1Oligo5 IBV 212 His Arg Arg Arg Arg DQ167148 CK CH LJL 04I S1Oligo5 IBV 212 His Arg Arg Arg Arg


id: cord-256859-7ixegm72
type: DNA
entity:
  CK CH LGD 04III S1Oligo5 IBV 212 Arg Arg Leu Arg Arg DQ167135 CK CH LHLJ 04XI S1Oligo5 IBV 212 His Arg Arg Arg Arg


id: cord-256859-7ixegm72
type: PROTEIN
entity:
  alanine N asparagine H histidine E glutamic acid T threonine Y tyrosine P proline Q glutamine V valine I isoleucine K lysine R arginine M methionine b positions


id: cord-256859-7ixegm72
type: GGP
entity:
  asparagine H histidine E glutamic acid T threonine Y tyrosine P proline Q glutamine V valine I isoleucine K lysine R arginine M methionine b positions of residues in deduced amino acid sequences


id: cord-280442-jtvez46y
type: PROTEIN
entity:
  glycoprotein S small membrane protein E membrane glycoprotein M and phosphorylated nucleocapsid protein N


id: cord-280442-jtvez46y
type: PROTEIN
entity:
  nucleocapsid N matrix protein M phosphoprotein P fusion protein F hemagglutinin neuraminidase protein HN


id: cord-280442-jtvez46y
type: DNA
entity:
  primer pairs 5 ATCACACTAGCCTTGC GCTAGA 3 5 GCAAAAGCATCAGCGTAATCC 3 and 5 AATCTGTATTACATGTCTAGG 3 5 AGA GAGAATATATCCTTTCGC 3


id: cord-003208-lwirkob3
type: PROTEIN
entity:
  glycosylated spike protein S membrane protein M phosphorylated nucleoprotein N and envelope protein E 3 and 15 nonstructural proteins nsp2 nsp16


id: cord-003208-lwirkob3
type: GGP
entity:
  glycosylated spike protein S membrane protein M phosphorylated nucleoprotein N and envelope protein E 3


id: cord-260042-cs0wp99n
type: PROTEIN
entity:
  PGC 1α Peroxisome proliferator activated receptor gamma coactivator 1 alpha SDHA Succinate dehydrogenase complex subunit A flavoprotein


id: cord-260042-cs0wp99n
type: GGP
entity:
  Peroxisome proliferator activated receptor gamma coactivator 1 alpha SDHA Succinate dehydrogenase complex subunit A flavoprotein variant


id: cord-007648-tm0hn0hz
type: GGP
entity:
  glycopolypeptides S 1 and 2 which have molecular weights of 90 kDa and 84 kDa respectively Cavanagh 1981 The membrane protein


id: cord-010608-eaa2znom
type: DNA
entity:
  consensus sequences IBV Universal S1 4 IBV S1 adap Fwd 5ʹ TTTCTGTTGGTGCTGATATTGCTGAAC CTGAACAAAAGAC 3ʹ S1 Nanopore 1 672


id: cord-256444-grw5s2pf
type: DNA
entity:
  L leader sequence HE hemagglutinin esterase S spike E small membrane protein M integral membrane protein N nucleocapsid protein An poly A tail G


id: cord-256444-grw5s2pf
type: TAXON
entity:
  bovine coronavirus BCV turkey coronavirus TCV bluecomb virus feline coronavirus FCV canine coronavirus CCV


id: cord-256444-grw5s2pf
type: SO
entity:
  L leader sequence HE hemagglutinin esterase S spike E small membrane protein M integral membrane protein N nucleocapsid protein


id: cord-256444-grw5s2pf
type: CHEMICAL
entity:
  N linked glycosylation of the N terminal domain Identification of the coronavirus MHV JHM mRNA 4 product Complete sequence 20 kilobases of the polyprotein encoding gene 1 of


id: cord-252048-ftbjsoup
type: DNA
entity:
  IBV 5 RACE SP1 5 CGTATAGAAAAACAAAGCGTCAC 3 IBV 5 RACE SP2 5 GTCACTGTCTATTGTATGTCTGCTC 3 and IBV 5 RACE SP3 5 TAGCCGACCTTATGCGAGAACG 3


id: cord-252048-ftbjsoup
type: DNA
entity:
  Cal99 NE15172 95 IBV CK CA99 99 CA CA557 03 IBV Conn 66 IBV Conn 72 IBV Conn 83 IBV Conn 91 IBV Mass 65 IBV Mass 72 IBV Mass 79 IBV Mass 85 IBV Mass 06 and the IBV CK A2 China


id: cord-252048-ftbjsoup
type: DNA
entity:
  S1 gene b CAL 1 0 10 2 9 4 10 4 2 0 10 2 2 4 10 3 Conn 1 5 10 4 1 7 10 4 2 6 10 4 3 5 10 4 Mass 1 9 10 3 2 4 10 4 3 3 10 3 5 8 10 4


id: cord-252048-ftbjsoup
type: DNA
entity:
  envelope and membrane genes Coronavirus avian infectious bronchitis virus Infectious bronchitis virus evidence for recombination


id: cord-252048-ftbjsoup
type: WORK_OF_ART
entity:
  A Laboratory Manual for the Isolation Identification and Characterization of Avian Pathogens Recombinant


id: cord-266585-jfjrk9gy
type: DNA
entity:
  nucleotides 1 5751 lane 2 5752 8693 lane 3 8694 15 520 lane 4 15 521 20 900 lane 5 and 20 901 27 608 lane 6


id: cord-266585-jfjrk9gy
type: GGP
entity:
  proteins i e spike glycoprotein S envelope protein E membrane protein M and nucleocapsid protein N The 5 two third region of mRNA 1


id: cord-284501-5i0w74q4
type: WORK_OF_ART
entity:
  The Replicase Gene of Avian Coronavirus Infectious Bronchitis Virus Is a Determinant of Pathogenicity


id: cord-255870-gmq5zs2d
type: PERCENT
entity:
  3 M protein gene gene 5 and N protein gene in this order from the 5 end to the 3 end were very similar to those detected in the corresponding genomic areas of the IBV pf CH LKQ3 03


id: cord-263785-0iift8zy
type: DNA
entity:
  AceQ qPCR Probe Master Mix Kit Vazyme Biotech Nanjing China For haematoxylin eosin staining the collected samples


id: cord-002407-25cawzi0
type: ORG
entity:
  the National Institute of Allergy and Infectious Diseases NIAID Centers of Excellence for Influenza Research


id: cord-002407-25cawzi0
type: DISEASE
entity:
  influenza and respiratory syncytial virus in the united states Clinical and genetic characterization of severe influenza B


id: cord-002407-25cawzi0
type: DISEASE
entity:
  influenza A virus Influenza virus assembly and budding Selective packaging of the influenza A genome


id: cord-002407-25cawzi0
type: DISEASE
entity:
  influenza B viruses Influenza drug resistance Assessment of pandemic and seasonal influenza A H1N1 virus


id: cord-277804-ujabzic4
type: ORG
entity:
  Chicken Embryos United States Department of Agriculture Animal and Plant Health Inspection Service Protection


id: cord-004680-u3cnsdl8
type: PROTEIN
entity:
  Kudou Y Umeda K Ueda S title Typing of recent infectious bronchitis virus isolates causing nephritis


id: cord-279495-zxerb7de
type: CELL_LINE
entity:
  China High frequency RNA recombination of murine coronaviruses The molecular biology of coronaviruses Isolation and characterization of a novel antigenic subtype of infectious bronchitis virus serotype DE072 Stem loop III


id: cord-279495-zxerb7de
type: ORG
entity:
  the International Committee on Taxonomy of Viruses International Union of Microbiological Societies Virology Division Molecular


id: cord-269150-d1sgnxc0
type: PROTEIN
entity:
  RNase P RP buffer 50 mM KCl 1 mM MgCl 2 10 mM HEPES pH 8 0 suspended in 25 ml of sodium dodecyl sulfate SDS sample


id: cord-269150-d1sgnxc0
type: CL
entity:
  stem and the absence of bulges although the structure may be as unstable thermodynamically as that of SARS CoV and HCoV OC43


id: cord-259505-7hiss0j3
type: PROTEIN
entity:
  molecular chaperone 18 macromolcular biosynthesis proteins 17 cytoskeletal proteins 15 signal transport proteins 15 protein degradation 8 chromosome associated proteins 2 ribosomal proteins 2


id: cord-259505-7hiss0j3
type: PROTEIN
entity:
  aldehyde dehydrogenase 9 family member A1 ALDH9A1 glyceraldehyde 3 phosphate dehydrogenase GAPDH alpha enolase


id: cord-259505-7hiss0j3
type: DNA
entity:
  hepatitis B virus posttranscriptional regulatory element Glyceraldehyde 3 phosphate dehydrogenase GAPDH


id: cord-259505-7hiss0j3
type: GGP
entity:
  Kaposi s sarcoma associated herpesvirus KSHV 8 9 Marek s disease virus MDV 10 Epstein Barr virus EBV 11 human


id: cord-265258-2rmtsyns
type: PROTEIN
entity:
  12Á5 ll 29 QuantiTect Probe RT PCR Master Mix QuantiTect Probe RT PCR Kit Qiagen 0Á25 ll QuantiTect RT Mix primers


id: cord-001083-vy1nxax2
type: DNA
entity:
  IBV spacer sequence IBV Podo 1 sp6 59 TATTTAAACGGGTACGGGAGGTGGTCAAGGTGGTC GGCCACGAGCTCCCAAATTTTCGCCCC 39


id: cord-001083-vy1nxax2
type: DNA
entity:
  P anserina pseudoknot IBV Podo0 59 TTATTTAA ACGGGTACGGGAGGTGGTCAAGGTGGTCGGCCACGAG CTCCCAAATTTTCGCCCCAT 39 The b galactosidase and


id: cord-293651-96cmduez
type: DNA
entity:
  5 primer A Beau U30 5 TACACTAGCCTTGCGC TAGA 3 and 3 primer A Beau L5447 5 GCACGCCA AAGTCCCATAG 3 Briefly RNA


id: cord-271897-9oqzsd70
type: DNA
entity:
  Swedish National Veterinary Institute SVA Uppsala Sweden four subsequent virus strains 80 1989 162 1997 255 1997 and G225 2017


id: cord-273661-egpyvqrw
type: WORK_OF_ART
entity:
  Molecular Characterization of Major Structural Protein Genes of Avian Coronavirus Infectious Bronchitis Virus Isolates in Southern China


id: cord-286473-sl5zy8nj
type: PROTEIN
entity:
  protein membrane M protein ORF5 ORFs X 5a 5b nucleocapsid N protein 3 UTR poly A TCoV genome structure


id: cord-286473-sl5zy8nj
type: DNA
entity:
  TCoV genome S spike glycoprotein gene 3a 3b and 3c E tricistronic gene 3 M membrane protein gene ORF X unique ORF


id: cord-286473-sl5zy8nj
type: PROTEIN
entity:
  FeCoV 46 43 59 40 37 43 38 HCoV 229E 60 45 59 40 40 43 40 HCoV NL63 50 45 60 41 42 44 39 BCoV NC 46 46 59 45 41 50 44 HCoV OC43 48 46 59 44 42 51 44 MHV JHM 46 43 58 43 43 51 42 SARS CoV 45 41 59 44 31 45 41 IBV Beaudette 94 90 93 57 90 94 92 IBV p65 87 90 93 57 88 92 92 IBV M41 87 90 93 57 88 92 93 TCoV MG10 100 100 100 100 100 100 100 TCoV G1


id: cord-286473-sl5zy8nj
type: DNA
entity:
  murine hepatitis virus MHV BCoV HCoV OC43 rat sialodacryoadenyleitis virus SADV canine respiratory coronavirus CRCoV


id: cord-286473-sl5zy8nj
type: PROTEIN
entity:
  ORF1b spike S protein ORF3 ORFs 3a and 3b small envelop E or 3c protein membrane M protein ORF X ORF5 ORFs 5a and 5b nucleocapsid N protein 3 UTR poly A


id: cord-286473-sl5zy8nj
type: CHEBI
entity:
  protein membrane M protein ORF5 ORFs X 5a 5b nucleocapsid N protein 3 UTR poly A TCoV genome structure and sequence


id: cord-272666-3uidpr79
type: PROTEIN
entity:
  coronavirus nonstructural proteins 3 and 4 Virology Mobility and Interactions of Coronavirus Nonstructural Protein 4 Severe Acute Respiratory Syndrome Coronavirus Nonstructural Proteins 3 4 and 6 Induce Double Membrane Vesicles Targeting Membrane Bound Viral RNA


id: cord-272666-3uidpr79
type: ORG
entity:
  Associated Nuclear Transport Machinery Limit Access of Pattern Recognition Receptors to Viral Replication Sites Ultrastructure


id: cord-272666-3uidpr79
type: ORG
entity:
  Zippered Endoplasmic Reticulum Membranes Expression and Cleavage of Middle East Respiratory Syndrome Coronavirus


id: cord-286332-cdg4im5h
type: DNA
entity:
  NGS rabbit anti MHV polyserum k134 diluted 1 400 and chicken anti IBV H120 serum diluted 1 400 or rabbit anti MHV polyserum k134 diluted 1 400 and mouse MAb Ch IBV 26


id: cord-291718-cz1bi0ym
type: PROTEIN
entity:
  cord 291718 cz1bi0ym authors Yu Liping Zhang Xiaorong Wu Tianqi Wang Yuyang Meng Jie Liu Qian Niu Xiaosai Wu Yantao title


id: cord-293081-40pa5g89
type: FAC
entity:
  the Beijing Synchrotron Radiation Facility BSRF Institute of High Energy Physics Beijing People s Republic of China


id: cord-259738-yuqc6dk0
type: DNA
entity:
  N forward primer 5 CATCTCGAGTCTT TTATCATGGCAAGC 3 reverse primer 5 GGCGAATTCA TTAGAGTTCATTTTCAC 3 IL 2 forward primer 5 CCAGGATCCACCATGATGTGCAAAG 3 reverse primer 5 GAAGCGGCCGCAGATTAGTTAGC 3


id: cord-259738-yuqc6dk0
type: CHEMICAL
entity:
  N gene and IL 2 as listed N forward primer 5 CATCTCGAGTCTT TTATCATGGCAAGC 3 reverse primer 5 GGCGAATTCA TTAGAGTTCATTTTCAC 3 IL 2 forward primer 5 CCAGGATCCACCATGATGTGCAAAG 3 reverse primer 5 GAAGCGGCCGCAGATTAGTTAGC 3 The medium


id: cord-285323-473d7zvg
type: ORG
entity:
  Cell Biology Molecular Immunology Laboratory Division of Biotechnology College of Environmental Bioresource Sciences Chonbuk National University


id: cord-272693-432ixb7g
type: DNA
entity:
  5 0 untranslated region UTR polyproteins 1a and 1ab spike 3a 3b envelope membrane 4b 5a 5b nucleocapsid and 3 0 UTR


id: cord-272693-432ixb7g
type: CHEMICAL
entity:
  MgCl 2 5 mM 109 RNA PCR buffer 19 dNTP mixture 1 mM RNase inhibitor 1 units ll reverse transcriptase 0 25 units ll 5 0 degenerate primer 2 5 lM and RNA 5 75 ll reaction then 10 ll per sample


id: cord-286658-9kco7qad
type: PROTEIN
entity:
  S2 4 8 12 16 20 24 28 4 8 12 16 20 24 28 32 36 40 44 I1101 16 10 10 3 10 10 b 9 10 7 10 6 10 2 10 1 10 1 10 7 10 8 10 10 10 7 10 7 10 5 10 6 10 6 10 6 10 2 10 0 10 ck CH LJL 140901 9 10 0 9 10 10 10 10 6 10 2 10 2 10 0 10 c 10 10 10 10 10 10 10 10 6 10 6 10 6 10 0 10 Negative 0 10 0 0 10 0 10 0 10 0 10 0 10 0 10 0 10 0 10 0 10 0 10 0 10 0 10 0 10 0 10 0 10 0 10 0 10 0 10


id: cord-271568-qgpi2kcs
type: ORG
entity:
  A Laboratory Manual for the Isolation Identification and Characterization of Avian Pathogens Coronaviruses


id: cord-291510-jh2fdks4
type: CELL_LINE
entity:
  China 10 11 12 13 Severe nephritis false layer syndrome and high mortality are observed in chickens infected with this viral genotype


id: cord-291510-jh2fdks4
type: ORG
entity:
  the Animal Welfare Conceptualization Methodology Software Investigation Validation Visualization Resources Writing


id: cord-298920-1lc2xf7u
type: PROTEIN
entity:
  PtdIns3K phosphatidylinositol 3 kinase Ptdins3P phosphatidylinositol 3 phosphate PTK2 FAK protein tyrosine kinase 2 RAB7 RAB7 member RAS oncogene family RB1CC1 FIP200 RB


id: cord-298920-1lc2xf7u
type: GGP
entity:
  PIK3C3 VPS34 phosphatidylinositol 3 kinase catalytic subunit type 3 PIK3R4 VPS15 phosphoinositide 3 kinase regulatory subunit 4 PtdIns3K phosphatidylinositol 3 kinase


id: cord-300104-855iw9wi
type: GGP
entity:
  specifi c pathogen free SPF fl ock killed by cervical dislocation see Note 1 13 Growth medium EMEM 10 NBBS 2


id: cord-301720-majpfxqn
type: DNA
entity:
  Kurdistan Sulaymania 12 Egypt Beni Suef 01 Turkey 10RS 3161 2010 IS VAR2 06 variant_2 Eg CLEVB 2 IBV 012 IR Bu variant2 SH1229 5


id: cord-309623-2ngr682l
type: DISEASE
entity:
  coronavirus infectious bronchitis virus infection Impaired cardiac microvascular endothelial cells function


id: cord-316525-uadfehr6
type: GGP
entity:
  HCoV 15633 15672 40 35 88 TGEV 15729 15770 42 40 96 MHV 15765 15817 53 46 87 HCoV 15852 15908 57 49 86 MHV 17088 17125 38 35 93 IBV 17688 17714 27 25 93 TGEV 17757 17800 44 39 89 PEDV 17783 17809 27 25 93 HCoV 18558 18577 20 20 100 PEDV 18771 18847 77 65 85 TGEV 18784 18833 50 44 88 HCoV 19102


id: cord-310372-qc6941pm
type: ORG
entity:
  Pathogenicity of Infectious Bronchitis Coronaviruses Complicated Evolution and Epidemiology in China


id: cord-303393-9zs3qqo4
type: WORK_OF_ART
entity:
  OIE Manual of Diagnostic Tests and Vaccines for Terrestrial Animals World Organisation for Animal Health


id: cord-319253-8bssrn9o
type: WORK_OF_ART
entity:
  A Real Time Reverse Transcription Polymerase Chain Reaction for Differentiation of Massachusetts Vaccine


id: cord-316153-wet0go35
type: DNA
entity:
  CU T2 genome POL RNA polymerase gene S S protein gene 1 S1 protein gene 2 2 protein gene N N protein gene U TR 3 end untranslated region HVR Hypervariabte region


id: cord-310536-u30cufg7
type: CHEMICAL
entity:
  MgCl 0 2 mM dNTPs 2 units of Taq DNA polymerase 1X reaction buffer 1 pmol of each primer and 5 M N N N trimethylglycine betaine


id: cord-307304-irji8owi
type: DNA
entity:
  dominant selectable marker gene Escherichia coli guanine Xanthine phosphoribosyltransferase Ecogpt Mulligan


id: cord-307304-irji8owi
type: DISEASE
entity:
  infectious positive stranded RNA viruses including picornaviruses caliciviruses alphaviruses flaviviruses arteriviruses


id: cord-306976-p2521bl4
type: DNA
entity:
  nrTW I strain 10 10 4 10 0 10 0 10 7 10 10 10 10 10 10 10 6 6 6 6 6 6 6 6 10 10 5 6 4 6 2 6 1 6 LDT3 A 0 10 0 10 0 10 2 10 6 10 9 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 8 10 1 10 1 10 0 10 4 91 1 10 1 10 0 10 0 10 2 10 8 10 10 10 10 10 10 10 9 9 9 9 9 9 10 10 9 10 5 9 3 9 0 9 Conn 4 10 1 10 0 10 4 10 7 10 10 10 10 10 10 10 9 9 9 9 9 9 9 9 9 10 6 9 4 9 0 9 LDL 091022 P120 0 10 0 10 0 10 4 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 8 10 10 10 2 10 0 10 LSD 120720 P90 3 10 2 10 0 10 0 10 3 10 7 10 10 10 10 10 10 10 8 8 8 8 8 8 10 10 8 10 4 8 0 8 LGX 100508 P70 2 10 2 10 0 10 0 10 3 10 8 10 10 10 10 10 10 10 9 9 8 8 8 8 9 10 3 10 2 9 0 8 LDL 97I P115 0 10 0 10 0 10 2 10 6 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 8 10 1 10 1 10 0 10 nrTW I d 10 10 7 10 0 10 6 10 10 10 10 10 10 10 0 10 3 3 3 3 3 3 3 3 10 10 3 3 1 3 0 3 Negative control 0 10 0 10 0 10 0 10 0 10 0 10 0 10 0 10 0 10 0 10 0 10 0 10 0 10 0 10 0 10 0 10 0 10


id: cord-306976-p2521bl4
type: GGP
entity:
  nrTW I strain 10 10 4 10 0 10 0 10 7 10 10 10 10 10 10 10 6 6 6 6 6 6 6 6 10 10 5 6 4 6 2 6 1 6 LDT3 A 0 10 0 10 0 10 2 10 6 10 9 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 8 10 1 10 1 10 0 10 4 91 1 10 1 10 0 10 0 10 2 10 8 10 10 10 10 10 10 10 9 9 9 9 9 9 10 10 9 10 5 9 3 9 0 9 Conn 4 10 1 10 0 10 4 10 7 10 10 10 10 10 10 10 9 9 9 9 9 9 9 9 9 10 6 9 4 9 0 9


id: cord-316234-vtjsfi2c
type: DISEASE
entity:
  influenza and respiratory syncytial viruses Rapid PCR based molecular pathotyping of H5 and H7 avian influenza viruses Rapid discrimination of H5 and H9 subtypes of avian influenza viruses and Newcastle disease


id: cord-329497-3jow4xbn
type: PROTEIN
entity:
  structural proteins phosphorylated nucleocapsid protein N membrane glycoprotein M spike glycoprotein S


id: cord-317587-rrx2r4n2
type: DNA
entity:
  CK CH LSC 99I GI 22 New 1 GVI 1 Mass GI 1 LX4 GI 19 4 91 GI 13 Taiwan GI 7 LDT3 A GI 28 and New 2 GVII 1


id: cord-317587-rrx2r4n2
type: CHEMICAL
entity:
  N gene Table S6 The selection profile and entropy values of S1 E M and N proteins of Guangxi IBV isolates Figure S1 Alignment of the deduced amino acid


id: cord-317587-rrx2r4n2
type: CHEMICAL
entity:
  N genes y axis shows the entropy of each amino acid site Figure S4 The location of positive selection sites and putative glycosylation sites of the S1 subunit of 91 IBV isolates


id: cord-322410-k23engcx
type: DNA
entity:
  Massachusetts D3128 D274 D 08880 and 4 91 genotypes Abdel Moneim et al 2006 Jackwood 2012 Sheble et al 1986 In 2001 a unique Egyptian variant type isolate Egypt Beni Suef 01 closely


id: cord-322410-k23engcx
type: ORG
entity:
  the National Laboratory for Veterinary Quality Control on Poultry Production NLQP Ministry of Agriculture Giza


id: cord-322410-k23engcx
type: DISEASE
entity:
  Egyptian variant II sequences Fig 2 Within HVR 1 2 sequences however the existence of two distinct Table 3 RT


id: cord-323568-s0wmll4q
type: PROTEIN
entity:
  IBV spike ectodomain S1 receptor binding subunit S2 membrane fusion subunit GCN4 His 6 GCN4 trimerization tag


id: cord-331740-yjt3q9ph
type: CELL_LINE
entity:
  MagNA Pure LC Total Nucleic Acid Isolation kit Roche Burgess Hill West Sussex UK Nucleic acid extractions were prepared from 200 ll of sample


id: cord-331740-yjt3q9ph
type: CELL_LINE
entity:
  primer CTA TCG CCA GGG AAA TGT C IBVRT2 reverse primer GCG TCC TAG TGC TGT ACC C IBVRT3 TaqMan Ò probe FAM CCT GGA AAC GAA CGG TAG ACC CT TAMRA


id: cord-331740-yjt3q9ph
type: CHEMICAL
entity:
  MgCl 2 1 ll 10 mm dNTP mix 0 8 lm IBVRT1 primer 0 8 lm IBVRT2 primer 0 2 lm IBVRT3 TaqMan probe 0 25 ll RNasin


id: cord-331740-yjt3q9ph
type: CHEMICAL
entity:
  MgCl 2 1 ll 10 mm dNTP mix 0 4 lm of primer S1for2 0 4 lm of primer S1rev3 0 04 lm of each of the remaining primers 0 25 ll RNasin


id: cord-342354-j10m2dfh
type: ORG
entity:
  the Key Subject of Traditional Chinese Medicine of Jilin Agricultural Science and Technology University


id: cord-331020-lyxje82u
type: LAW
entity:
  Pathogenesis of Oviduct Lesions in Immature Chickens Following Exposure to Infectious Bronchitis Virus


id: cord-331020-lyxje82u
type: WORK_OF_ART
entity:
  The Diagnosis of Certain Avian Diseases with the Fluorescent Antibody Technique Standardization of the Fluorescent Antibody Technique for the Detection of Avian Respiratory Viruses Effects of Infectious Bronchitis in Baby Chicks Persistence of Virus in the Tissues and Development of the Oviduct in the Fowl Following Infection at Day Old with Infectious Bronchitis Virus Induction


id: cord-330057-3vucm0s1
type: PRODUCT
entity:
  Improving the Accuracy of Demographic and Molecular Clock Model Comparison While Accommodating Phylogenetic Uncertainty Bayesian Coalescent Inference of Past Population Dynamics


id: cord-345630-bam3pa70
type: PROTEIN
entity:
  I I I I I I I I I I I I 1 2000 2500 3000 3500 3 ORF la lb 0 ORF lb I I I I I I I I I I I I I 1000 1500 2000 2500 FIG 2 Hydropathy


id: cord-339259-4oi7slk9
type: ORG
entity:
  the National Laboratory for Veterinary Quality Control on Poultry Production NLQP Ministry of Agriculture


id: cord-326319-3538jmqd
type: CHEMICAL
entity:
  N peptides by antigen presenting cells following effective uptake processing or presentation on MHC receptors of these cells 37 Therefore


id: cord-348660-qnbgywgy
type: LAW
entity:
  title Production of Recombinant N Protein of Infectious Bronchitis Virus Using the Baculovirus Expression System and Its Assessment as a Diagnostic Antigen date 2018


id: cord-353027-bc0un6kb
type: ORG
entity:
  the Reference Laboratory for Veterinary Quality Control on Poultry Production NLQP Animal Health Research Institute


id: cord-342176-tewfm8it
type: DNA
entity:
  High Capacity cDNA Archive kit Applied Biosystems Life Technologies Europe BV Naerum Denmark cat no 436881


id: cord-353310-19kzb6ag
type: DNA
entity:
  family Coronaviridae Beaudette Hudson 1937 Tyrell 1968 subfamily Coronavirinae and genus Gammacoronavirus group 3


id: cord-338307-vfutmwxq
type: DNA
entity:
  murine coronavirus JHM and A59 Antigenic relationships amongst coronaviruses The propagation of coronaviruses


id: cord-338307-vfutmwxq
type: CHEMICAL
entity:
  Sindbis virus glycoproteins Immunogenicity and antigenicity of human coronaviruses 2293 and OC43 Polypeptides


id: cord-356094-sbtigcfr
type: PROTEIN
entity:
  melanoma differentiation associated protein 5 A mitochondrial antiviral signaling gene B interferon alpha C interferon beta D nuclear factor kappa beta e IL 6 F and tumor necrosis factor alpha


id: cord-356094-sbtigcfr
type: EVENT
entity:
  International Conference on Harmonisation of Technical Requirements for Registration of Pharmaceuticals for


id: cord-343893-sophqqne
type: DNA
entity:
  human coronavirus strain OC43 phylogenetic relationships to bovine and murine coronaviruses and influenza C virus Sialic acids


id: cord-343893-sophqqne
type: DISEASE
entity:
  coronaviruses and influenza C virus The hemagglutinin esterase gene of human coronavirus strain OC43 phylogenetic


id: cord-334090-66d8c75g
type: ORG
entity:
  Slemani Governorate Council of College of Veterinary Medicine University of Sulaimani in Partial Fulfillment of the Requirements


# bib

id: cord-000924-wwuqxx1r
author: Yan, Fang
date: 2013-03-24
txt: ./txt/cord-000924-wwuqxx1r.txt
cache: ./cache/cord-000924-wwuqxx1r.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3615232/
doi: 10.4142/jvs.2013.14.1.53
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.

title:
  Protection of chickens against infectious bronchitis virus with a multivalent DNA vaccine and boosting with an inactivated vaccine

abstract:
  The protective efficacy of DNA plasmids encoding avian infectious bronchitis virus (IBV) S1, N, or M protein was investigated in chickens. Chickens were inoculated monovalently (with plasmid pVAX1-16S1, pVAX1-16M, or pVAX1-16N alone) or multivalently (combination of the three different plasmids, pVAX1-16S1/M/N). A prime-boost immunization protocol against IBV was developed. Chickens were immunized with the multivalent DNA vaccine twice and then boosted with an inactivated vaccine once. Antibody titers of the chickens immunized with pVAX1-16S1/M/N were much higher than those of the monovalent groups (p < 0.01). A protective rate up to 90% was observed in the pVAX1-16S1/M/N group. The serum antibody titers in the prime-boost birds were significantly higher than those of the multivalent DNA vaccine group (p < 0.01) but not significantly different compared to the inactivated vaccine group at 49 days of age. Additionally, the prime-boost group also showed the highest level of IBV-specific cellular proliferation compared to the monovalent groups (p < 0.01) but no significant difference was found compared to the multivalent DNA vaccine group, and the prime-boost group completely protected from followed viral challenge.


id: cord-001083-vy1nxax2
author: Malagnac, Fabienne
date: 2013-09-19
txt: ./txt/cord-001083-vy1nxax2.txt
cache: ./cache/cord-001083-vy1nxax2.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3777964/
doi: 10.1371/journal.pone.0073772
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) .

title:
  Rab-GDI Complex Dissociation Factor Expressed through Translational Frameshifting in Filamentous Ascomycetes

abstract:
  In the model fungus Podospora anserina, the PaYIP3 gene encoding the orthologue of the Saccharomyces cerevisiae YIP3 Rab-GDI complex dissociation factor expresses two polypeptides, one of which, the long form, is produced through a programmed translation frameshift. Inactivation of PaYIP3 results in slightly delayed growth associated with modification in repartition of fruiting body on the thallus, along with reduced ascospore production on wood. Long and short forms of PaYIP3 are expressed in the mycelium, while only the short form appears expressed in the maturing fruiting body (perithecium). The frameshift has been conserved over the evolution of the Pezizomycotina, lasting for over 400 million years, suggesting that it has an important role in the wild.


id: cord-001768-8vljd5cv
author: Awad, Faez
date: 2015-09-09
txt: ./txt/cord-001768-8vljd5cv.txt
cache: ./cache/cord-001768-8vljd5cv.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4567785/
doi: 10.1136/vetreco-2014-000111
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

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

abstract:
  The ability of the infectious bronchitis H120 (a Massachusetts strain) and CR88 (a 793B strain) live attenuated vaccine viruses to protect from two Middle East infectious bronchitis virus isolates, IS/885/00-like (IS/885) and IS/1494/06-like (IS/1494) in broiler chicks was investigated. Day-old chicks were separated into three groups, (I) vaccinated with H120 at day-old followed by CR88 at 14 days-old, (II) vaccinated with H120 and CR88 simultaneously at day-old and again with CR88 at 14 days-old, (III) control unvaccinated. At 30 days-old, each of the groups was challenged with virulent IS/885 or IS/1494. Protection was evaluated based on the clinical signs, tracheal and kidney gross lesions and tracheal ciliostasis. Results showed that administering combined live H120 and CR88 vaccines simultaneously at day-old followed by CR88 vaccine at 14 days-old gave more than 80 per cent tracheal ciliary protection from both of the Middle East isolates. In addition, this programme conferred 100 per cent protection from clinical signs and tracheal or kidney lesions. The other vaccination programme, H120 at day-old followed by CR88 at 14 days-old, the tracheal ciliary protection conferred were 60 per cent and 80 per cent from IS/885/00-like and IS/1494/06-like, respectively.


id: cord-002407-25cawzi0
title: Reverse Genetics Approaches for the Development of Influenza Vaccines
author: Nogales, Aitor
date: 2016-12-22
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5297655/
doi: 10.3390/ijms18010020
abstract:
  Influenza viruses cause annual seasonal epidemics and occasional pandemics of human respiratory disease. Influenza virus infections represent a serious public health and economic problem, which are most effectively prevented through vaccination. However, influenza viruses undergo continual antigenic variation, which requires either the annual reformulation of seasonal influenza vaccines or the rapid generation of vaccines against potential pandemic virus strains. The segmented nature of influenza virus allows for the reassortment between two or more viruses within a co-infected cell, and this characteristic has also been harnessed in the laboratory to generate reassortant viruses for their use as either inactivated or live-attenuated influenza vaccines. With the implementation of plasmid-based reverse genetics techniques, it is now possible to engineer recombinant influenza viruses entirely from full-length complementary DNA copies of the viral genome by transfection of susceptible cells. These reverse genetics systems have provided investigators with novel and powerful approaches to answer important questions about the biology of influenza viruses, including the function of viral proteins, their interaction with cellular host factors and the mechanisms of influenza virus transmission and pathogenesis. In addition, reverse genetics techniques have allowed the generation of recombinant influenza viruses, providing a powerful technology to develop both inactivated and live-attenuated influenza vaccines. In this review, we will summarize the current knowledge of state-of-the-art, plasmid-based, influenza reverse genetics approaches and their implementation to provide rapid, convenient, safe and more effective influenza inactivated or live-attenuated vaccines.


id: cord-003148-o7y3wygc
author: Shirvani, Edris
date: 2018-08-10
txt: ./txt/cord-003148-o7y3wygc.txt
cache: ./cache/cord-003148-o7y3wygc.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6086832/
doi: 10.1038/s41598-018-30356-2
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.

title:
  A Recombinant Newcastle Disease Virus (NDV) Expressing S Protein of Infectious Bronchitis Virus (IBV) Protects Chickens against IBV and NDV

abstract:
  Infectious bronchitis virus (IBV) causes a highly contagious respiratory, reproductive and urogenital tract disease in chickens worldwide, resulting in substantial economic losses for the poultry industry. Currently, live-attenuated IBV vaccines are used to control the disease. However, safety, attenuation and immunization outcomes of current vaccines are not guaranteed. Several studies indicate that attenuated IBV vaccine strains contribute to the emergence of variant viruses in the field due to mutations and recombination. Therefore, there is a need to develop a stable and safe IBV vaccine that will not create variant viruses. In this study, we generated recombinant Newcastle disease viruses (rNDVs) expressing the S1, S2 and S proteins of IBV using reverse genetics technology. Our results showed that the rNDV expressing the S protein of IBV provided better protection than the rNDV expressing S1 or S2 protein of IBV, indicating that the S protein is the best protective antigen of IBV. Immunization of 4-week-old SPF chickens with the rNDV expressing S protein elicited IBV-specific neutralizing antibodies and provided complete protection against virulent IBV and virulent NDV challenges. These results suggest that the rNDV expressing the S protein of IBV is a safe and effective bivalent vaccine candidate for both IBV and NDV.


id: cord-003208-lwirkob3
title: Novel protein chip for the detection of antibodies against infectious bronchitis virus
author: Yan, Liping
date: 2018-09-17
txt: ./txt/cord-003208-lwirkob3.txt
cache: ./cache/cord-003208-lwirkob3.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6142349/
doi: 10.1186/s12917-018-1586-x
summary:
  RESULTS: We have developed two indirect microarray methods to detect antibodies against IBV: a chemiluminescent immunoassay test (CIT) and a rapid diagnostic test (RDT). Compared with these methods, enzyme-linked immunosorbent assay (ELISA) has been widely used for testing IBV early infection and continuous infection, and this technique can be used for both antigenic and antibody detection. The data showed that 130 serum samples were positive for antibodies against IBV, and 14 samples were negative, similar to the results of the IDEXX IBV Ab Test kit with the nsp5 concentration of 0.2 mg/mL (Table 4 ). The specific experiments of the RDT showed that no cross-reaction Fig. 4 a Distribution of the SNRs of the IDEXX-positive (n = 142) and IDEXX-negative (n = 42) serum samples of the clinical sera obtained from the IBV protein microarray.

abstract:
  BACKGROUND: Infectious bronchitis (IB) caused by the IB virus (IBV) can cause acute damage to chickens around the world. Therefore, rapid diagnosis and immune status determination are critical for controlling IBV outbreaks. Enzyme-linked immunosorbent assays (ELISAs) have been widely used in the detection of IBV antibodies in the early infection and continuous infection of IB because they are more sensitive and quicker than other diagnostic methods. RESULTS: We have developed two indirect microarray methods to detect antibodies against IBV: a chemiluminescent immunoassay test (CIT) and a rapid diagnostic test (RDT). IBV nonstructural protein 5 (nsp5) was expressed, purified from Escherichia coli, and used to spot the initiator integrated poly(dimethylsiloxane), which can provide a near “zero” background for serological assays. Compared with the IDEXX IBV Ab Test kit, CIT and RDT have a sensitivity and specificity of at least 98.88% and 91.67%, respectively. No cross-reaction was detected with antibodies against avian influenza virus subtypes (H5, H7, and H9), Newcastle disease virus, Marek’s disease virus, infectious bursal disease virus, and chicken anemia virus. The coefficients of variation of the reproducibility of the intra- and inter-assays for CIT ranged from 0.8 to 18.63%. The reproducibility of RDT was consistent with the original results. The application of the IBV nsp5 protein microarray showed that the positive rate of the CIT was 96.77%, that of the nsp5 ELISA was 91.40%, and that of the RDT was 90.32%. Furthermore, the RDT, which was visible to the naked eye, could be completed within 15 min. Our results indicated that compared with nsp5 ELISA, the CIT was more sensitive, and the RDT had similar positive rates but was faster. Furthermore, the two proposed methods were specific and stable. CONCLUSIONS: Two microarray assays, which were rapid, specific, sensitive, and relatively simple, were developed for the detection of an antibody against IBV. These methods can be of great value for the surveillance of pathogens and monitoring the efficiency of vaccination.


id: cord-003334-ion97n4b
author: De Silva Senapathi, Upasama
date: 2018-11-15
txt: ./txt/cord-003334-ion97n4b.txt
cache: ./cache/cord-003334-ion97n4b.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6266937/
doi: 10.3390/v10110635
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.

title:
  The In Ovo Delivery of CpG Oligonucleotides Protects against Infectious Bronchitis with the Recruitment of Immune Cells into the Respiratory Tract of Chickens

abstract:
  The in ovo delivery of cytosine-guanosine (CpG) oligodeoxynucleotides (ODNs) protects chickens against many bacterial and viral infections, by activating the toll-like receptor (TLR)21 signaling pathway. Although the delivery of CpG ODNs in ovo at embryo day (ED) 18 has been shown to reduce infectious bronchitis virus (IBV) loads in embryonic chicken lungs pre-hatch, whether in ovo delivered CpG ODNs are capable of protecting chickens against a post-hatch challenge is unknown. Thus, our objectives were to determine the protective effect of the in ovo delivery of CpG ODNs at ED 18 against IBV infection encountered post-hatch and, then, to investigate the mechanisms of protection. We found significantly higher survival rates and reduced IBV infection in the chickens following the pre-treatment of the ED 18 eggs with CpG ODNs. At 3 days post infection (dpi), we found an increased recruitment of macrophages, cluster of differentiation (CD)8α+ and CD4+ T lymphocytes, and an up-regulation of interferon (IFN)-γ mRNA in the respiratory tract of the chickens. Overall, it may be inferred that CpG ODNs, when delivered in ovo, provide protection against IBV infection induced morbidity and mortality with an enhanced immune response.


id: cord-004680-u3cnsdl8
title: Typing of recent infectious bronchitis virus isolates causing nephritis in chicken
author: Lin, Z.
date: 1991
txt: ./txt/cord-004680-u3cnsdl8.txt
cache: ./cache/cord-004680-u3cnsdl8.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086593/
doi: 10.1007/bf01310957
summary:
  Four isolates of infectious bronchitis viruses (IBV) from chickens with nephritis, were characterized by polymerase chain reaction (PCR) and restriction enzyme fragment length polymorphism (RFLP), and were found to be genetically different from the other twelve strains which we previously studied. HinfI digested pUC 19 DNA was used as the molecular size markers (3//), and their sizes are indicated in base pairs (bp) on the left In this study, essentially the same procedure was used in an attempt to characterize four IBV isolates F-88, Y-4, M-l, and NI-1 from chickens with nephritis in different endemic areas of Japan between 1988 and 1989. The results of the present study, indicate that the four recently obtained IBV isolates causing nephritis are, by our genetic criteria, similar to each other but different from previous isolates, hence are classified together into a new subtype (group VI). Serological comparisons of strains of infectious bronchitis virus using plaque-purified isolants

abstract:
  Four isolates of infectious bronchitis viruses (IBV) from chickens with nephritis, were characterized by polymerase chain reaction (PCR) and restriction enzyme fragment length polymorphism (RFLP), and were found to be genetically different from the other twelve strains which we previously studied.


id: cord-004810-g0y7ied0
title: S1 glycoprotein gene analysis of infectious bronchitis viruses isolated in Korea
author: Lee, S. K.
date: 2003-11-13
txt: ./txt/cord-004810-g0y7ied0.txt
cache: ./cache/cord-004810-g0y7ied0.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087141/
doi: 10.1007/s00705-003-0225-3
summary:
  The S1 glycoprotein gene of IBV isolates were amplified by reverse transcriptase – polymerase chain reaction (RT-PCR) and analyzed by restriction fragment length polymorphism (RFLP) analysis. And these IBV isolates showed different patterns from each other and non-Korean IBV isolates in reverse transcriptase-polymerase chain reaction-restriction fragment length polymorphism (RT-PCR-RFLP) analysis [29] . Amplified S1 genes were first classified by RFLP analysis and then the representative strains were cloned, sequenced and compared to other non-Korean published IBV sequences. Phylogenetic trees were constructed from the nucleotide and deduced amino acid sequences of the S1 glycoprotein genes of Korean IBV isolates and non-Korean IBV strains (Fig. 3) . Korean IBV K281-01 and K210-02 isolates formed distinct clusters that were related to non-Korean IBV Ark99, Ark DPI, Gray and JMK strains although K281-01 and K210-02 isolates were classified into the Arkansas type by PCR-RFLP analysis.

abstract:
  Fifteen isolates of Infectious bronchitis virus (IBV) were obtained from the kidney, trachea, and cecal tonsil of IB suspected chickens between 2001 and 2002 years in Korea. The S1 glycoprotein gene of IBV isolates were amplified by reverse transcriptase – polymerase chain reaction (RT-PCR) and analyzed by restriction fragment length polymorphism (RFLP) analysis. Fifteen Korean IBV isolates were classified into 4 groups by their RFLP patterns using restriction enzymes, HaeIII, BstYI, and XcmI. The RFLP patterns for 3, 1, and 1 of 15 isolates corresponded to the patterns of IBV Arkansas, Connecticut, and Massachusetts strains, respectively. Ten of 15 isolates generated unique KM91 RFLP pattern that was observed in the IBV KM 91 strain previously isolated in Korea. To confirm genetic diversity in the S1 genes of IBV isolates, viral RNAs of representative 9 of 15 IBV isolates were amplified, cloned, sequenced and compared with published sequences for non-Korean IBV strains. Korean IBV isolates showed amino acid sequence similarity between 61.8% (K446-01 and K161-02) and 96.1% (K281-01 and K210-02) with each other and they showed amino acid sequence similarity between 42.9% (K161-02 and GA980470) and 96.5% (K203-02 and KB8523) compared to non-Korean IBV strains. By phylogenetic tree analysis, Korean IBV field isolates were branched into five clusters in which 3 clusters were differentiated from non-Korean IBV strains. Especially, Korean IBV isolates K069-01, K507-01, K774-01 and K142-02 formed a separate cluster. It seems that IBVs continue to evolve and IBVs showing various genetic differences may cocirculate in Korea.


id: cord-006991-2q5ore6g
title: Oral administration of tea saponins to relive oxidative stress and immune suppression in chickens
author: Chi, X.
date: 2017-06-15
txt: ./txt/cord-006991-2q5ore6g.txt
cache: ./cache/cord-006991-2q5ore6g.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7107189/
doi: 10.3382/ps/pex127
summary:
  The results showed that administration of tea saponins significantly increased total antioxidant capacity, total superoxide dismutase, catalase, glutathione peroxidase, glutathione, ascorbic acid, and α-tocopherol, and decreased malondialdehyde and protein carbonyl. Enhanced immune responses, such as lymphocyte proliferation induced by concanavalin A and lipopolysaccharides, and serum Newcastle disease virusand infectious bronchitis virus-specific antibodies were also observed in chickens injected with or without cyclophosphamide. At the present study, we evaluated the effect of TS on the antioxidative activities as well as the immune responses to a live bivalent vaccine of Newcastle disease virus (NDV) and infectious bronchitis virus (IBV) vaccine in chickens in oxidative stress induced by cyclophosphamide (Cy). In this study, injection of Cy generated oxidative stress and lowered immune responses by reducing antioxidant enzymes such as T-AOC, T-SOD, GSH, and CAT, as well as inhibiting lymphocyte proliferation and antibody responses to vaccination.

abstract:
  The present study was designed to evaluate the effects of tea saponins on oxidative stress induced by cyclophosphamide in chickens. One hundred twenty chickens were randomly divided into 5 groups. Groups 3 to 4 received intramuscular injection of cyclophosphamide to induce oxidative stress and immunosuppression. After that, groups 2 and 4 were orally administered tea saponins in drinking water for 7 d. Then, groups 1 to 4 were immunized with a live, bivalent vaccine of Newcastle disease virus and infectious bronchitis virus. Blood samples were collected for analysis of oxidative parameters and specific antibody titers, and splenocytes were prepared for lymphocyte proliferative assay. The results showed that administration of tea saponins significantly increased total antioxidant capacity, total superoxide dismutase, catalase, glutathione peroxidase, glutathione, ascorbic acid, and α-tocopherol, and decreased malondialdehyde and protein carbonyl. Enhanced immune responses, such as lymphocyte proliferation induced by concanavalin A and lipopolysaccharides, and serum Newcastle disease virus- and infectious bronchitis virus-specific antibodies were also observed in chickens injected with or without cyclophosphamide. In addition, no side effects were found in chickens throughout the study. Therefore, tea saponins may be a potential agent to improve imunosuppression induced by oxidative stress in chickens.


id: cord-007648-tm0hn0hz
title: Envelope proteins of avian infectious bronchitis virus: Purification and biological properties
author: Mockett, A.P.Adrian
date: 2002-12-20
txt: ./txt/cord-007648-tm0hn0hz.txt
cache: ./cache/cord-007648-tm0hn0hz.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7119818/
doi: 10.1016/0166-0934(85)90138-7
summary:
  Immunoadsorbents, made with monoclonal antibodies, were used to purify the spike and membrane proteins of infectious bronchitis virus (IBV). A second inoculation of virus at 42 days induced an anamnestic antibody response to the spike and membrane proteins and also for the neutralizing antibodies. The objectives of this work were to produce immunoadsorbents using monoclonal antibodies which have been prepared previously (Mockett et al., 1984) and to purify the virus-coded proteins of the viral envelope in a single step in relatively large amounts. In addition the sequential humoral antibody response of chickens after IBV infection has been studied using the purified viral proteins and whole virus in ELISAs and compared to the results using the neutralization test. Thc chicken, about 10 days after an IBV infection, has antibodies to both the spike and membrane proteins in its serum but only very low concentrations of neutralizing antibodies.

abstract:
  Immunoadsorbents, made with monoclonal antibodies, were used to purify the spike and membrane proteins of infectious bronchitis virus (IBV). The purified proteins were inoculated into rabbits to produce antisera. The rabbit anti-spike sera neutralized the infectivity of the virus whereas the anti-membrane sera did not. IBV-infected chickens produced antibodies to both the spike and membrane proteins. Both these antibodies were at their highest concentration about 9–11 days after inoculation, whereas neutralizing antibodies were present only at very low concentrations at that time. Neutralizing antibodies were at their highest concentration 21 days after inoculation. A second inoculation of virus at 42 days induced an anamnestic antibody response to the spike and membrane proteins and also for the neutralizing antibodies. The neutralizing, anti-spike and anti-membrane antibodies all reached highest concentrations 7–11 days after this inoculation. The advantages of purifying viral proteins using affinity chromatography with monoclonal antibodies are discussed.


id: cord-009487-7xb4huyz
title: Simple rapid method of rumen cannulation
author: GODWIN, IR
date: 2008-03-10
txt: ./txt/cord-009487-7xb4huyz.txt
cache: ./cache/cord-009487-7xb4huyz.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7159126/
doi: 10.1111/j.1751-0813.1988.tb14467.x
abstract: nan
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.


id: cord-010608-eaa2znom
author: Butt, Salman L.
date: 2020-03-05
txt: ./txt/cord-010608-eaa2znom.txt
cache: ./cache/cord-010608-eaa2znom.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7201198/
doi: 10.1177/1040638720910107
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.

title:
  Real-time, MinION-based, amplicon sequencing for lineage typing of infectious bronchitis virus from upper respiratory samples

abstract:
  Infectious bronchitis (IB) causes significant economic losses in the global poultry industry. Control of IB is hindered by the genetic diversity of the causative agent, infectious bronchitis virus (IBV), which has led to the emergence of several serotypes that lack complete serologic cross-protection. Although serotyping requires immunologic characterization, genotyping is an efficient means to identify IBVs detected in samples. Sanger sequencing of the S1 subunit of the spike gene is currently used to genotype IBV; however, the universal S1 PCR was created to work from cultured IBV, and it is inefficient at detecting multiple viruses in a single sample. We describe herein a MinION-based, amplicon-based sequencing (AmpSeq) method that genetically categorized IBV from clinical samples, including samples with multiple IBVs. Total RNA was extracted from 15 tracheal scrapings and choanal cleft swab samples, randomly reverse transcribed, and PCR amplified using modified S1-targeted primers. Amplicons were barcoded to allow for pooling of samples, processed per manufacturer’s instructions into a 1D MinION sequencing library, and then sequenced on the MinION. The AmpSeq method detected IBV in 13 of 14 IBV-positive samples. AmpSeq accurately detected and genotyped both IBV lineages in 3 of 5 samples containing 2 IBV lineages. Additionally, 1 sample contained 3 IBV lineages, and AmpSeq accurately detected 2 of the 3 lineages. Strain identification, including detection of different IBVs from the same lineage, was also possible with this AmpSeq method. Our results demonstrate the feasibility of using MinION-based AmpSeq for rapid and accurate identification and lineage typing of IBV from oral swab samples.


id: cord-017894-8iahlshj
author: Loa, Chien Chang
date: 2015-09-10
txt: ./txt/cord-017894-8iahlshj.txt
cache: ./cache/cord-017894-8iahlshj.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122580/
doi: 10.1007/978-1-4939-3414-0_12
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

title:
  A Multiplex Polymerase Chain Reaction for Differential Detection of Turkey Coronavirus from Chicken Infectious Bronchitis Virus and Bovine Coronavirus

abstract:
  A multiplex polymerase chain reaction (PCR) method for differential detection of turkey coronavirus (TCoV), infectious bronchitis virus (IBV), and bovine coronavirus (BCoV) is presented in this chapter. Primers are designed from the conserved or variable regions of nucleocapsid (N) or spike (S) protein genes of TCoV, IBV, and BCoV and used in the same PCR reaction. Reverse transcription followed by PCR reaction is used to amplify a portion of N or S gene of the corresponding coronaviruses. Two PCR products, a 356-bp band corresponding to N gene and a 727-bp band corresponding to S gene, are obtained for TCoV. In contrast, one PCR product of 356 bp corresponding to a fragment of N gene is obtained for IBV strains and one PCR product of 568 bp corresponding to a fragment of S gene is obtained for BCoV.


id: cord-022187-7c3wz6c6
author: Liu, Shengwang
date: 2010-10-19
txt: ./txt/cord-022187-7c3wz6c6.txt
cache: ./cache/cord-022187-7c3wz6c6.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7154297/
doi: 10.1080/0307945042000220697
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.

title:
  A new genotype of nephropathogenic infectious bronchitis virus circulating in vaccinated and non-vaccinated flocks in China

abstract:
  Five strains of infectious bronchitis virus (IBV) were isolated from five layer flocks that had nephropathogenic infection in four provinces in China. Among them, three of the five flocks had been vaccinated against infectious bronchitis. Virulence studies indicated that the five Chinese IBV isolates caused 10 to 30% mortality in 15-day-old specific pathogen free chickens and gross lesions were mainly confined to the kidneys in all of the dead chickens. Two oligonucleotide pairs, S1Uni2 and S1Oligo3′ or S1Oligo5′ and S1Oligo3′, were used after propagation of the isolates in embryonated eggs to amplify the S1 protein genes of the spike protein. The cDNA derived by reverse transcriptase-polymerase chain reaction was cloned and sequenced. The nucleotide and amino acid sequence of S1 protein gene had a similar degree of identity (≥92%) among the five Chinese IBV isolates. The nucleotide and amino acid identity of the S1 protein gene between the five Chinese IBV isolates and 16 strains of other IBVs varied from 60 to 81%. This clearly showed that the five Chinese IBV isolates comprised a separate genotype. These results demonstrated, for the first time, that there is a new genotype of nephropathogenic IBV circulating in vaccinated and non-vaccinated flocks in China.


id: cord-022378-ovxmy1as
title: Coronaviridae
author: Cook, Jane K.A.
date: 2009-05-15
txt: ./txt/cord-022378-ovxmy1as.txt
cache: ./cache/cord-022378-ovxmy1as.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155630/
doi: 10.1016/b978-0-7020-2862-5.50033-7
abstract: nan
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.


id: cord-252048-ftbjsoup
author: McKinley, Enid T.
date: 2011-04-22
txt: ./txt/cord-252048-ftbjsoup.txt
cache: ./cache/cord-252048-ftbjsoup.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.virusres.2011.04.006
doi: 10.1016/j.virusres.2011.04.006
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.

title:
  Attenuated live vaccine usage affects accurate measures of virus diversity and mutation rates in avian coronavirus infectious bronchitis virus

abstract:
  The full-length genomes of 11 infectious bronchitis virus (IBV) field isolates from three different types of the virus; Massachusetts (Mass), Connecticut (Conn) and California (CAL) isolated over a 41, 25 and 8 year period respectively, were sequenced and analyzed to determine the mutation rates and level of polymorphisms across the genome. Positive selection was not detected and mutation rates ranged from 10(−4) to 10(−6) substitutions/site/year for Mass and Conn IBV types where attenuated live vaccines are routinely used to control the disease. In contrast, for CAL type viruses, for which no vaccine exists, positive selection was detected and mutation rates were 10 fold higher ranging from 10(−2) to 10(−3) substitutions/site/year. Lower levels of genetic diversity among the Mass and Conn viruses as well as sequence similarities with vaccine virus genomes suggest that the origin of the Mass and all but one of the Conn viruses was likely vaccine virus that had been circulating in the field for an unknown but apparently short period of time. The genetic data also identified a recombinant IBV isolate with 7 breakpoints distributed across the entire genome suggesting that viruses within the same serotype can have a high degree of genetic variability outside of the spike gene. These data are important because inaccurate measures of genetic diversity and mutation rates could lead to underestimates of the ability of IBV to change and potentially emerge to cause disease.


id: cord-253695-tjdw2uta
title: Infection of the tracheal epithelium by infectious bronchitis virus is sialic acid dependent
author: Winter, Christine
date: 2007-12-28
txt: ./txt/cord-253695-tjdw2uta.txt
cache: ./cache/cord-253695-tjdw2uta.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/18396435/
doi: 10.1016/j.micinf.2007.12.009
summary:
  Avian Infectious bronchitis virus (IBV) is a coronavirus that infects chickens via the respiratory epithelium as primary target cells. Here we analyze the importance of the sialic acid binding activity for the infection of tracheal organ cultures (TOCs) by different IBV strains. Desialylation induced by neuraminidase treatment of tracheal organ cultures prior to infection by IBV delayed the ciliostatic effect or resulted in partial loss of ciliary activity. After having shown recently that sialic acid serves as a receptor determinant for IBV on cultured cells, we were interested to find out whether this type of sugar is also important for an infection in vivo. From this result we conclude that a2,3-linked sialic acid serves as a receptor determinant for the infection of avian tracheal epithelial cells by the Beaudette strain of IBV. Sialic acid is a receptor determinant for infection of cells by avian Infectious bronchitis virus

abstract:
  Avian Infectious bronchitis virus (IBV) is a coronavirus that infects chickens via the respiratory epithelium as primary target cells. The binding of coronaviruses to the cell surface is mediated by the viral surface protein S. Recently we demonstrated that α2,3-linked sialic acid serves as a receptor determinant for IBV on Vero cells and primary chicken embryo kidney cells. Here we analyze the importance of the sialic acid binding activity for the infection of tracheal organ cultures (TOCs) by different IBV strains. Our results show that α2,3-linked sialic acid also serves as a receptor determinant on chicken TOCs. Infection of TOCs by IBV results in ciliostasis. Desialylation induced by neuraminidase treatment of tracheal organ cultures prior to infection by IBV delayed the ciliostatic effect or resulted in partial loss of ciliary activity. This effect was observed with both respiratory and nephropathogenic strains. Inhibition of ciliostasis was also observed when TOCs were pretreated with an α2,3-specific neuraminidase. Analysis of the tracheal epithelium for reactivity with lectins revealed that the susceptible cells in the epithelium abundantly express α2,3-linked sialic acid. These results indicate that α2,3-linked sialic acid plays an important role for infection of the respiratory epithelium by IBV.


id: cord-255141-55ho9av4
title: Genomic and single nucleotide polymorphism analysis of infectious bronchitis coronavirus
author: Abolnik, Celia
date: 2015-04-03
txt: ./txt/cord-255141-55ho9av4.txt
cache: ./cache/cord-255141-55ho9av4.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S1567134815001185
doi: 10.1016/j.meegid.2015.03.033
summary:
  A QX-like strain was analysed by high-throughput Illumina sequencing and genetic variation across the entire viral genome was explored at the sub-consensus level by single nucleotide polymorphism (SNP) analysis. The E and 3b protein products play key roles in coronavirus virulence, and RNA folding demonstrated that the mutations in the 5′UTR did not alter the predicted secondary structure. Coronavirus accessory proteins are generally dispensable for virus replication, but they play vital roles in virulence and pathogenesis by affecting host innate immune responses, encoding pro-or anti-apoptotic activities, or by effecting other signalling pathways that influence disease outcomes (Susan & Julian, 2011) . Mapping of the receptor-binding domain and amino acids critical for attachment in the spike protein of avian coronavirus infectious bronchitis virus Analysis of a QX-like avian infectious bronchitis virus genome identified recombination in the region containing the ORF 5a, ORF 5b, and nucleocapsid protein gene sequences

abstract:
  Infectious bronchitis virus (IBV) is a Gammacoronavirus that causes a highly contagious respiratory disease in chickens. A QX-like strain was analysed by high-throughput Illumina sequencing and genetic variation across the entire viral genome was explored at the sub-consensus level by single nucleotide polymorphism (SNP) analysis. Thirteen open reading frames (ORFs) in the order 5′-UTR-1a-1ab-S-3a-3b-E-M-4b-4c-5a-5b-N-6b-3′UTR were predicted. The relative frequencies of missense: silent SNPs were calculated to obtain a comparative measure of variability in specific genes. The most variable ORFs in descending order were E, 3b, 5′UTR, N, 1a, S, 1ab, M, 4c, 5a, 6b. The E and 3b protein products play key roles in coronavirus virulence, and RNA folding demonstrated that the mutations in the 5′UTR did not alter the predicted secondary structure. The frequency of SNPs in the Spike (S) protein ORF of 0.67% was below the genomic average of 0.76%. Only three SNPS were identified in the S1 subunit, none of which were located in hypervariable region (HVR) 1 or HVR2. The S2 subunit was considerably more variable containing 87% of the polymorphisms detected across the entire S protein. The S2 subunit also contained a previously unreported multi-A insertion site and a stretch of four consecutive mutated amino acids, which mapped to the stalk region of the spike protein. Template-based protein structure modelling produced the first theoretical model of the IBV spike monomer. Given the lack of diversity observed at the sub-consensus level, the tenet that the HVRs in the S1 subunit are very tolerant of amino acid changes produced by genetic drift is questioned.


id: cord-255619-5h3l6nh6
author: Kuo, Shu-Ming
date: 2013-03-23
txt: ./txt/cord-255619-5h3l6nh6.txt
cache: ./cache/cord-255619-5h3l6nh6.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0378113512005597
doi: 10.1016/j.vetmic.2012.10.020
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) .

title:
  Evolution of infectious bronchitis virus in Taiwan: Positively selected sites in the nucleocapsid protein and their effects on RNA-binding activity

abstract:
  RNA recombination has been shown to underlie the sporadic emergence of new variants of coronavirus, including the infectious bronchitis virus (IBV), a highly contagious avian pathogen. We have demonstrated that RNA recombination can give rise to a new viral population, supported by the finding that most isolated Taiwanese (TW) IBVs, similar to Chinese (CH) IBVs, exhibit a genetic rearrangement with the American (US) IBV at the 5’ end of the nucleocapsid (N) gene. Here, we further show that positive selection has occurred at two sites within the putative crossover region of the N-terminal domain (NTD) of the TW IBV N protein. Based on the crystal structure of the NTD, the stereographic positions of both predicted selected sites do not fall close to the RNA-binding groove. Surprisingly, converting either of the two residues to the amino acid present in most CH IBVs resulted in significantly reduced affinity of the N protein for the synthetic RNA repeats of the viral transcriptional regulatory sequence. These results suggest that modulating the amino acid residue at either selected site may alter the conformation of the N protein and affect the viral RNA–N interaction. This study illustrates that the N protein of the current TW IBV variant has been shaped by both RNA recombination and positive selection and that the latter may promote viral survival and fitness, potentially by increasing the RNA-binding capacity of the N protein.


id: cord-255870-gmq5zs2d
title: Identification of the avian infectious bronchitis coronaviruses with mutations in gene 3
author: Liu, Shengwang
date: 2008-04-15
txt: ./txt/cord-255870-gmq5zs2d.txt
cache: ./cache/cord-255870-gmq5zs2d.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S037811190800005X
doi: 10.1016/j.gene.2008.01.004
summary:
  All the IBV field and vaccine strains were propagated once in 9 to 11-day-old embryonated chicken-specific pathogen-free (SPF) eggs (Harbin Veterinary Research Institute, China) and confirmed using negative contrast electronic microscopy (JEM-1200, EX) in the allantoic fluids of inoculated eggs as described previously (Liu and Kong, 2004) , before being used in sequence analysis. Each of the nine 9-day-old SPF chicken embryos was inoculated with the isolates CK/CH/LLN/98, CK/CH/LSD/03I, CK/CH/LJL/04I, CK/CH/LDL/97I, and CK/CH/LGD/04II passage level 3 (the latter 3 virus strains, each representing different IBV serotypes in China, were used as controls) with 10 2 EID 50 per embryo in 0.1 ml inoculum into the allantoic cavity. This mutation resulted in the virus lacking ORF 3a and changed the primary structure of the 3′-encoding regions of CK/CH/LLN/98I, leading to a novel genomic organization of the avian coronavirus that had the S-3b-3c-M-5a-5b-N gene order from the 5′-end to the 3′-end, instead of the typical gene order in the 3′-encoding regions of group 3 coronaviruses isolated from chicken (IBV) (Boursnell et al., 1987) , turkey (Breslin et al., 1999; Cavanagh et al., 2001; Lin et al., 2002) , and pheasants (Cavanagh et al., 2002) .

abstract:
  The sequence of a 6.0-kb fragment was compared in the 3′-encoding region of the genome in 27 infectious bronchitis virus (IBV) strains. All these strains have the same S-3-M-5-N gene order, as is the case for other IBVs. However, the sizes of the corresponding open reading frames (ORFs) of some genes varied among the virus strains. Phylogenetic analysis and sequence alignments demonstrated that recombination events had occurred in the origin and evolution of the strains CK/CH/LSD/03I and CK/CH/LLN/98I and the possible recombinant junction sites might be located at the 3c and M genes, respectively. The normal product of ORF 3a is 57 amino acids long, whereas a 43-bp deletion at the 3′-end of the CK/CH/LSD/03I 3a gene was detected, resulting in a frameshift event and C-terminally truncated protein with 47 amino acids. Comparison of the growth ability in embryos and replication and pathogenicity in chickens with IBV carrying the normal 3a gene indicated that this deleted sequence in the 3a gene of CK/CH/LSD/03I was not necessary for viral pathogenesis and replication either in vitro or in vivo. Occurrence of a mutation at the corresponding position of the CK/CH/LLN/98I start codon in the 3a gene led to the absence of ORF 3a in this virus, resulting in a novel genomic organization at the 3′-encoding regions: S-3b, 3c-M-5a, 5b-N. Comparison with other viruses carrying the normal 3a gene revealed that CK/CH/LLN/98I had replication and pathogenicity abilities in vivo similar to those of other IBVs; however, its growth ability in embryos was lower, although the relationship between the lower growth ability and the ORF 3a defect requires further confirmation.


id: cord-256444-grw5s2pf
title: The Molecular Biology of Coronaviruses
author: Lai, Michael M.C.
date: 1997-12-31
txt: ./txt/cord-256444-grw5s2pf.txt
cache: ./cache/cord-256444-grw5s2pf.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0065352708602869
doi: 10.1016/s0065-3527(08)60286-9
summary:
  Publisher Summary This chapter discusses the manipulation of clones of coronavirus and of complementary DNAs (cDNAs) of defective-interfering (DI) RNAs to study coronavirus RNA replication, transcription, recombination, processing and transport of proteins, virion assembly, identification of cell receptors for coronaviruses, and processing of the polymerase. This decade has seen the manipulation of these clones, and of complementary DNAs (cDNAs) of defective-interfering (DI) RNAs, to study coronavirus RNA replication, transcription, recombination, processing and transport of proteins, virion assembly, identification of cell receptors for coronaviruses, and processing of the polymerase. The species and tissue specificity of a coronavirus infection is a t least partially dictated by the nature and distribution of cellular receptors and other related molecules that regulate virus entry, as evidenced by the viral replication that results when viral RNA is directly introduced into cell types of other animal species.

abstract:
  Publisher Summary This chapter discusses the manipulation of clones of coronavirus and of complementary DNAs (cDNAs) of defective-interfering (DI) RNAs to study coronavirus RNA replication, transcription, recombination, processing and transport of proteins, virion assembly, identification of cell receptors for coronaviruses, and processing of the polymerase. The nature of the coronavirus genome is nonsegmented, single-stranded, and positive-sense RNA. Its size ranges from 27 to 32 kb, which is significantly larger when compared with other RNA viruses. The gene encoding the large surface glycoprotein is up to 4.4 kb, encoding an imposing trimeric, highly glycosylated protein. This soars some 20 nm above the virion envelope, giving the virus the appearance-with a little imagination-of a crown or coronet. Coronavirus research has contributed to the understanding of many aspects of molecular biology in general, such as the mechanism of RNA synthesis, translational control, and protein transport and processing. It remains a treasure capable of generating unexpected insights.


id: cord-256859-7ixegm72
author: Liu, S. W.
date: 2006-01-09
txt: ./txt/cord-256859-7ixegm72.txt
cache: ./cache/cord-256859-7ixegm72.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/16397751/
doi: 10.1007/s00705-005-0695-6
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.

title:
  Genetic diversity of avian infectious bronchitis coronavirus strains isolated in China between 1995 and 2004

abstract:
  Twenty-six avian infectious bronchitis (IB) viruses (IBV) were isolated from outbreaks in chickens in China between 1995 and 2004. They were characterized by comparison with twenty-six Chinese reference strains and five other IBV strains. Chinese IBVs, which were mainly nephropathogenic, were placed into seven genotypes. Fourteen Chinese IBV isolates were placed in genotype I, having small evolutionary distances from each other. Genotype II included 6 strains that were isolated in the 1990s in China. Genotype III consisted of eight Chinese isolates that showed close relationship with Korean IBV isolates. Another eight IBV isolates clustered in genotype IV and showed larger evolutionary distances. The Massachusetts serotype was present in China in 1990s and was in a separate genotype. Two isolates, HN99 and CK/CH/LHN/00I, which might be a reisolation of vaccine strains, clustered into genotype VI. Four Chinese IBV isolates formed another genotype and showed larger evolutionary distances from other Chinese IBV genotypes (genotype VII). IBVs in same genotypes showed more than 90% amino acid sequence similarities, whereas most of the viruses in different genotypes showed less than 90%. The results showed that IBVs in China came from genetic changes both in IBV populations that existed before the advent of vaccination and in the viruses that were introduced through live vaccines. IBVs showing various genetic differences are cocirculating in China.


id: cord-257064-iafm3pcc
title: Quantification of Infectious Bronchitis Coronavirus by Titration In Vitro and In Ovo
author: Kint, Joeri
date: 2014-12-18
txt: ./txt/cord-257064-iafm3pcc.txt
cache: ./cache/cord-257064-iafm3pcc.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/978-1-4939-2438-7_9
doi: 10.1007/978-1-4939-2438-7_9
summary:
  During a titration assay, tissue cultures or embryonated eggs are incubated with tenfold serial dilutions of a virus containing sample and several days later the cytopathic effect is scored. The virus titer is defined as the reciprocal of the dilution at which 50 % of the inoculated embryos or tissue cultures show CPE. Passaging of IBV in either embryonated eggs or primary cell cultures leads to attenuation of the virus in vivo [10] [11] [12] . IBV strains which have been adapted to grow in cultures of primary chicken cells can be titrated on these cells using either the TCID 50 method or plaque titration. Virus titers in the original sample, expressed as 10 log EID 50 /ml are calculated using the method described by Spearman and Kaerber [6, 7] , using the following formula: Plaque formation by infectious bronchitis virus in chicken embryo kidney cell cultures Growth kinetics of embryo-and organ-culture adapted Beaudette strain of infectious bronchitis virus in embryonated chicken eggs

abstract:
  Quantification of the number of infectious viruses in a sample is a basic virological technique. In this chapter we provide a detailed description of three techniques to estimate the number of viable infectious avian coronaviruses in a sample. All three techniques are serial dilution assays, better known as titrations.


id: cord-257999-apg4uhhq
title: Presence of Infectious Bronchitis Virus Strain CK/CH/LDL/97I in the Middle East
author: Ababneh, Mustafa
date: 2012-04-11
txt: ./txt/cord-257999-apg4uhhq.txt
cache: ./cache/cord-257999-apg4uhhq.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.5402/2012/201721
doi: 10.5402/2012/201721
summary:
  The sequenced fragment of the S1 gene of the CK/CH/LDL/97I strain had less than 80% nucleotide identity to the IBV vaccine strains commonly used in the Middle East (M41 and H120). In this study, the CK/CH/LDL/97I-like strains were isolated from three different Middle Eastern countries (Jordan, Saudi Arabia, and Iraq) in 2011. Pathogenicity of a QX strain of infectious bronchitis virus in specific pathogen free and commercial broiler chickens, and evaluation of protection induced by a vaccination programme based on the Ma5 and 4/91 serotypes Phylogenetic analysis of infectious bronchitis coronaviruses newly isolated in China, and pathogenicity and evaluation of protection induced by Massachusetts serotype H120 vaccine against QX-like strains Evaluation of the protection conferred by commercial vaccines and attenuated heterologous isolates in China against the CK/CH/LDL/97I strain of infectious bronchitis coronavirus Characterization of three infectious bronchitis virus isolates from China associated with proventriculus in vaccinated chickens

abstract:
  Infectious bronchitis virus (IBV) is a very dynamic and evolving virus, causing major economic losses to the global poultry industry. In early 2011, respiratory disease outbreaks were investigated in Iraq, Jordan, and Saudi Arabia. Five IBV isolates (JOA2, JOA4, Saudi-1, Saudi-2, and Iraqi IBV) were detected by diagnostic-nested nucleocapsid RT-PCR. Strain identification was characterised by sequencing and phylogenetic analysis of the amplified hypervariable region of the spike 1 (S1) gene. These five IBV isolates were found to be of the IBV strain CK/CH/LDL/97I. Nucleotide identity between these five IBV isolates ranged from 96.9% to 99.7%, and between these isolates and the CK/CH/LDL/97I strain in the range of 96.6–99.1%. The sequenced fragment of the S1 gene of the CK/CH/LDL/97I strain had less than 80% nucleotide identity to the IBV vaccine strains commonly used in the Middle East (M41 and H120). The presence of these CK/CH/LDL/97I-like strains may account for vaccination failure against IBV, since all IBV isolates were from vaccinated chickens. In this paper, we documented for the first time the presence of IBV strain CK/CH/LDL/97I in the Middle East. This strain is known to have originated in China and Taiwan.


id: cord-258379-v3lceirh
title: Association of the infectious bronchitis virus 3c protein with the virion envelope
author: Liu, D. X.
date: 1991-12-31
txt: ./txt/cord-258379-v3lceirh.txt
cache: ./cache/cord-258379-v3lceirh.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/1962461/
doi: 10.1016/0042-6822(91)90572-s
summary:
  There was considerably less evidence of contaminating cellular proteins in this gradient, and the relative proportion of the 12K protein to the other virion proteins appeared similar to that observed at the previous stage in purification, strongly supporting the idea of a specific association between the 12K protein and virus particles. In order to establish the identity of the 12K polypeptide as the product of the 3c gene, and to examine the possibility that IBV virions might contain other new virus polypeptides in amounts too small to detect directly, we next carried out immunoprecipitation experiments using monospecific antisera directed against the predicted products of the 3a, 3b, 3c, 5a, and 5b ORFs (17, 18, 23) . Messenger RNA 4 of mouse hepatitis virus (MHV) is known to encode a 15K polypeptide, the predicted amino acid sequence of which contains a highly hydrophobic region from residues 8 to 41 (9, 22) , although the protein has not so far been found in virions.

abstract:
  Abstract A highly purified radiolabeled preparation of the coronavirus infectious bronchitis virus (IBV) was analyzed, by immunoprecipitation with monospecific antisera, for the presence of a series of small virus proteins recently identified as the products of I BV mRNAs 3 and 5. One of these, 3c, a 12.4K protein encoded by the third open reading frame of the tricistronic mRNA3 was clearly detectable and was found to cofractionate with virion envelope proteins on detergent disruption of virus particles. These results, together with the hydrophobic nature of 3c and its previously demonstrated association with the membranes of infected cells, suggest strongly that 3c represents a new virion envelope protein, which may have counterparts in other coronaviruses.


id: cord-259480-1tqfoecc
author: Li, Huixin
date: 2016-03-02
txt: ./txt/cord-259480-1tqfoecc.txt
cache: ./cache/cord-259480-1tqfoecc.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.antiviral.2016.03.003
doi: 10.1016/j.antiviral.2016.03.003
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).

title:
  Recombinant duck enteritis viruses expressing major structural proteins of the infectious bronchitis virus provide protection against infectious bronchitis in chickens

abstract:
  To design an alternative vaccine for control of infectious bronchitis in chickens, three recombinant duck enteritis viruses (rDEVs) expressing the N, S, or S1 protein of infectious bronchitis virus (IBV) were constructed using conventional homologous recombination methods, and were designated as rDEV-N, rDEV-S, and rDEV-S1, respectively. Chickens were divided into five vaccinated groups, which were each immunized with one of the rDEVs, covalent vaccination with rDEV-N & rDEV-S, or covalent vaccination with rDEV-N & rDEV-S1, and a control group. An antibody response against IBV was detectable and the ratio of CD4(+)/CD8(+) T-lymphocytes decreased at 7 days post-vaccination in each vaccinated group, suggesting that humoral and cellular responses were elicited in each group as early as 7 days post-immunization. After challenge with a homologous virulent IBV strain at 21 days post-immunization, vaccinated groups showed significant differences in the percentage of birds with clinical signs, as compared to the control group (p < 0.01), as the two covalent-vaccination groups and the rDEV-S group provided better protection than the rDEV-N- or rDEV-S1-vaccinated group. There was less viral shedding in the rDEV-N & rDEV-S- (2/10) and rDEV-N & rDEV-S1- (2/10) vaccinated groups than the other three vaccinated groups. Based on the clinical signs, viral shedding, and mortality rates, rDEV-N & rDEV-S1 covalent vaccination conferred better protection than use of any of the single rDEVs.


id: cord-259505-7hiss0j3
title: Proteomic analysis of purified coronavirus infectious bronchitis virus particles
author: Kong, Qingming
date: 2010-06-09
txt: ./txt/cord-259505-7hiss0j3.txt
cache: ./cache/cord-259505-7hiss0j3.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/20534109/
doi: 10.1186/1477-5956-8-29
summary:
  It is an important prerequisite for the functional studies to know the protein composition of the purified viral particles, as it allows the analysis of specific proteins and their roles during the virus life cycle, resulting in better understanding of the infection process and the pathogenesis of viruses. To date, there have been no reports about TENP associated with virus, but it''s an enriched and abundant protein identified in purified infectious bronchitis particles which suggests to us that it may be a requisite host protein in IBV life cycles. The present study 1) provides the first proteomic analysis of infectious bronchitis particles, 2) establishes the most comprehensive proteomic index of IBV and 3) shows that most of the virion incorporated host proteins have central roles in virus life cycle.

abstract:
  BACKGROUND: Infectious bronchitis virus (IBV) is the coronavirus of domestic chickens causing major economic losses to the poultry industry. Because of the complexity of the IBV life cycle and the small number of viral structural proteins, important virus-host relationships likely remain to be discovered. Toward this goal, we performed two-dimensional gel electrophoresis fractionation coupled to mass spectrometry identification approaches to perform a comprehensive proteomic analysis of purified IBV particles. RESULTS: Apart from the virus-encoded structural proteins, we detected 60 host proteins in the purified virions which can be grouped into several functional categories including intracellular trafficking proteins (20%), molecular chaperone (18%), macromolcular biosynthesis proteins (17%), cytoskeletal proteins (15%), signal transport proteins (15%), protein degradation (8%), chromosome associated proteins (2%), ribosomal proteins (2%), and other function proteins (3%). Interestingly, 21 of the total host proteins have not been reported to be present in virions of other virus families, such as major vault protein, TENP protein, ovalbumin, and scavenger receptor protein. Following identification of the host proteins by proteomic methods, the presence of 4 proteins in the purified IBV preparation was verified by western blotting and immunogold labeling detection. CONCLUSIONS: The results present the first standard proteomic profile of IBV and may facilitate the understanding of the pathogenic mechanisms.


id: cord-259738-yuqc6dk0
author: Tang, Mengjun
date: 2008-03-07
txt: ./txt/cord-259738-yuqc6dk0.txt
cache: ./cache/cord-259738-yuqc6dk0.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/18329109/
doi: 10.1016/j.jviromet.2008.01.017
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

title:
  Enhancement of the immunogenicity of an infectious bronchitis virus DNA vaccine by a bicistronic plasmid encoding nucleocapsid protein and interleukin-2

abstract:
  A DNA vaccine against infectious bronchitis virus (IBV) can induce specific humoral and cell-mediated immunity. However, compared to conventional vaccines, DNA vaccines usually induce poor antibody responses. To develop a more potent IBV DNA vaccine formulations, a monocistronic vector encoding the nucleocapsid protein of IBV and a bicistronic vector separately encoding the nucleocapsid protein and immune-stimulatory interleukin-2 were constructed. When the DNA vaccines were administered to the quadriceps muscle of chickens, the induced humoral and cellular responses were evaluated. There was a significant difference in ELISA antibody levels elicited by either monocistronic or bicistronic DNA vaccines. The percentage of CD3(+), CD3(+)CD8(+) and CD3(+)CD4(+) subgroups of peripheral blood T-lymphocytes in chickens immunized with bicistronic DNA vaccine were higher than those in chickens immunized with monocistronic DNA vaccine. When chickens were challenged with a virulent strain of IBV, the protective efficacy could be enhanced significantly after immunization with bicistronic DNA vaccine. These results demonstrated that bicistronic DNA vaccine is an effective approach to increase IBV DNA vaccine immunogenicity.


id: cord-259959-qzd3hf8y
author: Alhatami, Abdullah O.
date: 2020-07-16
txt: ./txt/cord-259959-qzd3hf8y.txt
cache: ./cache/cord-259959-qzd3hf8y.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32848311/
doi: 10.14202/vetworld.2020.1358-1362
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.

title:
  Sequencing and phylogenetic analysis of infectious bronchitis virus variant strain from an outbreak in egg-layer flocks in Baghdad, Iraq

abstract:
  BACKGROUND AND AIM: Infectious bronchitis (IB) has an influential economic impact on the poultry industry, causing huge losses each year due to the condemnation of infected chickens. Despite the use of many kinds of vaccines in Iraq, it is common to find IB problems in vaccinated chickens. Information about the strains that affect Iraqi chickens is very limited. Therefore, we aimed to detect the currently circulating strains of IB virus that cause frequent outbreaks in egg layers despite the use of vaccination against the virus. MATERIALS AND METHODS: Isolate detection, sequencing, and phylogenetic analysis were performed using a rapid IB virus antigen kit (32 tracheal swabs), flinders technology associates (FTA) card (32 tracheal swabs), and partial gene sequencing (16 positive FTA samples). RESULTS: The isolated strain was different from other strains, especially the strain isolated in the North of Iraq (Sulemania Strain) and shares 98% homology with an Israeli strain (Israel variant 2, IS 1494). CONCLUSION: Although more studies are needed to detect IB virus strains circulating in Iraq, this work lays the foundation for making a good strategy to control the disease and selecting vaccines that should be used in farms.


id: cord-260042-cs0wp99n
author: Khan, Samiullah
date: 2019-04-01
txt: ./txt/cord-260042-cs0wp99n.txt
cache: ./cache/cord-260042-cs0wp99n.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/s12860-019-0190-7
doi: 10.1186/s12860-019-0190-7
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.

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

abstract:
  BACKGROUND: Egg formation takes place in the oviduct of laying hens over a 24 h period. Infectious bronchitis virus (IBV) causes pathological lesions in the chicken oviduct. In the current study, mitochondrial counts were determined in three different segments of the oviduct during egg formation in laying chickens challenged with IBV T strain. Nuclear DNA encoded genes that are involved in mitochondrial biogenesis, fission and function were studied in the shell gland of the oviduct undergoing virus multiplication. RESULTS: In the shell gland, the mitochondrial count was significantly lower (P < 0.05) in the challenged group, compared with the control group. However, it did not vary in response to IBV challenge in the isthmus and magnum regions of the oviduct. The gene succinate dehydrogenase complex, subunit A, flavoprotein variant (SDHA) was down-regulated in the shell gland by IBV challenge (P < 0.05), while other genes being studied did not show responses to the challenge (P > 0.05). Differential expression of the genes was observed at different time-points of egg-shell formation. The expression levels of citrate synthase (CS), cytochrome C, somatic (CYC, S) and sodium-potassium adenosine triphosphatase (Na(+)-K(+)ATPase) genes were significantly higher, while those of SDHA and dynamin related protein 1 (Drp1) genes were significantly lower, at 15 h compared with 5 h following oviposition of the previous egg. The expression level of peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α) did not show significant change at different time-points. CONCLUSIONS: It was concluded that IBV T strain infection in laying hens reduced mitochondrial counts only in the shell gland region of the oviduct. The genes involved in mitochondrial biogenesis or function may not show synchronised responses to that of mitochondria in the shell gland of chickens under T strain of IBV challenge.


id: cord-260145-grz0fe9l
author: Liu, Shengwang
date: 2009-07-23
txt: ./txt/cord-260145-grz0fe9l.txt
cache: ./cache/cord-260145-grz0fe9l.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.vaccine.2009.05.072
doi: 10.1016/j.vaccine.2009.05.072
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] .

title:
  Altered pathogenicity, immunogenicity, tissue tropism and 3′-7 kb region sequence of an avian infectious bronchitis coronavirus strain after serial passage in embryos

abstract:
  In this study, we attenuated a Chinese LX4-type nephropathogenic infectious bronchitis virus (IBV) strain, CK/CH/LHLJ/04V, by serial passage in embryonated chicken eggs. Based on sequence analysis of the 3′-7 kb region, the CK/CH/LHLJ/04V virus population contained subpopulations with a mixture of genetic mutants. The titers of the virus increased gradually during serial passage, but the replication capacity decreased in chickens. The virus was partially attenuated at passage 40 (P40) and P70, and was fully attenuated at P110. It lost immunogenicity and kidney tropism at P110 and P70, respectively. Amino acid substitutions were found in the 3′-7 kb region, primarily in the spike (S) protein. Substitutions in the S1 subunit occurred between P3 and P40 and all subpopulations in a virus passage showed the same substitutions. Other substitutions that occurred between P70 and P110, however, were found only in some subpopulations of the virus passages. A 109-bp deletion in the 3′-UTR was observed in most subpopulations of P70 and P110, and might be related to virus replication, transcription and pathogenicity. The changes described in the 3′-7 kb region of the virus are possibly responsible for virus attenuation, immunogenicity decrease and tissue tropism changes; however, we cannot exclude the possibility that other parts of the genome may also be involved in those changes.


id: cord-260667-5aurua6o
author: Falchieri, Marco
date: 2013-05-24
txt: ./txt/cord-260667-5aurua6o.txt
cache: ./cache/cord-260667-5aurua6o.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.vaccine.2013.03.055
doi: 10.1016/j.vaccine.2013.03.055
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

title:
  Avian metapneumoviruses expressing Infectious Bronchitis virus genes are stable and induce protection

abstract:
  The study investigates the ability of subtype A Avian metapneumovirus (AMPV) to accept foreign genes and be used as a vector for delivery of Infectious bronchitis virus (IBV) QX genes to chickens. Initially the GFP gene was added to AMPV at all gene junctions in conjunction with the development of cassetted full length DNA AMPV copies. After recombinant virus had been recovered by reverse genetics, GFP positions supporting gene expression while maintaining virus viability in vitro, were determined. Subsequently, either S1 or nucleocapsid (N) genes of IBV were positioned between AMPV M and F genes, while later a bivalent recombinant was prepared by inserting S1 and N at AMPV MF and GL junctions respectively. Immunofluorescent antibody staining showed that all recombinants expressed the inserted IBV genes in vitro and furthermore, all recombinant viruses were found to be highly stable during serial passage. Eyedrop inoculation of chickens with some AMPV-IBV recombinants at one-day-old induced protection against virulent IBV QX challenge 3 weeks later, as assessed by greater motility of tracheal cilia from chickens receiving the recombinants. Nonetheless evidence of AMPV/IBV seroconversion, or major recombinant tracheal replication, were largely absent.


id: cord-260799-kx6hfpu0
author: Mahmood, Zana H.
date: 2011-05-12
txt: ./txt/cord-260799-kx6hfpu0.txt
cache: ./cache/cord-260799-kx6hfpu0.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0378113510005882
doi: 10.1016/j.vetmic.2010.12.015
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.

title:
  Isolation and molecular characterization of Sul/01/09 avian infectious bronchitis virus, indicates the emergence of a new genotype in the Middle East

abstract:
  Infectious bronchitis virus (IBV) was isolated from trachea and kidney tissues of eight broiler farms in Kurdistan region of North Iraq from 2008 to 2010. The birds were suffering from respiratory and nephropathological symptoms and lesions. A 1116 bp hyper mutable spike glycoprotein (S1) gene was amplified and sequenced using conventional RT-PCR. Sequence analysis and BLAST homology search in GenBank data base indicate that two of the farms were infected with the 4/91 strain, one with an unidentified IBV and five were infected with Sul/01/09. The birds in the latter five farms were suffering from nephropathogenic lesions, however, the virus was isolated from kidney but not from trachea in these cases. The birds were vaccinated regularly with 4/91 or MA5 vaccine. The deduced amino acid sequence of the isolated and amplified S1 subunit (372 aa) of Sul/01/09 was differed in 27–28% from that of all three vaccine strains (4/91, MA5, and H120) used in the region. This dissimilarity is most likely the cause of poor efficacy of vaccines used in the region, at least in five of these farms. Amino acid sequence comparison and phylogenetic tree analysis with other published IBV genotypes indicate that this newly isolated virus together with other regionally related and recently published isolates from Israel (IS/720/99, IS/885) and Egypt (egypt/Benisuef/01) belong to a new genotype. This is the first report of identification and genotyping of IBV isolate in Iraq, which indicate the circulation of 4/91 along with a new variant (Sul/01/09) of IBV in vaccinated broiler farms.


id: cord-261388-d56ci0hl
author: Tibbles, K.W
date: 1999-05-28
txt: ./txt/cord-261388-d56ci0hl.txt
cache: ./cache/cord-261388-d56ci0hl.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0168170299000118
doi: 10.1016/s0168-1702(99)00011-8
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

title:
  Activity of a purified His-tagged 3C-like proteinase from the coronavirus infectious bronchitis virus

abstract:
  Previous studies in vitro of the processing of cloned polyprotein fragments from the coronavirus infectious bronchitis virus (IBV) large open reading frame (ORF1), confirmed the activity of a predicted 3C-like proteinase (3CLP) domain and suggested that the proteinase is released autocatalytically from the polyprotein in the form of a 35 kDa protein, 3CLpro, capable of further cleavages in trans. In order to identify such cleavages within the ORF1 polyprotein mediated by 3CLpro, the proteinase was expressed in bacteria, purified and used in trans cleavage assays with polyprotein fragments lacking the 3CLP domain as targets. The proteinase was expressed as a polyprotein fragment which was able to process during expression in bacterial cells, releasing mature 3CLpro. A histidine (His(6)) tag was introduced close to the C-terminus of the proteinase to aid purification. Processing demonstrated by the tagged proteinase was indistinguishable from that of the wild-type enzyme indicating that the site chosen for the tag was permissive. From these studies we were able to demonstrate trans cleavages consistent with the use of most of the previously predicted or identified sites within the open reading frame of gene 1. This tentatively completes the processing map for the ORF1 region with respect to 3CLpro.


id: cord-262226-7kwkla73
author: Fang, Shouguo
date: 2013-07-09
txt: ./txt/cord-262226-7kwkla73.txt
cache: ./cache/cord-262226-7kwkla73.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0042682213003632
doi: 10.1016/j.virol.2013.06.014
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) .

title:
  Identification of two ATR-dependent phosphorylation sites on coronavirus nucleocapsid protein with nonessential functions in viral replication and infectivity in cultured cells

abstract:
  Coronavirus encodes an extensively phosphorylated and highly basic nucleocapsid (N) protein. Previous studies have identified Ser190, Ser192, Thr378 and Ser379 as the phosphorylation sites for coronavirus infectious bronchitis virus (IBV) N protein. In this study, we show that phosphorylation at Thr378 and Ser379 sites is dependent on the ataxia-telangiectasia mutated (ATM) and Rad3-related (ATR), a kinase activated during IBV replication. Introduction of Ala substitutions at these two sites individually, in combination of the two and together with other two sites (Ser190 and Ser192) into an infectious IBV clone did not affect recovery of the recombinant viruses containing the mutations. A mutant virus (rIBV-Nm4) carrying the four Ala substitutions grew at a similar, if not better, growth rate as wild type virus. This study reveals a cellular kinase responsible for phosphorylation of a coronavirus N protein at two positions and the functional consequence of this modification on coronavirus replication.


id: cord-262940-eyejnexx
author: Liu, Genmei
date: 2013-11-12
txt: ./txt/cord-262940-eyejnexx.txt
cache: ./cache/cord-262940-eyejnexx.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0264410X13012656
doi: 10.1016/j.vaccine.2013.09.024
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.

title:
  Assembly and immunogenicity of coronavirus-like particles carrying infectious bronchitis virus M and S proteins

abstract:
  Infectious bronchitis virus (IBV) as an avian coronavirus is still posing a persistent and imminent threat to the poultry industry worldwide. Here we report that transfection of Sf9 cells with a single recombinant baculovirus encoding M and S proteins resulted in the assembly of IBV VLPs; this is the first report that S protein plus M protein alone were able to be assembled into VLPs for coronaviruses. We further showed that the generated IBV VLPs could induce humoral immune responses in a level comparable to that of inactivated IBV vaccine, and more importantly the IBV VLPs could elicit significantly higher cellular immune responses than the inactivated IBV vaccine. In summary, the assembly of IBV VLPs with M and S proteins provided a simple strategy for generating VLPs for coronaviruses, and the generated IBV VLPs laid a feasible foundation for the development of an effective vaccine against infection of IBV in the future.


id: cord-263178-lvxxdvas
author: Shan, Dan
date: 2018-05-02
txt: ./txt/cord-263178-lvxxdvas.txt
cache: ./cache/cord-263178-lvxxdvas.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0168170217309103
doi: 10.1016/j.virusres.2018.04.013
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.

title:
  Effects of hypervariable regions in spike protein on pathogenicity, tropism, and serotypes of infectious bronchitis virus

abstract:
  To study the roles of hypervariable regions (HVRs) in receptor-binding subunit S1 of the spike protein, we manipulated the genome of the IBV Beaudette strain using a reverse genetics system to construct seven recombinant strains by separately or simultaneously replacing the three HVRs of the Beaudette strain with the corresponding fragments from a QX-like nephropathogenic isolate ck/CH/LDL/091022 from China. We characterized the growth properties of these recombinant IBVs in Vero cells and embryonated eggs, and their pathogenicity, tropism, and serotypes in specific pathogen-free (SPF) chickens. All seven recombinant IBVs proliferated in Vero cells, but the heterogenous HVRs could reduce their capacity for adsorption during in vitro infection. The recombinant IBVs did not significantly increase the pathogenicity compared with the Beaudette strain in SPF chickens, and they still shared the same serotype as the Beaudette strain, but the antigenic relatedness values between the recombinant strain and Beaudette strain generally decreased with the increase in the number of the HVRs exchanged. The results of this study demonstrate the functions of HVRs and they may help to develop a vaccine candidate, as well as providing insights into the prevention and control of IBV.


id: cord-263193-paeosfiu
title: Infectious bronchitis virus inhibits activation of the TLR7 pathway, but not the TLR3 pathway
author: Zhu, Jinyan
date: 2020-06-10
txt: ./txt/cord-263193-paeosfiu.txt
cache: ./cache/cord-263193-paeosfiu.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32524263/
doi: 10.1007/s00705-020-04690-8
summary:
  Here, primary chicken embryo kidney (CEK) cells and specific-pathogen-free (SPF) chickens were infected with three pathogenic IBV strains, and it was observed that the TLR7-MYD88 pathway was inhibited but the TLR3-TIRF pathway was activated. To investigate the effect of innate immune molecules, agonists of TLR3, TLR7, and MDA5 and inhibitors of key molecules of the TLR3 pathway were added to CEK cells that had grown to 80-90% as instructed by the reagent manufacturer (InvivoGen, CA, USA) as follows: 5 μg of imiquimod (a TLR7 agonist) per mL for 12 h, 10 μg of low-molecular-weight (LMW) polyinosinic-polycytidylic acid (poly(I:C)) (a TLR3 agonist) per mL for 12 h, 0.5 μg of poly (I:C)-LMW/LyoVec (an MDA5 agonist) per mL for 12 h, 10 μM Pepinh-TRIF (a TRIF inhibitor) for 6 h, 5 μM celastrol (an NF-κB inhibitor) for 1 h, 50 μM chloroquine (an inhibitor of endosomal acidification) for 0.5 h, and 5 μM BX795 (a TBK1 inhibitor) for 6 h.

abstract:
  Various strains of infectious bronchitis virus (IBV) cause different forms of infectious bronchitis with different clinical signs. Here, primary chicken embryo kidney (CEK) cells and specific-pathogen-free (SPF) chickens were infected with three pathogenic IBV strains, and it was observed that the TLR7-MYD88 pathway was inhibited but the TLR3-TIRF pathway was activated. After treatment with poly(I:C)-LMW, poly (I:C)-LMW/LyoVec, and Imiquimod, the replication of IBV was significantly suppressed after 24 h. However, treatment with TLR3 pathway inhibitors such as Pepinh-TRIF, celastrol, chloroquine, and BX795 resulted in increased replication of IBV after 36 h. These results also showed that chloroquine and celastrol were most effective inhibitors of the antiviral response at 48 hpi.


id: cord-263476-ju7xqwa7
author: Xia, Jing
date: 2016-08-13
txt: ./txt/cord-263476-ju7xqwa7.txt
cache: ./cache/cord-263476-ju7xqwa7.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/27530216/
doi: 10.1016/j.meegid.2016.08.011
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.

title:
  Phylogenetic and antigenic analysis of avian infectious bronchitis virus in southwestern China, 2012–2016

abstract:
  The aim of this study was to decipher the molecular epidemiological and antigenic characteristics of infectious bronchitis virus strains (IBVs) isolated in recent years in southwestern China. A total of 24 field strains were isolated from diseased chickens between 2012 and 2016. Phylogenetic analysis based on S1 nucleotide sequences showed that 16 of the 24 isolates were clustered into four distinct genotypes: QX (37.5%), TW (16.7%, TWI and TWII), Mass (8.3%), and J2 (4.2%). The QX genotype was still the prevalent genotype in southwestern China. Recombination analysis of the S1 subunit gene showed that eight of the 24 field strains were recombinant variants that originated from field strains and vaccine strains. A new potential recombination hotspot [ATTTT(T/A)] was identified, implying that recombination events may become more and more common. The antigenicity of ten IBVs, including seven field strains and commonly used vaccine strains, were assayed with a viral cross-neutralization assay in chicken embryonated kidney cells (CEK). The results showed that the ten IBVs could be divided into four serotypes (Massachusetts, 793B, Sczy3, and SCYB). Sczy3 and 793B were the predominant serotypes. Six of the seven field isolates (all except for cK/CH/SCYB/140913) cross-reacted well with anti-sera against other field strains. In conclusion, the genetic and antigenic features of IBVs from southwestern China in recent years have changed when compared to the previous reports. The results could provide a reference for vaccine development and the prevention of infectious bronchitis in southwestern China.


id: cord-263785-0iift8zy
author: Zhang, Xiaorong
date: 2020-07-31
txt: ./txt/cord-263785-0iift8zy.txt
cache: ./cache/cord-263785-0iift8zy.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32736651/
doi: 10.1186/s13567-020-00819-4
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.

title:
  Evaluation of the reproductive system development and egg-laying performance of hens infected with TW I-type infectious bronchitis virus

abstract:
  The prevalence of TW I-type infectious bronchitis virus (IBV) has been increasing rapidly, and it has become the second most common genotype of IBV in China threatening the poultry industry. In this study, 1-day-old specific-pathogen-free (SPF) chickens infected with TW I-type IBV were continuously observed for 200 days. TW I-type IBV affected the respiratory, urinary, and female reproductive systems, resulting in a mortality rate of 10% as well as a decrease in egg quantity and an increase in inferior eggs. During the monitoring period, serious lesions occurred in the female reproductive system, such as yolk peritonitis, a shortened oviduct, and cysts of different sizes with effusion in the degenerated right oviduct. The infective viruses persisted in vivo for a long time, and due to the stress of laying, virus shedding was detected again after the onset of egg production. Our findings suggest that TW I-type IBV is deadly to chickens and could cause permanent damage to the oviduct, resulting in the poor laying performance of female survivors and decreasing the breeding value and welfare of the infected flock.


id: cord-264716-igl25jhg
author: Koo, B.S.
date: 2013-11-01
txt: ./txt/cord-264716-igl25jhg.txt
cache: ./cache/cord-264716-igl25jhg.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3382/ps.2013-03280
doi: 10.3382/ps.2013-03280
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.

title:
  Molecular survey of enteric viruses in commercial chicken farms in Korea with a history of enteritis

abstract:
  Several enteric viruses have increasingly received attention as potential causative agents of runting-stunting syndrome (RSS) in chickens. A molecular survey was performed to determine the presence of a broad range of enteric viruses, namely chicken astrovirus (CAstV), avian nephritis virus (ANV), chicken parvovirus (ChPV), infectious bronchitis virus (IBV), avian rotavirus (AvRV), avian reovirus (ARV), and fowl adenovirus (FAdV), in intestinal samples derived from 34 commercial chicken flocks that experienced enteritis outbreaks between 2010 and 2012. Using techniques such as PCR and reverse-transcription PCR, enteric viruses were identified in a total of 85.3% of investigated commercial chicken flocks in Korea. Furthermore, diverse combinations of 2 or more enteric viruses were simultaneously identified in 51.7% of chicken farms positive for enteric viruses. The rank order of positivity for enteric viruses was as follows: ANV (44.1%), CAstV (38.2%), ChPV (26.5%), IBV (20.6%), ARV (8.8%), AvRV (5.9%), and FAdV (2.9%). Additionally, other pathogens such as Escherichia coli, Salmonella spp., Eimeria spp., and FAdV were detected in 79% of chicken flocks positive for enteric viruses using PCR, bacterial isolation, and microscopic examination. The results of our study indicate the presence of several enteric viruses with various combinations in commercial chicken farms that experienced enteritis outbreaks. Experimental studies are required to further understand the roles of enteric viruses in RSS in commercial chickens.


id: cord-265258-2rmtsyns
title: Specific detection of GII‐1 lineage of infectious bronchitis virus
author: Domanska‐Blicharz, K.
date: 2017-07-03
txt: ./txt/cord-265258-2rmtsyns.txt
cache: ./cache/cord-265258-2rmtsyns.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/28493279/
doi: 10.1111/lam.12753
summary:
  The real-time RT-PCR assays seem to be effective tools for IBV-type identification and although S1 coding region is prone to mutations, methods aimed in this gene detection has been recently developed and used for GI-1 (Mass, Connecticut), GI-9 (Arkansas), GI-11 (SAI), G1-16 (ASAII) and GIV-1 (DE072/GA98) lineages (Acevedo et al. Here, we describe the development of a TaqMan probe-based real-time RT-PCR for the detection of GII-1 (D1466-like) IBV lineage. Moreover, the assay developed in the present study showed to be highly specific as no fluorescent signals were detected with other tested IBV lineages or chicken RNA viral pathogens. In conclusion, the TaqMan probe-based real-time RT-PCR assay described here is a time-saving, specific, sensitive and reliable method of detection of GII-1 lineage (D1466-like) of IBV which could successfully replace standard nested RT-PCR. Development and evaluation of a real-time Taqman RT-PCR assay for the detection of infectious bronchitis virus from infected chickens

abstract:
  Infectious bronchitis virus (IBV) is a worldwide prevalent RNA virus that causes highly contagious and economically devastating disease in chicken. The virus exists in many different genetic forms which made the disease control very difficult. The present study describes the development and validation of TaqMan probe‐based real‐time reverse transcription‐polymerase chain reaction (real‐time RT‐PCR) targeting the S1 coding region of S gene characteristic for the GII‐1 lineage (formerly the D1466‐like variant) of IBV. These strains are quite different from other European IBV belonging to different lineages of the GI genotype. The developed method was 30‐fold more sensitive than used so far for standard nested RT‐PCR with detection limit of 56 RNA copies per reaction. The specificity of the assay was also evaluated with a panel of different poultry pathogens. Repeatability and reproducibility of the method was very high with coefficients of variation lower than 4%. One hundred and twenty‐seven IBV‐positive samples were tested by this method and GII‐1 strains were detected in four of them (3·15%) which indicate a decrease in the GII‐1 IBV prevalence in Poland. The assay was proven to be a valuable tool for rapid diagnosis of GII‐1 lineage of IBV strains and moreover it enabled the monitoring of viral loads which can be used to assess disease progression. SIGNIFICANCE AND IMPACT OF THE STUDY: This study reports a TaqMan probe‐based real‐time reverse transcription‐polymerase chain reaction (real‐time RT‐PCR) for rapid and accurate identification of GII‐1 lineage (formerly D1466‐like variant) of infectious bronchitis virus (IBV). The assay revealed to be more sensitive than standard nested RT‐PCR assay, previously used for this purpose. The developed assay has been tested on numerous field samples and revealed 3·15% prevalence of this lineage of IBV in Polish chicken population. Moreover, this new assay enables the assessment of viral load measurement which might be useful for epidemiology and pathogenesis studies.


id: cord-265499-pbf11zy1
author: Dove, Brian K.
date: 2006-03-03
txt: ./txt/cord-265499-pbf11zy1.txt
cache: ./cache/cord-265499-pbf11zy1.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/16819967/
doi: 10.1111/j.1462-5822.2006.00698.x
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) .

title:
  Changes in nucleolar morphology and proteins during infection with the coronavirus infectious bronchitis virus

abstract:
  The nucleolus is a dynamic subnuclear structure involved in ribosome subunit biogenesis, cell cycle control and mediating responses to cell stress, among other functions. While many different viruses target proteins to the nucleolus and recruit nucleolar proteins to facilitate virus replication, the effect of infection on the nucleolus in terms of morphology and protein content is unknown. Previously we have shown that the coronavirus nucleocapsid protein will localize to the nucleolus. In this study, using the avian infectious bronchitis coronavirus, we have shown that virus infection results in a number of changes to the nucleolus both in terms of gross morphology and protein content. Using confocal microscopy coupled with fluorescent labelled nucleolar marker proteins we observed changes in the morphology of the nucleolus including an enlarged fibrillar centre. We found that the tumour suppressor protein, p53, which localizes normally to the nucleus and nucleolus, was redistributed predominately to the cytoplasm.


id: cord-265508-t1nfyzf5
title: Sequencing of coronavirus IBV genomic RNA: a 195-base open reading frame encoded by mRNA B
author: Boursnell, M.E.G.
date: 1984-08-31
txt: ./txt/cord-265508-t1nfyzf5.txt
cache: ./cache/cord-265508-t1nfyzf5.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/6092234/
doi: 10.1016/0378-1119(84)90169-0
summary:
  authors: Boursnell, M.E.G.; Brown, T.D.K. title: Sequencing of coronavirus IBV genomic RNA: a 195-base open reading frame encoded by mRNA B Abstract DNA sequencing of genomic cDNA clones of avian infectious bronchitis virus (IBV) has been carried out. The organisation of the messenger RNAs and in vitro translation studies have led to the hypothesis that the 5''-most sequences of each mRNA, which are not present in the next smallest mRNA, contain the complete coding sequences for the major protein product produced by that messenger species (Stern and Kennedy, 1980b; Lai et al., 1981) . In this paper we report the nucleotide sequence of a cloned cDNA copy of IBV genomic RNA in the region corresponding to the 5'' end of mRNA B. The region of the IBV sequence presented in this paper contains the 5'' ends, on the viral genome, of mRNAs A and B.

abstract:
  Abstract DNA sequencing of genomic cDNA clones of avian infectious bronchitis virus (IBV) has been carried out. 770 bases have been determined which include genomic sequences spanning the 5' termini of the two smallest mRNAs of the 3'-coterminal “nested” set: mRNA A and mRNA B. This region contains the complete coding sequences for mRNA B which are additional to those present in mRNA A. Two open reading frames are present, predicting proteins of M rs 7500 and 9500.


id: cord-265681-ab8j4o1u
author: Boroomand, Zahra
date: 2012-04-01
txt: ./txt/cord-265681-ab8j4o1u.txt
cache: ./cache/cord-265681-ab8j4o1u.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1100/2012/402537
doi: 10.1100/2012/402537
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

title:
  Pathogenesis and Tissue Distribution of Avian Infectious Bronchitis Virus Isolate IRFIBV32 (793/B Serotype) in Experimentally Infected Broiler Chickens

abstract:
  Infectious bronchitis (IB) is one of the most important viral diseases of poultry. The aim of this study was to investigate the distribution of avian infectious bronchitis virus isolate IRFIBV32 (793/B serotype) in experimentally infected chicken. Ninety-one-day-old commercial broilers were divided randomly into two groups (seventy in the experimental and twenty in the control group). Chicks in the experimental group were inoculated intranasally with 10(5) ELD50/0.1 mL of the virus at three weeks of age. The samples from various tissues were collected at1, 2, 3, 5, 7, 11, 13, 15, and 20 days postinoculation. Chickens exhibited mild respiratory signs and depression. Viral RNA was detected in the kidney, lung and tracheas on days 1 to 13 PI, in the oviduct between, days 3 and 13, in testes between days 1 and 11 PI, and in the caecal tonsil consistently up to day 20 PI. The most remarkable clinical signs and virus detection appeared on day 1 PI. Data indicated that the number of infected chickens and viral RNA detection from tissues was reduced with increasing antibody titer on day 20 PI. The results demonstrated that the IRFIBV32 virus has wide tissue distribution for respiratory, urogenital, and digestive systems.


id: cord-266585-jfjrk9gy
author: Fang, Shouguo
date: 2007-02-05
txt: ./txt/cord-266585-jfjrk9gy.txt
cache: ./cache/cord-266585-jfjrk9gy.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0042682206005745
doi: 10.1016/j.virol.2006.08.020
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.

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

abstract:
  Genetic manipulation of the RNA genomes by reverse genetics is a powerful tool to study the molecular biology and pathogenesis of RNA viruses. During construction of an infectious clone from a Vero cell-adapted coronavirus infectious bronchitis virus (IBV), we found that a G–C point mutation at nucleotide position 15526, causing Arg-to-Pro mutation at amino acid position 132 of the helicase protein, is lethal to the infectivity of IBV on Vero cells. When the in vitro-synthesized full-length transcripts containing this mutation were introduced into Vero cells, no infectious virus was rescued. Upon correction of the mutation, infectious virus was recovered. Further characterization of the in vitro-synthesized full-length transcripts containing the G15526C mutation demonstrated that this mutation may block the transcription of subgenomic RNAs. Substitution mutation of the Arg132 residue to a positively charged amino acid Lys affected neither the infectivity of the in vitro-synthesized transcripts nor the growth properties of the rescued virus. However, mutation of the Arg132 residue to Leu, a conserved residue in other coronaviruses at the same position, reduced the recovery rate of the in vitro-synthesized transcripts. The recovered mutant virus showed much smaller-sized plaques. On the contrary, a G–C and a G–A point mutations at nucleotide positions 4330 and 9230, respectively, causing Glu–Gln and Gly–Glu mutations in or near the catalytic centers of the papain-like (Nsp3) and 3C-like (Nsp5) proteinases, did not show detectable detrimental effect on the rescue of infectious viruses and the infectivity of the rescued viruses.


id: cord-268454-w4qca90s
author: Rim, Aouini
date: 2019-06-17
url: https://www.sciencedirect.com/science/article/pii/S0147957119301109
doi: 10.1016/j.cimid.2019.06.004
title:
  Viral interference between H9N2-low pathogenic avian influenza virus and avian infectious bronchitis virus vaccine strain H120 in vivo

abstract:
  The interaction between a low pathogenic avian influenza virus (A/CK/TUN/145/2012), a H9N2 Tunisian isolate, and a vaccine strain (H120) of avian infectious bronchitis, administered simultaneously or sequentially three days apart to chicks during 20 days, was evaluated using ELISA antibody levels, quantitative reverse transcription–polymerase chain reaction (qRT-PCR) analyses and histopathology examination. First, the in vivo replication interference of avian influenza virus (AIV) and infectious bronchitis virus (IBV) was evaluated using qRT-PCR to detect accurately either AIV or IBV genomes or viral copy numbers during dual infections. Second, we have determined the amount of specific antibodies in sera of chick’s infected with AIV alone, IBV alone, mixed AIV + IBV, IBV then AIV or AIV IBV 3 days later using an ELISA test. Finally, histopathological analyses of internal organs from inoculated chicks were realized. Quantitative results of AIV and IBV co-infection showed that interferences between the two viruses yielded decreased viral growth. However, in the case of super-infection, the second virus, either AIV or IBV, induced a decrease in the growth of the first inoculated virus. According to our results, vaccine application was safe and do not interfere with AIV H9N2 infection, and does not enhance such infection. In conclusion, co-infection of chicks with AIV and IBV, simultaneously or sequentially, affected the clinical signs, the virus replication dynamics as well as the internal organ integrity. The results proposed that infection with heterologous virus may result in temporary competition for cell receptors or competent cells for replication, most likely interferon-mediated.


id: cord-268788-jcu3pasy
title: Recombination in Avian Gamma-Coronavirus Infectious Bronchitis Virus
author: Thor, Sharmi W.
date: 2011-09-23
txt: ./txt/cord-268788-jcu3pasy.txt
cache: ./cache/cord-268788-jcu3pasy.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3390/v3091777
doi: 10.3390/v3091777
summary:
  In this study, the full-length genomes of eight avian gamma-coronavirus infectious bronchitis virus (IBV) isolates were sequenced and along with other full-length IBV genomes available from GenBank were analyzed for recombination. In this study we sequenced and analyzed the entire genome of eight IBV strains that represent different serotypes that have not been previously sequenced, and we compared these sequences with other gamma-coronavirus full-length genome sequences available in GenBank for evidence of recombination [16] . A phylogenetic compatibility matrix constructed at the 70% bootstrap level for 250 bp sequence fragments at 100 bp intervals also showed that recombination breakpoints were distributed throughout the IBV genomes (data not shown). Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus Complete genome sequence and recombination analysis of infectious bronchitis virus attenuated vaccine strain H120

abstract:
  Recombination in the family Coronaviridae has been well documented and is thought to be a contributing factor in the emergence and evolution of different coronaviral genotypes as well as different species of coronavirus. However, there are limited data available on the frequency and extent of recombination in coronaviruses in nature and particularly for the avian gamma-coronaviruses where only recently the emergence of a turkey coronavirus has been attributed solely to recombination. In this study, the full-length genomes of eight avian gamma-coronavirus infectious bronchitis virus (IBV) isolates were sequenced and along with other full-length IBV genomes available from GenBank were analyzed for recombination. Evidence of recombination was found in every sequence analyzed and was distributed throughout the entire genome. Areas that have the highest occurrence of recombination are located in regions of the genome that code for nonstructural proteins 2, 3 and 16, and the structural spike glycoprotein. The extent of the recombination observed, suggests that this may be one of the principal mechanisms for generating genetic and antigenic diversity within IBV. These data indicate that reticulate evolutionary change due to recombination in IBV, likely plays a major role in the origin and adaptation of the virus leading to new genetic types and strains of the virus.


id: cord-269024-re0hyolh
author: Bande, Faruku
date: 2016-09-07
txt: ./txt/cord-269024-re0hyolh.txt
cache: ./cache/cord-269024-re0hyolh.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1155/2016/5484972
doi: 10.1155/2016/5484972
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

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

abstract:
  Bioinformatic analysis was used to predict antigenic B-cell and T-cell epitopes within the S1 glycoprotein of M41 and CR88 IBV strains. A conserved linear B-cell epitope peptide, YTSNETTDVTS(175–185), was identified in M41 IBV strains while three such epitopes types namely, VSNASPNSGGVD(279–290), HPKCNFRPENI(328–338), and NETNNAGSVSDCTAGT(54–69), were predicted in CR88 IBV strains. Analysis of MHCI binding peptides in M41 IBV strains revealed the presence of 15 antigenic peptides out of which 12 were highly conserved in 96–100% of the total M41 strains analysed. Interestingly three of these peptides, GGPITYKVM(208), WFNSLSVSI(356), and YLADAGLAI(472), relatively had high antigenicity index (>1.0). On the other hand, 11 MHCI binding epitope peptides were identified in CR88 IBV strains. Of these, five peptides were found to be highly conserved with a range between 90% and 97%. However, WFNSLSVSL(358), SYNISAASV(88), and YNISAASVA(89) peptides comparably showed high antigenicity scores (>1.0). Combination of antigenic B-cells and T-cells peptides that are conserved across many strains as approach to evoke humoral and CTL immune response will potentially lead to a broad-based vaccine that could reduce the challenges in using live attenuated vaccine technology in the control of IBV infection in poultry.


id: cord-269150-d1sgnxc0
author: Tan, Yong Wah
date: 2012-02-22
txt: ./txt/cord-269150-d1sgnxc0.txt
cache: ./cache/cord-269150-d1sgnxc0.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/nar/gks165
doi: 10.1093/nar/gks165
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.

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

abstract:
  Coronaviruses RNA synthesis occurs in the cytoplasm and is regulated by host cell proteins. In a screen based on a yeast three-hybrid system using the 5′-untranslated region (5′-UTR) of SARS coronavirus (SARS-CoV) RNA as bait against a human cDNA library derived from HeLa cells, we found a positive candidate cellular protein, zinc finger CCHC-type and RNA-binding motif 1 (MADP1), to be able to interact with this region of the SARS-CoV genome. This interaction was subsequently confirmed in coronavirus infectious bronchitis virus (IBV). The specificity of the interaction between MADP1 and the 5′-UTR of IBV was investigated and confirmed by using an RNA pull-down assay. The RNA-binding domain was mapped to the N-terminal region of MADP1 and the protein binding sequence to stem–loop I of IBV 5′-UTR. MADP1 was found to be translocated to the cytoplasm and partially co-localized with the viral replicase/transcriptase complexes (RTCs) in IBV-infected cells, deviating from its usual nuclear localization in a normal cell using indirect immunofluorescence. Using small interfering RNA (siRNA) against MADP1, defective viral RNA synthesis was observed in the knockdown cells, therefore indicating the importance of the protein in coronaviral RNA synthesis.


id: cord-271359-dpa8zzc3
title: Novel Variation in the N Protein of Avian Infectious Bronchitis Virus
author: Sapats, S. I.
date: 1996-12-15
txt: ./txt/cord-271359-dpa8zzc3.txt
cache: ./cache/cord-271359-dpa8zzc3.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0042682296906704
doi: 10.1006/viro.1996.0670
summary:
  Despite the considerable variation observed between the two virus groups, all N proteins contained a high proportion of basic residues, 80% of which were conserved in position. The N protein of all coronaviruses virus lacks a sequence of 184-196 nucleotides that has is overall very basic and in IBV contains 409 amino acids been detected in five other IBV strains. located downstream of the HVR (315 nucleotides ending The N protein of 27 strains of IBV isolated over a period at the poly(A) tail) is highly conserved in strains of IBV, of 60 years from diverse locations such as the U.S.A., the probably indicative of its role in the synthesis of negative-UK, Holland, Saudi Arabia, and Japan has been shown to strand RNA. For each virus two or more for the N proteins of IBV also contain a region of complete independent cDNA clones were sequenced using the conservation between positions 242 and 296 (4).

abstract:
  Abstract The nucleocapsid protein of coronaviruses has been considered highly conserved, showing greater than 94% conservation within strains of a given species. We determined the nucleotide sequence of the N gene and the 3′ untranslated region (UTR) of eight naturally occurring strains of IBV which differed in pathogenicity and tissue tropism. In pairwise comparisons, the deduced amino acid sequences of N of five strains Vic S, N1/62, N9/74, N2/75, and V5/90 (group I) shared 92.3–98.8% identity. The three strains N1/88, Q3/88, and V18/91 (group II) shared 85.8–89.2% identity with each other, but only 60.0–63.3% identity with viruses of group I. Amino acid substitutions, deletions, and insertions occurred throughout the N protein and involved regions previously identified as being conserved. Despite the considerable variation observed between the two virus groups, all N proteins contained a high proportion of basic residues, 80% of which were conserved in position. In addition, all strains contained approximately 30 serine residues of which 10 were conserved, the majority occurring between positions 168 and 194. As for all other coronaviruses, the region between positions 92 and 103 was highly conserved. Hence, a large number of amino acid changes can be tolerated within the N protein without affecting its integrity or functioning. The 3′ UTR immediately downstream from the N gene was highly heterogeneous with extensive deletions occurring in the group II strains.


id: cord-271568-qgpi2kcs
author: Jackwood, M.W.
date: 2010-01-21
url: https://doi.org/10.1016/j.virusres.2010.01.006
doi: 10.1016/j.virusres.2010.01.006
title:
  Avian coronavirus infectious bronchitis virus susceptibility to botanical oleoresins and essential oils in vitro and in vivo

abstract:
  Anti-coronaviral activity of a mixture of oleoresins and essential oils from botanicals, designated QR448(a), was examined in vitro and in vivo. Treatment of avian infectious bronchitis virus (IBV) with QR448(a) reduced the virus titer as measured in two laboratory host systems, Vero E6 cells and embryonating eggs. The effect of QR448(a) on IBV in chickens was also investigated. Administering QR448(a) to chickens at a 1:20 dilution by spray, 2 h before challenge with IBV was determined to be the most effective treatment. Treatment decreased the severity of clinical signs and lesions in the birds, and lowered the amount of viral RNA in the trachea. Treatment with QR448(a) protected chickens for up to 4 days post-treatment from clinical signs of disease (but not from infection) and decreased transmission of IBV over a 14-day period. Anti-IBV activity of QR448(a) was greater prior to virus attachment and entry indicating that the effect is virucidal. In addition, QR448(a) had activity against both Massachusetts and Arkansas type IB viruses, indicating that it can be expected to be effective against IBV regardless of serotype. To our knowledge, this is the first report on the in vivo use of a virucidal mixture of compounds effective against the coronavirus IBV.


id: cord-271897-9oqzsd70
title: Molecular epidemiology of infectious bronchitis virus in Poland from 1980 to 2017
author: Domanska-Blicharz, Katarzyna
date: 2020-01-07
url: https://www.ncbi.nlm.nih.gov/pubmed/31917362/
doi: 10.1016/j.meegid.2020.104177
abstract:
  The presence of infectious bronchitis virus (IBV) was identified for the first time in the poultry population in Poland at the end of the 1960s. From this time a few waves of epidemics caused by different IBV variants spread across the country. In order to gain more insight into the molecular epidemiology of IBV in Poland, in the present study the S1 coding region of 34 IBV isolates and nearly whole genome of 10 strains collected over a period of 38 years was characterized. Phylogenetic analysis showed that these strains belonged to five recently established IBV lineages: GI-1, GI-12, GI-13, GI-19 and GI-23. Additionally, two strains from 1989 and 1997 formed a separate branch of the phylogenetic tree categorized as unique early Polish variants, and one strain was revealed to be the recombinant of these and GI-1 lineage viruses. Irrespective of year of isolation and S1-dependent genotype, the genome sequences of Polish IBV strains showed the presence of six genes and 13 ORFs: 5′UTR-1a-1b-S-3a-3b-E-M-4b-4c-5a-5b-N-6b-3′UTR, however their individual genes and putative proteins had different lengths. The phylogenetic analyses performed on the genome of ten Polish IBV strains revealed that they cluster into different groups. The Polish GI-1, GI-19 and GI-23 strains cluster with other similar viruses of these lineages, with the exception of the two strains from 1989 and 1997 which are different. It seems that in Poland in the 1980s and 1990s IBV strains with a unique genome backbone circulated in the field, which were then replaced by other strains belonging to other IBV lineages with a genome backbone specific to these lineages. The recombination analysis showed that some Polish strains resulted from a recombination event involving different IBV lineages, most frequently GI-13 and GI-19.


id: cord-272305-eniovfwy
author: Zhao, Ye
date: 2015-10-22
txt: ./txt/cord-272305-eniovfwy.txt
cache: ./cache/cord-272305-eniovfwy.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.vetmic.2015.07.036
doi: 10.1016/j.vetmic.2015.07.036
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

title:
  Safety and efficacy of an attenuated Chinese QX-like infectious bronchitis virus strain as a candidate vaccine

abstract:
  Infectious bronchitis (IB) is a highly contagious respiratory and urogenital disease of chickens caused by infectious bronchitis virus (IBV). This disease is of considerable economic importance and is primarily controlled through biosecurity and immunization with live attenuated and inactivated IB vaccines of various serotypes. In the present study, we tested the safety and efficacy of an attenuated predominant Chinese QX-like IBV strain. The results revealed that the attenuated strain has a clear decrease in pathogenicity for specific-pathogen-free (SPF) chickens compared with the parent strain. Strain YN-inoculated birds had clinical signs of varying severity with 30% mortality, while the attenuated group appeared healthy, with less tissue damage. The attenuated strain also had relatively low tissue replication rates and higher antibody levels. The superior protective efficacy of the attenuated strain was observed when vaccinated birds were challenged with a homologous or heterologous field IBV strain, indicating the potential of the attenuated YN (aYN) as a vaccine. Producing a vaccine targeting the abundant serotype in China is essential to reducing the economic impact of IB on the poultry industry.


id: cord-272437-gvzfl8c3
author: Zhao, Jing
date: 2020-08-20
txt: ./txt/cord-272437-gvzfl8c3.txt
cache: ./cache/cord-272437-gvzfl8c3.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0042682220301628
doi: 10.1016/j.virol.2020.08.009
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

title:
  Replicase 1a gene plays a critical role in pathogenesis of avian coronavirus infectious bronchitis virus

abstract:
  Avian coronavirus infectious bronchitis virus (IBV) is an important pathogen threatening poultry production worldwide. Here, two recombinant IBVs (rYN-1a-aYN and rYN-1b-aYN) were generated in which ORF1a or ORF1b of the virulent YN genome were replaced by the corresponding regions from the attenuated strain aYN. The pathogenicity and virulence of rIBVs were evaluated in ovo and in vivo. The results revealed that mutations in the ORF1a gene during passage in embryonated eggs caused the decreased pathogenicity of virulent IBV YN strain, proven by determination of virus replication in ECEs and CEK cells, the observation of clinical signs, gross lesions, microscopic lesions, tracheal ciliary activity and virus distribution in chickens following exposure to rIBVs. However, mutations in ORF1b had no obvious effect on virus replication in both ECEs and CEK cells, or pathogenicity in chickens. Our findings demonstrate that the replicase 1a gene of avian coronavirus IBV is a determinant of pathogenicity.


id: cord-272666-3uidpr79
title: Infectious Bronchitis Virus Nonstructural Protein 4 Alone Induces Membrane Pairing
author: Doyle, Nicole
date: 2018-09-06
url: https://doi.org/10.3390/v10090477
doi: 10.3390/v10090477
abstract:
  Positive-strand RNA viruses, such as coronaviruses, induce cellular membrane rearrangements during replication to form replication organelles allowing for efficient viral RNA synthesis. Infectious bronchitis virus (IBV), a pathogenic avian Gammacoronavirus of significant importance to the global poultry industry, has been shown to induce the formation of double membrane vesicles (DMVs), zippered endoplasmic reticulum (zER) and tethered vesicles, known as spherules. These membrane rearrangements are virally induced; however, it remains unclear which viral proteins are responsible. In this study, membrane rearrangements induced when expressing viral non-structural proteins (nsps) from two different strains of IBV were compared. Three non-structural transmembrane proteins, nsp3, nsp4, and nsp6, were expressed in cells singularly or in combination and the effects on cellular membranes investigated using electron microscopy and electron tomography. In contrast to previously studied coronaviruses, IBV nsp4 alone is necessary and sufficient to induce membrane pairing; however, expression of the transmembrane proteins together was not sufficient to fully recapitulate DMVs. This indicates that although nsp4 is able to singularly induce membrane pairing, further viral or host factors are required in order to fully assemble IBV replicative structures. This study highlights further differences in the mechanism of membrane rearrangements between members of the coronavirus family.


id: cord-272693-432ixb7g
author: Phillips, J. E.
date: 2011-09-10
txt: ./txt/cord-272693-432ixb7g.txt
cache: ./cache/cord-272693-432ixb7g.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/21909766/
doi: 10.1007/s11262-011-0668-7
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.

title:
  Changes in nonstructural protein 3 are associated with attenuation in avian coronavirus infectious bronchitis virus

abstract:
  Full-length genome sequencing of pathogenic and attenuated (for chickens) avian coronavirus infectious bronchitis virus (IBV) strains of the same serotype was conducted to identify genetic differences between the pathotypes. Analysis of the consensus full-length genome for three different IBV serotypes (Ark, GA98, and Mass41) showed that passage in embryonated eggs, to attenuate the viruses for chickens, resulted in 34.75–43.66% of all the amino acid changes occurring in nsp 3 within a virus type, whereas changes in the spike glycoprotein, thought to be the most variable protein in IBV, ranged from 5.8 to 13.4% of all changes. The attenuated viruses did not cause any clinical signs of disease and had lower replication rates than the pathogenic viruses of the same serotype in chickens. However, both attenuated and pathogenic viruses of the same serotype replicated similarly in embryonated eggs, suggesting that mutations in nsp 3, which is involved in replication of the virus, might play an important role in the reduced replication observed in chickens leading to the attenuated phenotype. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11262-011-0668-7) contains supplementary material, which is available to authorized users.


id: cord-273366-xd84f8ct
title: Infectious Bronchitis Virus Regulates Cellular Stress Granule Signaling
author: Brownsword, Matthew J.
date: 2020-05-14
txt: ./txt/cord-273366-xd84f8ct.txt
cache: ./cache/cord-273366-xd84f8ct.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32422883/
doi: 10.3390/v12050536
summary:
  Interestingly, we found that IBV is able to inhibit multiple cellular stress granule signaling pathways, whilst at the same time, IBV replication also results in the induction of seemingly canonical stress granules in a proportion of infected cells. Moreover, IBV infection uncouples translational repression and stress granule formation and both processes are independent of eIF2α phosphorylation. Vero cells were infected with IBV and at the indicated time points, cells were fixed and labelled with anti-dsRNA to detect virus infection and with anti-G3BP1 to detect SG. Following identification of SG in IBV infected cells, the requirement for active virus replication in induction of granules was assessed. At 24 hpi, cells were fixed and labelled with anti-G3BP1 (red) to detect stress granules (SG) and IBV infected cells were detected with an anti-dsRNA antibody (green). Junin virus infection impairs stress-granule formation in Vero cells treated with arsenite via inhibition of eIF2alpha phosphorylation

abstract:
  Viruses must hijack cellular translation machinery to express viral genes. In many cases, this is impeded by cellular stress responses. These stress responses result in the global inhibition of translation and the storage of stalled mRNAs, into RNA-protein aggregates called stress granules. This results in the translational silencing of the majority of mRNAs excluding those beneficial for the cell to resolve the specific stress. For example, the expression of antiviral factors is maintained during viral infection. Here we investigated stress granule regulation by Gammacoronavirus infectious bronchitis virus (IBV), which causes the economically important poultry disease, infectious bronchitis. Interestingly, we found that IBV is able to inhibit multiple cellular stress granule signaling pathways, whilst at the same time, IBV replication also results in the induction of seemingly canonical stress granules in a proportion of infected cells. Moreover, IBV infection uncouples translational repression and stress granule formation and both processes are independent of eIF2α phosphorylation. These results provide novel insights into how IBV modulates cellular translation and antiviral stress signaling.


id: cord-273661-egpyvqrw
author: Mo, Mei-Lan
date: 2013-12-04
txt: ./txt/cord-273661-egpyvqrw.txt
cache: ./cache/cord-273661-egpyvqrw.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3390/v5123007
doi: 10.3390/v5123007
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.

title:
  Molecular Characterization of Major Structural Protein Genes of Avian Coronavirus Infectious Bronchitis Virus Isolates in Southern China

abstract:
  To gain comprehensive genetic information of circulating avian coronavirus infectious bronchitis virus (IBV) isolates in China, analysis of the phylogenetic tree, entropy of the amino acid sequences, and the positive selection as well as computational recombinations of S1, M and N genes of 23 IBV isolates was conducted in the present study. The phylogenetic trees based on the S1, M and N genes exhibited considerably different topology and the CK/CH/LSC/99I-type isolates were the predominant IBVs based on the phylogenetic analysis of S1 gene. Results of entropy of amino acid sequences revealed that the S1 gene had the largest variation; the M gene had less variation than the N gene. Positive selections were detected in not only S1 but also M and N gene proteins. In addition, five S1 gene recombinants between vaccine strain 4/91 and CK/CH/LSC/99I-type field isolate were confirmed. In conclusion, multiple IBV genotypes co-circulated; genetic diversity and positive selections existed in S1, M and N genes; 4/91 vaccine recombinants emerged in China. Our results show that field IBVs in China are continuing to evolve and vaccine strains may have an important role in the appearance of new IBV strains via recombination. In addition, the present study indicates that IBV evolution is driven by both generations of genetic diversity and selection.


id: cord-273846-l0elcfe8
author: Ganapathy, Kannan
date: 2005-02-24
txt: ./txt/cord-273846-l0elcfe8.txt
cache: ./cache/cord-273846-l0elcfe8.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/15847923/
doi: 10.1016/j.jviromet.2005.01.024
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

title:
  Effects of cold storage on detection of avian infectious bronchitis virus in chicken carcasses and local antibodies in tracheal washes

abstract:
  In order to test the survivability of infectious bronchitis virus (IBV) in dead chicken carcasses during 24 h of cold storage, 7 week-old specific-pathogen-free chickens were infected with virulent IBV Massachusetts strain M41, and were killed humanely 10 days later. Carcasses were stored in a cold room at 4 °C. After 1, 3, 6, 9, 12 or 24 h of storage, necropsies were carried out. Trachea, lung, kidney and rectum were collected for virus isolation by tracheal organ culture (TOC) or embryonated chicken eggs (ECE), and detection by nested reverse-transcriptase polymerase chain reaction (RT-PCR). IBV was detected by RT-PCR at all sampling times, except for 1 and 6 h of storage in kidney and 9 h of storage in kidney and rectum. For ECE, isolation was obtained at all sampling points, except at 1 and 24 h of storage in lungs. Isolation by tracheal organ cultures was less successful, except from rectum. In addition to sampling for virus, tracheal washes were collected from each carcass to measure the ability to detect local antibodies after storage. Levels of IgA in tracheal washes remained high for up to 9 h of storage, suggesting that accurate sampling for research purposes when required must be carried out within this time.


id: cord-276550-1in7m56w
author: Abdel-Moneim, Ahmed S
date: 2006-09-20
txt: ./txt/cord-276550-1in7m56w.txt
cache: ./cache/cord-276550-1in7m56w.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/16987422/
doi: 10.1186/1743-422x-3-78
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

title:
  S1 gene sequence analysis of a nephropathogenic strain of avian infectious bronchitis virus in Egypt

abstract:
  BACKGROUND: Infectious bronchitis is highly contagious and constitutes one of the most common and difficult poultry diseases to control. IBV is endemic in probably all countries that raise chickens. It exists as dozens of serotypes/genotypes. Only a few amino acid differences in the S1 protein of vaccine and challenge strains of IBV may result in poor protection. Tropism of IBV includes the respiratory tract tissues, proventriculus and caecal tonsils of the alimentary tract, the oviduct and the kidney. RESULTS: Infectious bronchitis virus (IBV) strain closely related to Massachusetts (Mass) serotype was isolated from broiler chickens suffering from severe renal and respiratory distresses. The isolate was serologically identified by Dot-ELISA and further characterized by RT-PCR then genotyped using S1 gene sequence analysis. Alignment of the S1 sequence of the isolate with 16 IBV strains revealed high homology to isolates related to Mass serotype. Inoculation with the strain reproduced the disease in experimental 1-day-old chickens and resulted in 20% mortality, severe renal and moderate respiratory distresses. Marked histopathological changes in both kidney and trachea were observed in experimentally infected chickens. A protection study using the H120 live attenuated vaccine showed low protection rate in spite of high S1 sequence homology (97%). Protection based criteria were: virus re-isolation attempts from trachea, tracheal and renal histopathology as well as IBV antigens detection by immunofluorescent antibody technique in kidney sections. CONCLUSION: Periodical evaluation of cross-protective capabilities of IBV vaccine(s) versus recently recovered field isolates should be performed to ensure optimum control of IBV.


id: cord-276755-ctzrgqe7
author: Emmott, Edward
date: 2010-09-08
txt: ./txt/cord-276755-ctzrgqe7.txt
cache: ./cache/cord-276755-ctzrgqe7.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1002/pmic.201000139
doi: 10.1002/pmic.201000139
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.

title:
  Elucidation of the avian nucleolar proteome by quantitative proteomics using SILAC and changes in cells infected with the coronavirus infectious bronchitis virus

abstract:
  The nucleolus is a dynamic subnuclear compartment involved in ribosome subunit biogenesis, regulation of cell stress and modulation of cellular growth and the cell cycle, among other functions. The nucleolus is composed of complex protein/protein and protein/RNA interactions. It is a target of virus infection with many viral proteins being shown to localize to the nucleolus during infection. Perturbations to the structure of the nucleolus and its proteome have been predicted to play a role in both cellular and infectious disease. Stable isotope labeling with amino acids in cell culture coupled to LC‐MS/MS with bioinformatic analysis using Ingenuity Pathway Analysis was used to investigate whether the nucleolar proteome altered in virus‐infected cells. In this study, the avian nucleolar proteome was defined in the absence and presence of virus, in this case the positive strand RNA virus, avian coronavirus infectious bronchitis virus. Data sets, potential protein changes and the functional consequences of virus infection were validated using independent assays. These demonstrated that specific rather than generic changes occurred in the nucleolar proteome in infectious bronchitis virus‐infected cells.


id: cord-277804-ujabzic4
author: Yuk, Seong-su
date: 2016-01-21
txt: ./txt/cord-277804-ujabzic4.txt
cache: ./cache/cord-277804-ujabzic4.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.jviromet.2016.01.008
doi: 10.1016/j.jviromet.2016.01.008
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) .

title:
  Comparison between dot-immunoblotting assay and clinical sign determination method for quantifying avian infectious bronchitis virus vaccine by titration in embryonated eggs

abstract:
  A sensitive and specific method for measuring the vaccine titer of infectious bronchitis virus (IBV) is important to commercial manufacturers for improving vaccine quality. Typically, IBV is titrated in embryonated chicken eggs, and the infectivity of the virus dilutions is determined by assessing clinical signs in the embryos as evidence of viral propagation. In this study, we used a dot-immunoblotting assay (DIA) to measure the titers of IBV vaccines that originated from different pathogenic strains or attenuation methods in embryonated eggs, and we compared this assay to the currently used method, clinical sign evaluation. To compare the two methods, we used real-time reverse transcription-PCR, which had the lowest limit of detection for propagated IBV. As a clinical sign of infection, dwarfism of the embryo was quantified using the embryo: egg (EE) index. The DIA showed 9.41% higher sensitivity and 15.5% higher specificity than the clinical sign determination method. The DIA was particularly useful for measuring the titer of IBV vaccine that did not cause apparent stunting but propagated in embryonated chicken eggs such as a heat-adapted vaccine strain. The results of this study indicate that the DIA is a rapid, sensitive, reliable method for determining IBV vaccine titer in embryonated eggs at a relatively low cost.


id: cord-278324-eqqvwwh6
author: Wang, Huanan
date: 2018-09-21
txt: ./txt/cord-278324-eqqvwwh6.txt
cache: ./cache/cord-278324-eqqvwwh6.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/s12985-018-1048-x
doi: 10.1186/s12985-018-1048-x
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 .

title:
  Development of a sensitive and specific xMAP assay for detection of antibodies against infectious laryngotracheitis and bronchitis viruses

abstract:
  BACKGROUND: A serological method to simultaneously detect antibodies against infectious laryngotracheitis virus (ILTV) and infectious bronchitis virus (IBV) is imperative for the differential diagnosis and evaluation of antibodies titers after vaccination. METHOD: The microspheres coated with purified recombinant glycoprotein D (gD) of ILTV or nucleocapsid (N) protein of IBV were incubated with serum samples. The simultaneous quantification of ILTV and IBV antibodies were achieved through the interrogation of microspheres by Luminex 200 detection system. . RESULTS: This xMAP detection demonstrated no nonspecific reactions with avian influenza virus (AIV), avian leukosis virus (ALV), newcastle disease virus (NDV), and Marek’s disease virus (MDV). The results also demonstrated that the xMAP assay was four times more sensitive than the enzyme-linked immunosorbent assay (ELISA) for ILTV detection and two times more sensitive for IBV detection. A total of 90 chicken serum samples from a chicken farm were tested by xMAP and ELISA assays. The results showed that the coincidence rates were 84.44 and 100% for ILTV and IBV detection, respectively. CONCLUSION: This study exhibited an opportunity for the differential diagnosis through simultaneous detection of multiplex antibodies in serum and can be used for the multiplex antibodies evaluation after vaccination.


id: cord-279495-zxerb7de
author: Liu, Xiaoli
date: 2012-11-21
txt: ./txt/cord-279495-zxerb7de.txt
cache: ./cache/cord-279495-zxerb7de.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1567134812003292
doi: 10.1016/j.meegid.2012.09.016
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

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

abstract:
  Four Massachusetts-type (Mass-type) strains of infectious bronchitis coronavirus (IBV) were compared genetically with the pathogenic M41 and H120 vaccine strains using the complete genomic sequences. The results revealed that strains ck/CH/LNM/091017 and ck/CH/LDL/101212 were closely related to the H120 vaccine, which suggests that they might represent re-isolations of vaccine strains or variants of vaccine strains that have resulted from the accumulated point mutations after several passages in chickens. In contrast, strains ck/CH/LHLJ/07VII and ck/CH/LHLJ/100902 had a close genetic relationship with the pathogenic M41 strain. In addition, molecular markers have been identified that distinguish between field and vaccine (or vaccine-like) Mass-type viruses, which may be able to differentiate between field and vaccine strains for diagnostic purposes. Phylogenetic analysis, and pairwise comparison of full-length genomes and the nine genes, identified the occurrence of recombination events in the genome of strain CK/VH/LHLJ/07VII, which suggests that this virus originated from recombination events between M41- and H120-like strains at the switch site located at the 3′ end of the nucleocapsid (N) genes. To our knowledge, this is the first time that evidence for the evolution and natural recombination under field conditions between Mass-type pathogenic and vaccinal IBV strains has been documented. These findings provide insights into the emergence and evolution of the Mass-type IB coronaviruses and may help to explain the emergence of Mass-type IBV in chicken flocks all over the world.


id: cord-280442-jtvez46y
author: Wu, Xuan
date: 2019-11-01
txt: ./txt/cord-280442-jtvez46y.txt
cache: ./cache/cord-280442-jtvez46y.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/31265112/
doi: 10.3382/ps/pez372
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) .

title:
  Simultaneous and visual detection of infectious bronchitis virus and Newcastle disease virus by multiple LAMP and lateral flow dipstick

abstract:
  ABSTRACT Infectious bronchitis virus (IBV) and Newcastle disease virus (NDV) are both important viruses seriously affecting poultry industry worldwide. In this study, reverse-transcription LAMP (RT-LAMP) was combined with lateral flow dipstick (LFD) forming a novel detection tool which could simultaneously detect IBV and NDV visually. Primers targeted the 5′-untranslated region (5′-UTR) of IBV genome and the conserved region of NDV large polymerase gene (LP). The specificity and sensitivity of this multiple reverse transcription-LAMP-LFD (mRT-LAMP-LFD) assay were compared with those of conventional RT-PCR, nested RT-PCR (nRT-PCR), quantification RT-PCR (qRT-PCR), and RT-LAMP monitored by electrophoresis. No non-specific amplifications were observed when the assays were tested with unrelated viruses. According to the sensitivity study, when detecting IBV or NDV alone, the lowest detection limits of mRT-LAMP-LFD were 100.8 IBV RNA copies/reaction and 100.7 NDV RNA copies/reaction. Furthermore, when detecting IBV and NDV simultaneously, the lowest detection limit was the same as that of the single detection assays. In the clinical sample study, mRT-LAMP-LFD performed the best among these assays. When tested with IBV or NDV single infected samples, the mean detection rates were 98.65% and 97.25%, respectively. In the IBV and NDV co-infected sample study, the mean detection rates of IBV and NDV were both 95%. This study showed that mRT-LAMP-LFD was a promising qualitative detection tool suitable for field single or multiple IBV and NDV detection.


id: cord-281526-7t9e4lgn
author: Yin, Lijuan
date: 2016-09-02
txt: ./txt/cord-281526-7t9e4lgn.txt
cache: ./cache/cord-281526-7t9e4lgn.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S016817021630274X
doi: 10.1016/j.virusres.2016.07.010
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

title:
  Immunogenicity and protective efficacy of recombinant fusion proteins containing spike protein of infectious bronchitis virus and hemagglutinin of H3N2 influenza virus in chickens

abstract:
  Infectious bronchitis (IB) is an acute and highly contagious viral respiratory disease of chickens and vaccination is the main method for disease control. The S1 protein, which contains several virus neutralization epitopes, is considered to be a target site of vaccine development. However, although protective immune responses could be induced by recombinant S1 protein, the protection rate in chickens was still low (<50%). Here, we generated fused S1 proteins with HA2 protein (rS1-HA2) or transmembrane domain and cytoplasmic tail (rS1-H3(TM)) from hemagglutinin of H3N2 influenza virus. After immunization, animals vaccinated with fusion proteins rS1-HA2 and rS1-H3(TM) demonstrated stronger robust humoral and cellular immune responses than that of rS1 and inactivated M41 vaccine. The protection rates of groups immunized with rS1-HA2 (87%) were significantly higher than the groups inoculated with rS1 (47%) and inactivated M41 vaccine (53%). And chickens injected with rS1-H3(TM) had similar level of protection (73%) comparing to chickens vaccinated with rS1 (47%) (P = 0.07). Our data suggest that S1 protein fused to the HA2 or TM proteins from hemagglutinin of H3N2 influenza virus may provide a new strategy for high efficacy recombinant vaccine development against IBV.


id: cord-282314-9cua2jzg
author: Albanese, Grace A.
date: 2018-10-01
txt: ./txt/cord-282314-9cua2jzg.txt
cache: ./cache/cord-282314-9cua2jzg.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0264410X18312283
doi: 10.1016/j.vaccine.2018.08.078
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.

title:
  Biological and molecular characterization of ArkGA: A novel Arkansas serotype vaccine that is highly attenuated, efficacious, and protective against homologous challenge

abstract:
  Almost all commercial poultry are vaccinated against avian coronavirus infectious bronchitis virus (IBV) using live attenuated vaccines mass administered by spray at day of hatch. Although many different types of IBV vaccines are used successfully, the ArkDPI serotype vaccine, when applied by spray, does not infect and replicate sufficiently to provide protection against homologous challenge. In this study, we examined a different Ark vaccine strain (Ark99), which is no longer used commercially due to its reactivity in one day old chicks, to determine if it could be further attenuated by passage in embryonated eggs but still provide adequate protection. Further attenuation of the Ark99 vaccine was achieved by passage in embryonated eggs but ArkGA P1, P20, and P40 (designated ArkGA after P1) were still too reactive to be suitable vaccine candidates. However, ArkGA P60 when given by spray had little or no vaccine reaction in one day old broiler chicks, and it induced protection from clinical signs and ciliostasis following homologous challenge. In addition, vaccinated and challenged birds had significantly less challenge virus, an important measure of protection, compared to non-vaccinated and challenged controls. The full-length genomes of viruses from egg passages 1, 20, 40, and 60 were sequenced using the Illumina platform and the data showed single nucleotide polymorphisms (SNPs) had accumulated in regions of the genome associated with viral replication, pathogenicity, and cell tropism. ArkGA P60 accumulated the most SNPs in key genes associated with pathogenicity (polyprotein gene 1ab) and cell tropism (spike gene), compared to previous passages, which likely resulted in its more attenuated phenotype. These results indicate that the ArkGA P60 vaccine is safe for spray vaccination of broiler chicks and induces suitable protection against challenge with pathogenic Ark-type virus.


id: cord-284501-5i0w74q4
author: Armesto, Maria
date: 2009-10-09
txt: ./txt/cord-284501-5i0w74q4.txt
cache: ./cache/cord-284501-5i0w74q4.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1371/journal.pone.0007384
doi: 10.1371/journal.pone.0007384
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.

title:
  The Replicase Gene of Avian Coronavirus Infectious Bronchitis Virus Is a Determinant of Pathogenicity

abstract:
  We have previously demonstrated that the replacement of the S gene from an avirulent strain (Beaudette) of infectious bronchitis virus (IBV) with an S gene from a virulent strain (M41) resulted in a recombinant virus (BeauR-M41(S)) with the in vitro cell tropism of the virulent virus but that was still avirulent. In order to investigate whether any of the other structural or accessory genes played a role in pathogenicity we have now replaced these from the Beaudette strain with those from M41. The recombinant IBV was in effect a chimaeric virus with the replicase gene derived from Beaudette and the rest of the genome from M41. This demonstrated that it is possible to exchange a large region of the IBV genome, approximately 8.4 kb, using our transient dominant selection method. Recovery of a viable recombinant IBV also demonstrated that it is possible to interchange a complete replicase gene as we had in effect replaced the M41 replicase gene with the Beaudette derived gene. Analysis of the chimaeric virus showed that it was avirulent indicating that none of the structural or accessory genes derived from a virulent isolate of IBV were able to restore virulence and that therefore, the loss of virulence associated with the Beaudette strain resides in the replicase gene.


id: cord-285052-aql0vrzv
author: Kamble, Nitin Machindra
date: 2016-02-12
txt: ./txt/cord-285052-aql0vrzv.txt
cache: ./cache/cord-285052-aql0vrzv.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1002/bab.1298
doi: 10.1002/bab.1298
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.

title:
  Evolutionary and bioinformatic analysis of the spike glycoprotein gene of H120 vaccine strain protectotype of infectious bronchitis virus from India

abstract:
  The infectious bronchitis virus is a causative agent of avian infectious bronchitis (AIB), and is is an important disease that produces severe economic losses to the poultry industry worldwide. Recent AIB outbreaks in India have been associated with poor growth in broilers, drop in egg production, and thin egg shells in layers. The complete spike gene of Indian AIB vaccine strain was amplified and sequenced using a conventional reverse transcription polymerase chain reaction and is submitted to the GenBank (accession no KF188436). Phylogenetic analysis revealed that the vaccine strain currently used belongs to H120 genotype, an attenuated strain of Massachusetts (Mass) serotype. Nucleotide and amino acid sequence comparisons have shown that the reported spike gene from Indian isolates have 71.8%–99% and 71.4%–96.9% genetic similarity with the sequenced H120 strain. The study identifies live attenuated IBV vaccine strain, which is routinely used for vaccination, for the first time. Based on nucleotide and amino acid relatedness studies of the vaccine strain with reported IBV sequences from India, it is shown that the current vaccine strain is efficient in controlling the IBV infection. Continuous monitoring of IBV outbreaks by sequencing for genotyping and in vivo cross protection studies for serotyping is not only important for epidemiological investigation but also for evaluation of efficacy of the current vaccine.


id: cord-285323-473d7zvg
title: Altered pro-inflammatory cytokine mRNA levels in chickens infected with infectious bronchitis virus
author: Jang, Hyesun
date: 2013-09-01
txt: ./txt/cord-285323-473d7zvg.txt
cache: ./cache/cord-285323-473d7zvg.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0032579119394404
doi: 10.3382/ps.2013-03116
summary:
  The KIIa genotype (Kr/ADL110002/2011) induced clinical signs accompanied by the excessive production of pro-inflammatory cytokines and a higher viral load. In chickens infected with this isolate, simultaneous peaks in the viral copy number and cytokine production were observed at 7 dpi in the trachea and 9 d postinoculation in the kidney. In chickens infected with this isolate, simultaneous peaks in the viral copy number and cytokine production were observed at 7 dpi in the trachea and 9 d postinoculation in the kidney. In this study, we observed changes in the transcriptional levels of 3 pro-inflammatory cytokines that are known to be involved in the innate immune response in chickens (Hong et al., 2006; Davison et al., 2008) after inoculation with 2 IB isolates. On the other hand, an active infection of the ChVI genotype isolate kr/ADL120003/2012, which resulted in an increase in serum AGP level at 9 dpi (Table 3) , evoked only a limited range of pro-inflammatory responses.

abstract:
  Infectious bronchitis virus (IBV) replicates primarily in the respiratory tract and grows in various organs in chickens, with or without pathological effects. The diversity of this virus has been verified by sequence analysis of the S1 glycoprotein gene, but this method must be supplemented with further analysis for characterization of the agent. To increase our understanding of the pathogenesis of the disease caused by this virus, we investigated the response of chickens to 2 IBV with different genotypes, KIIa and ChVI. The clinical signs induced by the viruses were observed. In addition, the mRNA levels of the pro-inflammatory cytokines, IL-6, IL-1β, and lipopolysaccharide-induced tumor necrosis factor-α factor and the serum levels of α(1)-acid glycoprotein, which is a major acute phase protein, were measured. The KIIa genotype (Kr/ADL110002/2011) induced clinical signs accompanied by the excessive production of pro-inflammatory cytokines and a higher viral load. In chickens infected with this isolate, simultaneous peaks in the viral copy number and cytokine production were observed at 7 dpi in the trachea and 9 d postinoculation in the kidney. On the other hand, the chickens infected with the ChVI genotype (Kr/ADL120003/2012) did not show a response other than a mild upregulation of cytokines at 1 d postinoculation, which appears to indicate the invasion of the virus. In summary, we confirmed a differential innate response following infection with distinct IBV. We hypothesize that an excessive innate response contributes to the scale of the pathophysiologic effect in chickens.


id: cord-285330-td4vr0zv
author: Mohammadi, Ali
date: 2015-11-12
txt: ./txt/cord-285330-td4vr0zv.txt
cache: ./cache/cord-285330-td4vr0zv.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/26645044/
doi: 10.1007/s13337-015-0286-4
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

title:
  Viral quantity and pathological changes in broilers experimentally infected by IRFIBV32 isolate of infectious bronchitis virus

abstract:
  An Iranian isolate of avian infectious bronchitis virus IRFIBV32 was quantified in experimentally infected broilers using real-time reverse transcriptase polymerase chain reaction and histopathological changes was investigated. Thirty-six 3-week-old commercial broilers were inoculated by 10(5) ELD50/0.1 ml of the virus. On the various days post inoculation (dpi) different tissues were collected. The virus strongly started the replication in trachea at 1 dpi and reached to the maximum titer at 3 dpi. The highest IBV RNA level was shown in this organ. In lung, the virus was replicated with the titer lower than that of the trachea, but it rose up more at 5 dpi. The kidneys were the tissues with the least viral genome copy number, although the duration of the virus presence was considerable. The virus replicated in testes sooner than ovaries also disappeared sooner but the maximum viral yield in the ovaries was more. The virus titer in the studied tissues had an interesting fluctuation especially in caecal tonsils. Testes and ovaries were the organs that the virus could reactivate without using any chemical. The most severe lesions were observed in tracheae but they appeared in the lungs later. Lymphocyte infiltration in the kidneys was noted from 5 dpi even sooner than the lungs. There were no lesions in the caecal tonsils, testes and ovaries in spite of the virus replication in a high titer.


id: cord-285942-mb1xwdqw
author: Feng, K. Y.
date: 2018-10-01
txt: ./txt/cord-285942-mb1xwdqw.txt
cache: ./cache/cord-285942-mb1xwdqw.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3382/ps/pey237
doi: 10.3382/ps/pey237
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

title:
  Molecular characteristic and pathogenicity analysis of a virulent recombinant avain infectious bronchitis virus isolated in China

abstract:
  ABSTRACT A virulent infectious bronchitis virus (IBV), designated as CK/CH/GD/QY16 (referred as QY16), was isolated from a diseased chicken farm in Guangdong province, China, in 2016. The complete genome of the strain was sequenced and analyzed. The results show that the genome of QY16 consists of 27,670 nucleotides, excluding poly (A) tail, and that its genome organization is 5’ UTR-1a-1b-S-3a-3b-E-M-4b-4c-5a-5b-N-6b-3’ UTR-poly (A) tail. Sequence comparison among QY16 and other IBV strains was conducted and its results demonstrate that the S1 gene of QY16 has the highest nucleotide sequence identity with that of 4/91, and the other part of its genome is highly similar to that of YX10. The results of the phylogenic analysis show that the entire genome of QY16 and most of the QY16 genes are located in the same cluster as those of YX10, except for the S1 gene which is located in the same cluster with that of 4/91. It has been further confirmed by the RDP and SimPlot analysis that QY16 is a recombinant strain deriving from YX10 (as the major parental sequence) and 4/91 (as the minor parental sequence), and that the recombination occurs in a region which includes the 3’-terminal 1b sequence (85 nt) and the 5’-terminal S1 protein gene sequence (1,466 nt). The results of the vaccination-challenge test suggest that QY16 is a nephropathogenic strain of IBV and that the vaccine strains–H120 and 4/91—cannot provide effective protection against it. These results indicate that the continuing evolution of IBV strains by genetic drift and genetic recombination may lead to IBV outbreaks even among the vaccinated chickens in China.


id: cord-286332-cdg4im5h
author: van Beurden, Steven J.
date: 2017-06-12
url: https://www.ncbi.nlm.nih.gov/pubmed/28606144/
doi: 10.1186/s12985-017-0775-8
title:
  A reverse genetics system for avian coronavirus infectious bronchitis virus based on targeted RNA recombination

abstract:
  BACKGROUND: Avian coronavirus infectious bronchitis virus (IBV) is a respiratory pathogen of chickens that causes severe economic losses in the poultry industry worldwide. Major advances in the study of the molecular biology of IBV have resulted from the development of reverse genetics systems for the highly attenuated, cell culture-adapted, IBV strain Beaudette. However, most IBV strains, amongst them virulent field isolates, can only be propagated in embryonated chicken eggs, and not in continuous cell lines. METHODS: We established a reverse genetics system for the IBV strain H52, based on targeted RNA recombination in a two-step process. First, a genomic and a chimeric synthetic, modified IBV RNA were co-transfected into non-susceptible cells to generate a recombinant chimeric murinized (m) IBV intermediate (mIBV). Herein, the genomic part coding for the spike glycoprotein ectodomain was replaced by that of the coronavirus mouse hepatitis virus (MHV), allowing for the selection and propagation of recombinant mIBV in murine cells. In the second step, mIBV was used as the recipient. To this end a recombination with synthetic RNA comprising the 3′-end of the IBV genome was performed by introducing the complete IBV spike gene, allowing for the rescue and selection of candidate recombinants in embryonated chicken eggs. RESULTS: Targeted RNA recombination allowed for the modification of the 3′-end of the IBV genome, encoding all structural and accessory genes. A wild-type recombinant IBV was constructed, containing several synonymous marker mutations. The in ovo growth kinetics and in vivo characteristics of the recombinant virus were similar to those of the parental IBV strain H52. CONCLUSIONS: Targeted RNA recombination allows for the generation of recombinant IBV strains that are not able to infect and propagate in continuous cell lines. The ability to introduce specific mutations holds promise for the development of rationally designed live-attenuated IBV vaccines and for studies into the biology of IBV in general. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12985-017-0775-8) contains supplementary material, which is available to authorized users.


id: cord-286473-sl5zy8nj
title: Complete genomic sequence of turkey coronavirus
author: Gomaa, M.H.
date: 2008-05-12
txt: ./txt/cord-286473-sl5zy8nj.txt
cache: ./cache/cord-286473-sl5zy8nj.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0168170208001317
doi: 10.1016/j.virusres.2008.03.020
summary:
  Turkey coronavirus (TCoV), one of the least characterized of all known coronaviruses, was isolated from an outbreak of acute enteritis in young turkeys in Ontario, Canada, and the full-length genomic sequence was determined. The RdRp motif was highly conserved among all coronaviruses, and TCoV-MG10 also showed a high degree of sequence identity for RdRp by 64%, 62%, 94% at the amino acid level to HCoV-229E, BCoV, IBV, respectively. The M gene seemed to be highly conserved within group III coronaviruses since TCoV M showed a 94% nucleotide identity to IBV M. This ORF is unique to TCoV and IBV, the only Group III coronaviruses for which sequence data in this region of the genome are available. In addition, we have identified a putatively functional gene (ORF-X) shared among all sequenced IBV and TCoV strains that may be a shared feature of all group III coronaviruses.

abstract:
  Turkey coronavirus (TCoV), one of the least characterized of all known coronaviruses, was isolated from an outbreak of acute enteritis in young turkeys in Ontario, Canada, and the full-length genomic sequence was determined. The full-length genome was 27,632 nucleotides plus the 3′ poly(A) tail. Two open reading frames, ORFs 1a and 1b, resided in the first two thirds of the genome, and nine additional downstream ORFs were identified. A gene for hemagglutinin-esterase was absent in TCoV. The region between the membrane (M) and nucleocapsid (N) protein genes contained three potential small ORFs: ORF-X, a previously uncharacterized ORF with an associated putative TRS within the M gene (apparently shared among all group III coronaviruses), and previously described ORFs 5a and 5b. The TCoV genome is organized as follows: 5′ UTR – replicase (ORFs 1a, 1b) – spike (S) protein – ORF3 (ORFs 3a, 3b) – small envelop (E or 3c) protein – membrane (M) protein – ORF5 (ORFs X, 5a, 5b) – nucleocapsid (N) protein −3′ UTR – poly(A). TCoV genome structure and sequence was most similar, but distinct from, avian infectious bronchitis virus (IBV). This is the first complete genome sequence for a TCoV and confirms that TCoV belongs to group III coronaviruses.


id: cord-286658-9kco7qad
author: Jiang, Lei
date: 2018-01-15
url: https://api.elsevier.com/content/article/pii/S0168170217307098
doi: 10.1016/j.virusres.2017.11.007
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

abstract:
  In this study, we isolated an infectious bronchitis virus, designated I1101/16, from broiler breeders in China. Analysis of the S1 gene showed that isolate I1101/16 was genetically close to strain ck/CH/LJL/140901, which belongs to the TW I genotype (also known as lineage GI-7 based on the recent IBV classification), however the S2 gene showed genetic diversity comparing to that of S1 gene. Comparison of the genomic sequences showed that the genome of isolate I1101/16 was similar to that of strain ck/CH/LJL/140901 from the 5′ end of the genome to the 5′ end of the S2 gene and from the 5′ end of the 3a gene to the end of the genome, whereas the remaining parts of the genome sequences were more closely related to those of strain 4/91 than those of ck/CH/LJL/140901, thereby suggesting that recombination might have occurred during the origin of the virus. SimPlot and Bootscan analysis of the complete genomic sequence confirmed this hypothesis, where it showed that isolate I1101/16 arose through recombination events between ck/CH/LJL/140901- and 4/91-like viruses. Isolate I1101/16 and strain ck/CH/LJL/140901 shared identical amino acids in almost all five of their B cell epitopes, but the two viruses had a serotype relatedness value of 65, which is well below 80, i.e., the lower cutoff value for viruses of the same serotype. In addition, pathogenicity tests demonstrated that isolate I1101/16 was more pathogenic to 1-day-old specific-pathogen-free chickens than strain ck/CH/LJL/140901, according to analysis of the clinical signs, whereas strain ck/CH/LJL/140901 exhibited prolonged replication and shedding after challenge compared with isolate I1101/16. This study did not provide evidence that recombination can directly alter the antigenicity, virulence, replication, shedding, and tissue tropism of a virus, but it did show that recombination events are likely to be major determinants of viral evolution.


id: cord-288309-6pw7t512
author: Kusters, J. G.
date: 1990-12-31
txt: ./txt/cord-288309-6pw7t512.txt
cache: ./cache/cord-288309-6pw7t512.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/0264410X9090018H
doi: 10.1016/0264-410x(90)90018-h
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

title:
  Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus

abstract:
  Abstract Under laboratory conditions coronaviruses were shown to have a high frequency of recombination. In The Netherlands, vaccination against infectious bronchitis virus (IBV) is performed with vaccines that contain several life-attenuated virus strains. These highly effective vaccines may create ideal conditions for recombination, and could therefore be dangerous in the long term. This paper addresses the question of the frequency of recombination of avian coronavirus IBV in the field. A method was sought to detect and quantify recombination from sequence data. Nucleotide sequences of eight IBV isolates in a region of the genome suspected to contain recombination, were aligned and compared. Phylogenetic trees were constructed for different sections of this region. Differences in topology between these trees were observed, suggesting that in three out of eight strains in vivo RNA recombinant had occurred.


id: cord-290638-7ro72sv3
title: Antigenicity of the peplomer protein of infectious bronchitis virus
author: Lenstra, Johannes A.
date: 1989-01-31
txt: ./txt/cord-290638-7ro72sv3.txt
cache: ./cache/cord-290638-7ro72sv3.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/016158908990014X
doi: 10.1016/0161-5890(89)90014-x
summary:
  Abstract To study the antigenic structure of the peplomer protein of the avian coronavirus infectious bronchitis virus, fragments from the peplomer gene were generated by restriction-enzyme cleavage or by limited DNase digestion and inserted in the Escherichia coli expression plasrnid pEX (Stanley and Luzio, 1984). Recombinants expressing the IBV gene fragments were selected by immunoscreening with a rabbit antiserum or, when the expression product was not recognized antigenically, by hybridization followed by gel electrophoresis of the protein expression products. Figure 2 (C) shows a Western blot of hybrid proteins screened with this MAb. The strong binding to fragments p2, s4, psl and ps2 localizes the epitope of MAb 26.1 between residues 390 and 612, the same region that is recognized by all polyclonal sera. The localization of epitopes within stretches of 10-20 residues in several coronaviruses (Fig. 4 , unpublished results) demonstrates that the binding of antibody does not depend on particular flanking sequences, and that any nativelike folding of the epitope in the hybrid protein is confined to the same small region.

abstract:
  Abstract To study the antigenic structure of the peplomer protein of the avian coronavirus infectious bronchitis virus, fragments from the peplomer gene were generated by restriction-enzyme cleavage or by limited DNase digestion and inserted in the Escherichia coli expression plasrnid pEX (Stanley and Luzio, 1984). The antigenicity of the expression products was tested using a number of polyclonal antisera and monoclonal antibodies. The polyclonal antisera recognized different sets of epitopes in the 1162-residue sequence. The N-terminal region of one of the two subunits, S2, was recognized by all polyclonal sera and by two monoclonal antibodies. This clearly immunodominant region contains at least two adjacent or overlapping epitopes, one of which has been localized within 18 residues. The epitopes found as antigenic pEX expression products do not coincide with the regions in the S1 subunit that have been found to contain hypervariable sequences. We suggest that these regions constitute conformation dependent neutralization epitopes that cannot be detected in the pEX system. The relevance of our finclings for vaccine development is discussed.


id: cord-291174-rym84kni
author: Yang, Yazhi
date: 2020-10-23
txt: ./txt/cord-291174-rym84kni.txt
cache: ./cache/cord-291174-rym84kni.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s00604-020-04582-3
doi: 10.1007/s00604-020-04582-3
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.

title:
  A label-free electrochemical assay for coronavirus IBV H120 strain quantification based on equivalent substitution effect and AuNPs-assisted signal amplification

abstract:
  A label-free electrochemical strategy is proposed combining equivalent substitution effect with AuNPs-assisted signal amplification. According to the differences of S1 protein in various infectious bronchitis virus (IBV) strains, a target DNA sequence that can specifically recognize H120 RNA forming a DNA-RNA hybridized double-strand structure has been designed. Then, the residual single-stranded target DNA is hydrolyzed by S1 nuclease. Therefore, the content of target DNA becomes equal to the content of virus RNA. After equivalent coronavirus, the target DNA is separated from DNA-RNA hybridized double strand by heating, which can partly hybridize with probe 2 modified on the electrode surface and probe 1 on AuNPs’ surface. Thus, AuNPs are pulled to the surface of the electrode and the abundant DNA on AuNPs’ surface could adsorb a large amount of hexaammineruthenium (III) chloride (RuHex) molecules, which produce a remarkably amplified electrochemical response. The voltammetric signal of RuHex with a peak near − 0.28 V vs. Ag/AgCl is used as the signal output. The proposed method shows a detection range of 1.56e(−9) to 1.56e(−6) μM with the detection limit of 2.96e(−10) μM for IBV H120 strain selective quantification detection, exhibiting good accuracy, stability, and simplicity, which shows a great potential for IBV detection in vaccine research and avian infectious bronchitis diagnosis. [Figure: see text] ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00604-020-04582-3) contains supplementary material, which is available to authorized users.


id: cord-291510-jh2fdks4
author: Jiang, Yi
date: 2020-02-11
url: https://doi.org/10.1016/j.vaccine.2020.01.001
doi: 10.1016/j.vaccine.2020.01.001
title:
  Recombinant infectious bronchitis coronavirus H120 with the spike protein S1 gene of the nephropathogenic IBYZ strain remains attenuated but induces protective immunity

abstract:
  Infectious bronchitis (IB) is a highly infectious viral disease responsible for major economic losses in the poultry industry. A reverse genetic vaccine is a safe, rapid, and effective method of achieving IB prevention and control. In this study, we constructed the recombinant strain, rH120-S1/YZ, using a reverse genetic system, based on the backbone of the H120 vaccine strain, with the S1 gene replaced with that of the QX-like nephropathogenic strain, ck/CH/IBYZ/2011, isolated in China. The results of dwarf chicken embryos, growth kinetics, and viral titration in the embryos demonstrated that the biological characteristics of the recombinant virus remained unchanged. Like the rH120-infected group and in contrast to the rIBYZ-infected group, no mortality, clinical signs, or lesions were observed in the lungs or kidneys of young chickens inoculated with rH120-S1/YZ. The viral loads in various tissues, cloacal, and oral swabs was lower in most types of samples, indicating that the rH120-S1/YZ strain was highly safe in chicks. Compared to rH120 vaccination group, when the efficacy of this strain was evaluated against the QX-like IBV strain, better protection, with 100% survival rate and no disease symptom or gross lesion was observed in the chickens vaccinated with rH120-S1/YZ. Increased levels of IBV-specific antibodies were detected in the serum of the rH120-S1/YZ-vaccinated animals 14 days post-vaccination. Collectively, our results suggest that the recombinant strain, rH120-S1/YZ, may represent a promising vaccine candidate against QX-like IBVs.


id: cord-291718-cz1bi0ym
title: The papain-like protease of avian infectious bronchitis virus has deubiquitinating activity
author: Yu, Liping
date: 2017-03-18
txt: ./txt/cord-291718-cz1bi0ym.txt
cache: ./cache/cord-291718-cz1bi0ym.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s00705-017-3328-y
doi: 10.1007/s00705-017-3328-y
summary:
  Furthermore, the IBV replicase-encoded PLP, including the downstream transmembrane (TM) domain, is a DUB enzyme and dramatically reduced the level of Ub-conjugated proteins, while processing both K48and K63-linked polyubiquitin chains. Overall, these results demonstrate that the IBV-encoded PLP-TM functions as a DUB enzyme and suggest that IBV may interfere with the activation of host antiviral signaling pathway by degrading polyubiquitin-associated proteins. Further experiments indicated that the proteinase PLP-TM plays an important role in IBV DUB activity and can process both K48-and K63-linked polyubiquitin chains. Overall, the results of our study show that IBV has DUB activity and confirm that PLP-TM is not only a classic papain-like protease encoded by IBV but is also a multifunctional protein that plays important roles in the regulation of interactions between IBV and host antiviral innate immune response proteins. IBV PLP-TM may prevent the activation of host antiviral signaling pathways by degrading polyubiquitin chains associated with ubiquitin proteins.

abstract:
  Coronavirus papain-like proteases (PLPs) can act as proteases that process virus-encoded large replicase polyproteins and also as deubiquitinating (DUB) enzymes. Like the PLPs of other coronaviruses (CoVs), the avian infectious bronchitis virus (IBV) PLP catalyzes proteolysis of Gly-Gly dipeptide bonds to release mature cleavage products. However, the other functions of the IBV PLP are not well understood. In this study, we found that IBV exhibits strong global DUB activity with significant reductions of the levels of ubiquitin (Ub)-, K48-, and K63-conjugated proteins. The DUB activity exhibited a clear time dependence, with stronger DUB activity in the early stage of viral infection. Furthermore, the IBV replicase-encoded PLP, including the downstream transmembrane (TM) domain, is a DUB enzyme and dramatically reduced the level of Ub-conjugated proteins, while processing both K48- and K63-linked polyubiquitin chains. By contrast, PLP did not cause any reduction of haemagglutinin (HA)-Ub-conjugated proteins. In addition, mutations of the catalytic residues of PLP-TM, Cys1274Ser and His1437Lys, reduced DUB activity against Ub-, K48- and K63- conjugated proteins, indicating that the DUB activity of the PLP-TM wild-type protein is not completely dependent on its catalytic activity. Overall, these results demonstrate that the IBV-encoded PLP-TM functions as a DUB enzyme and suggest that IBV may interfere with the activation of host antiviral signaling pathway by degrading polyubiquitin-associated proteins.


id: cord-291754-1zxztadu
author: Zhao, Ye
date: 2019-10-15
txt: ./txt/cord-291754-1zxztadu.txt
cache: ./cache/cord-291754-1zxztadu.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/31430502/
doi: 10.1016/j.virusres.2019.197726
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.

title:
  Successful establishment of a reverse genetic system for QX-type infectious bronchitis virus and technical improvement of the rescue procedure

abstract:
  In this study, a pathogenic avian infectious bronchitis virus (IBV) QX-type strain YN was successfully rescued by vaccinia virus based reverse genetic technology. Ten fragments contiguously spanning the complete IBV genome were amplified and cloned into the vaccinia virus genome by homologous recombination. The full-length genomic cDNA was transcribed in vitro, and its transcript was transfected into BHK-21/N cells that could stably express IBV N protein. At 48 h post transfection, the culture medium was harvested and inoculated into 10-day-old specific-pathogen-free embryonated chicken eggs to replicate the rescued virus. This strategy was chosen to facilitate the rescue procedure and to ensure that the recombinant rYN virus will not require any cell culture adaptations. After only one in ovo passage, the recombinant YN virus (rYN) was successfully recovered and confirmed to possess the introduced silent marker mutation in its genome. Biological characteristics of rYN such as the EID(50), TCID(50), replication in ovo, and replication kinetcs in vitro were tested and all were similar to its parental strain YN. Our findings demonstrate the successful construction of highly-pathogenic QX-type IBV using a modified rescue procedure, allowing for future studies of the molecular biology and pathogenicity of IBV field strains.


id: cord-292428-j3wdlpp6
author: Zhou, J.‐Y.
date: 2004-06-30
url: https://www.ncbi.nlm.nih.gov/pubmed/15228547/
doi: 10.1111/j.1439-0450.2004.00744.x
title:
  Characterization of an Avian Infectious Bronchitis Virus Isolated in China from Chickens with Nephritis

abstract:
  One IBV isolate, SC021202, was isolated from the kidneys of the infected young chickens by inoculating embryonated eggs, and its morphology, physiochemical and haemagglutonating properties were detected. Virulence of the isolate SC021202 was determined with specific pathogen‐free (SPF) chicken inoculation. Nucleotide acid sequence of S1 gene of the isolate SC021202 was further sequenced and analysed. The physiochemical and morphological properties of the isolate SC021202 were in accordance to that of typical infectious bronchitis virus (IBV). In a pathogenicity experiment, the clinical signs and related gross lesions resembling those of field outbreak were reproduced and the virus isolate SC021202 was re‐isolated from the kidneys of the infected chicken. Sequence data demonstrated that the full length of the amplified S1 gene of the isolate SC021202 was composed of 1931 nucleotides, coding a polypeptide of 543 amino acid residues. Compared with IBV strains from GenBank, the nucleotide and deduced amino acid sequence of S1 gene of the isolate SC021202 shared 60.0–91.4% and 49.1–88.9% identities, respectively. A nucleotide fragment of ′CTTTTTAATTATACTAACGGA′ was inserted at nucleotide site 208 in the S1 gene of the isolate. These results indicated that IBV isolate SC021202 was a new variant IBV isolate and responsible for field outbreak of nephritis.


id: cord-293081-40pa5g89
title: Preliminary crystallographic analysis of avian infectious bronchitis virus main protease
author: Li, Jun
date: 2006-12-16
txt: ./txt/cord-293081-40pa5g89.txt
cache: ./cache/cord-293081-40pa5g89.txt
extension: .txt
mime: text/plain
url: http://europepmc.org/articles/pmc2330114?pdf=render
doi: 10.1107/s1744309106052341
summary:
  IBV belongs to group III (Lai & Holmes, 2001) , which only infects avian species, and leads to a highly contagious disease affecting the respiratory, reproductive, neurological and renal systems of chickens, resulting in a drop in egg production in adult birds and damaging the developing reproductive system in young birds. To date, several crystal structures of coronavirus M pro s have been reported for group I and II coronaviruses, which mostly infect mammals (Anand et al., 2002 Yang et al., 2003) . The crystals belong to space group P6 1 22, with unit-cell parameters a = b = 119.1, c = 270.7 Å , = = 90, = 120 (see Table 1 Typical crystals of IBV M pro grown by the hanging-drop method in 2.5% PEG 4000, 12% 2-propanol, 0.1 M sodium cacodylate pH 6.5.

abstract:
  Infectious bronchitis virus (IBV) is the prototype of the genus Coronavirus. It causes a highly contagious disease which affects the respiratory, reproductive, neurological and renal systems of chickens, resulting great economic losses in the poultry industry worldwide. The coronavirus (CoV) main protease (M(pro)), which plays a pivotal role in viral gene expression and replication through a highly complex cascade involving the proteolytic processing of replicase polyproteins, is an attractive target for antiviral drug design. In this study, IBV M(pro) was overexpressed in Escherichia coli. Crystals suitable for X-ray crystallography have been obtained using microseeding techniques and belong to space group P6(1)22. X-ray diffraction data were collected in-house to 2.7 Å resolution from a single crystal. The unit-cell parameters were a = b = 119.1, c = 270.7 Å, α = β = 90, γ = 120°. Three molecules were predicted to be present in the asymmetric unit from a calculated self-rotation function.


id: cord-293651-96cmduez
author: Callison, Scott A.
date: 2006-08-28
txt: ./txt/cord-293651-96cmduez.txt
cache: ./cache/cord-293651-96cmduez.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0166093406002734
doi: 10.1016/j.jviromet.2006.07.018
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.

title:
  Development and evaluation of a real-time Taqman RT-PCR assay for the detection of infectious bronchitis virus from infected chickens

abstract:
  It is important to rapidly differentiate infectious bronchitis virus (IBV) from disease agents like highly pathogenic avian influenza virus and exotic Newcastle disease virus, which can be extremely similar in the early stages of their pathogenesis. In this study, we report the development and testing of a real-time RT-PCR assay using a Taqman(®)-labeled probe for early and rapid detection of IBV. The assay amplifies a 143-bp product in the 5′-UTR of the IBV genome and has a limit of detection and quantification of 100 template copies per reaction. All 15 strains of IBV tested as well as two Turkey coronavirus strains were amplified, whereas none of the other pathogens examined, tested positive. Evaluation of the assay was completed with 1329 tracheal swab samples. A total of 680 samples collected from IBV antibody negative birds were negative for IBV by the real-time RT-PCR assay. We tested 229 tracheal swabs submitted to two different diagnostic laboratories and found 79.04% of the tracheal swabs positive for IBV by real-time RT-PCR, whereas only 27.51% of the samples were positive by virus isolation, which is the reference standard test. We also collected a total of 120 tracheal swabs at six different time points from birds experimentally infected with different dosages of IBV and found that, independent of the dose given, the viral load in the trachea plateau at 5 days post-inoculation. In addition, an inverse relationship between the dose of virus given and the viral load at 14 days post-inoculation was observed. Finally, we tested 300 total tracheal swab samples, from a flock of commercial broilers spray vaccinated for IBV in the field. The percentage of birds infected with the IBV vaccine at 3, 7, and 14 days post-vaccination was 58%, 65%, and 83%, respectively, indicating that only slightly more than half the birds were initially infected then the vaccine was subsequently transmitted to other birds in the flock. This observation is significant because coronaviruses, which have a high mutation rate, can revert to pathogenicity when bird-to-bird transmission occurs. The real-time RT-PCR test described herein can be used to rapidly distinguish IBV from other respiratory pathogens, which is important for control of this highly infectious virus. The test was extremely sensitive and specific, and can be used to quantitate viral genomic RNA in clinical samples.


id: cord-294679-7pklrmz5
author: Wei, Lei
date: 2008-08-09
txt: ./txt/cord-294679-7pklrmz5.txt
cache: ./cache/cord-294679-7pklrmz5.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1107/s1744309108024391
doi: 10.1107/s1744309108024391
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

title:
  Purification, crystallization and preliminary crystallographic analysis of avian infectious bronchitis virus nsp3 ADRP domain

abstract:
  Avian infectious bronchitis virus (IBV) encodes 15 nonstructural proteins (nsps) which play crucial roles in RNA transcription and genome replication. One of them, nsp3, contains an ADRP (adenosine diphosphate-ribose-1′-phosphatase) domain which was revealed in recent studies to have ADP-ribose-1′-monophos­phatase (Appr-1′-pase) activity. Appr-1′-pase catalyzes the conversion of ADP-ribose-1′-monophosphate (Appr-1′-p) to ADP-ribose in the tRNA-splicing pathway. The gene segment encoding the IBV nsp3 ADRP domain has been cloned and expressed in Escherichia coli. The protein has been crystallized and the crystals diffracted to 1.8 Å resolution. They belonged to space group P1, with unit-cell parameters a = 41.1, b = 43.2, c = 48.9 Å, α = 78.0, β = 80.0, γ = 73.6°. Each asymmetric unit contains two molecules.


id: cord-296167-np0b9a7o
title: Naturally occurring recombination between distant strains of infectious bronchitis virus
author: Mardani, Karim
date: 2010-06-24
url: https://doi.org/10.1007/s00705-010-0731-z
doi: 10.1007/s00705-010-0731-z
abstract:
  New variants of infectious bronchitis virus (IBV) have emerged in Australia despite its geographical isolation and intensive vaccination programs. In the present study, the 3′ terminal 7.2 kb of the genome of a recently isolated variant of IBV (N1/03) was sequenced and compared with the sequences of classical and novel strains of IBV, the two main groups of these viruses in Australia. The comparison revealed that recombination between classical and novel IBVs was responsible for the emergence of the new variant. It was concluded that novel IBVs, which have not been detected since 1993, and which are phylogenically more distant from classical IBVs than turkey coronaviruses, might still be circulating and contributing to the evolution of IBV in Australia.


id: cord-296364-7rp60d2m
author: Youn, Soonjeon
date: 2005-02-05
url: https://www.sciencedirect.com/science/article/pii/S0042682204007421
doi: 10.1016/j.virol.2004.10.045
title:
  In vitro assembled, recombinant infectious bronchitis viruses demonstrate that the 5a open reading frame is not essential for replication

abstract:
  Molecular clones of infectious bronchitis virus (IBV), derived from the Vero cell adapted Beaudette strain, were constructed, using an in vitro assembly method. In vitro transcribed RNA from a cDNA template that had been constructed from seven cDNA fragments, encompassing the entire genome of IBV, was electroporated into BHK-21 cells. The cells were overlaid onto the susceptible Vero cells and viable virus was recovered from the molecular clone. The molecularly cloned IBV (MIBV) demonstrated growth kinetics, and plaque size and morphology that resembled the parental Beaudette strain IBV. The recombinant virus was further manipulated to express enhanced green fluorescent protein (EGFP) by replacing an open reading frame (ORF) of the group-specific gene, ORF 5a, with the EGFP ORF. The rescued recombinant virus, expressing EGFP (GIBV), replicated to lower viral titers and formed smaller plaques compared to the parental virus and the MIBV. After six passages of GIBV, a minority of plaques were observed that had reverted to the larger plaque size and virus from these plaques no longer expressed EGFP. Direct sequencing of RT-PCR products derived from cells infected with the plaque-purified virus, which had lost expression of EGFP, confirmed loss of the EGFP ORF. The loss of EGFP expression (Δ5a IBV) was also accompanied by reversion to growth kinetics resembling the standard virus and intact recombinant virus. This study demonstrates that the 5a ORF is not essential for viral multiplication in Vero cells.


id: cord-296611-ma32oz4o
title: Novel genotype of infectious bronchitis virus isolated in China
author: Ma, Tianxin
date: 2019-01-29
url: https://www.ncbi.nlm.nih.gov/pubmed/30827386/
doi: 10.1016/j.vetmic.2019.01.020
abstract:
  Recombination events are known to contribute to the emergence of novel infectious bronchitis virus (IBV) genotypes. In this study, we carried out detailed phylogenetic analysis and sequence comparisons based on 74 complete nucleotide sequences of the IBV S1 gene, including strain I0636/16 and 73 representative sequences from each genotype and lineage. The results showed that strain I0636/16 represented a novel genotype, designated as lineage 1 within genotype VII (GVII-1). Further comparative genomic analysis revealed at least two recombination sites that replaced the spike gene in a lineage 18 within genotype I (GI-18)-like virus with an as-yet-unidentified sequence, likely derived from another IBV strain, resulting a novel serotype with a lower affinity to the respiratory tract in chickens. To the best of our knowledge, this provides the first evidence for recombination leading to replacement of the complete spike gene and the emergence of a novel genotype/serotype with a lower affinity to the respiratory tract in chickens comparing to one of its parental virus ck/CH/LGX/111119. These results emphasize the importance of limiting exposure to novel IBVs that may serve as a source of genetic material for emerging viruses, as well as the importance of IBV surveillance in chicken flocks.


id: cord-296831-wdpatr2z
author: Matoo, Javaid Jeelani
date: 2018-04-07
url: https://api.elsevier.com/content/article/pii/S0882401018302948
doi: 10.1016/j.micpath.2018.04.012
title:
  Resiquimod enhances mucosal and systemic immunity against avian infectious bronchitis virus vaccine in the chicken

abstract:
  Adjuvant enhancing mucosal immune response is preferred in controlling many pathogens at the portal of entry. Earlier, we reported that a toll-like-receptor 7 (TLR7) agonist, resiquimod (R-848), stimulated the systemic immunity when adjuvanted with the inactivated Newcastle disease virus vaccine in the chicken. Here, we report the effect of R-848 when adjuvanted with live or inactivated avian infectious bronchitis virus (IBV) vaccines with special emphasis on mucosal immunity. Specific pathogen free (SPF) chicks (n = 60) were equally divided into six groups at two weeks of age and immunized with either inactivated or live IBV vaccine adjuvanted with or without R-848. Groups that received either PBS or R-848 served as control. A booster was given on 14 days post-immunization (dpi). R-848 enhanced the antigen specific humoral and cellular immune responses when co-administered with the vaccines as evidenced by an increase in the antibody titre in ELISA and stimulation index in lymphocyte transformation test (LTT) till 35 dpi and increased proportion of CD4(+) and CD8(+) T cells on 21 dpi in the flow cytometry. Interestingly, it potentiated the IgA responses in the tear and intestinal secretions when used with both live and inactivated IBV vaccines. The combination of IBV vaccine with R-848 significantly up-regulated the transforming growth factor beta 4 (TGFβ4) transcripts in the peripheral blood mononuclear cells (PBMCs) than that of the respective vaccine per se. An enhanced secretory IgA response is likely due to the up-regulation of TGFβ4, which is responsible for class switching to IgA. In conclusion, co-administration of R-848 with inactivated or live IBV vaccine enhanced the systemic as well as mucosal immune responses in the chicken.


id: cord-298078-uqrwq5qk
title: Annexin A2 Binds RNA and Reduces the Frameshifting Efficiency of Infectious Bronchitis Virus
author: Kwak, Hoyun
date: 2011-08-30
url: https://doi.org/10.1371/journal.pone.0024067
doi: 10.1371/journal.pone.0024067
abstract:
  Annexin A2 (ANXA2) is a protein implicated in diverse cellular functions, including exocytosis, DNA synthesis and cell proliferation. It was recently proposed to be involved in RNA metabolism because it was shown to associate with some cellular mRNA. Here, we identified ANXA2 as a RNA binding protein (RBP) that binds IBV (Infectious Bronchitis Virus) pseudoknot RNA. We first confirmed the binding of ANXA2 to IBV pseudoknot RNA by ultraviolet crosslinking and showed its binding to RNA pseudoknot with ANXA2 protein in vitro and in the cells. Since the RNA pseudoknot located in the frameshifting region of IBV was used as bait for cellular RBPs, we tested whether ANXA2 could regulate the frameshfting of IBV pseudoknot RNA by dual luciferase assay. Overexpression of ANXA2 significantly reduced the frameshifting efficiency from IBV pseudoknot RNA and knockdown of the protein strikingly increased the frameshifting efficiency. The results suggest that ANXA2 is a cellular RBP that can modulate the frameshifting efficiency of viral RNA, enabling it to act as an anti-viral cellular protein, and hinting at roles in RNA metabolism for other cellular mRNAs.


id: cord-298920-1lc2xf7u
title: Canonical and Noncanonical Autophagy as Potential Targets for COVID-19
author: Bello-Perez, Melissa
date: 2020-07-05
url: https://www.ncbi.nlm.nih.gov/pubmed/32635598/
doi: 10.3390/cells9071619
abstract:
  The SARS-CoV-2 pandemic necessitates a review of the molecular mechanisms underlying cellular infection by coronaviruses, in order to identify potential therapeutic targets against the associated new disease (COVID-19). Previous studies on its counterparts prove a complex and concomitant interaction between coronaviruses and autophagy. The precise manipulation of this pathway allows these viruses to exploit the autophagy molecular machinery while avoiding its protective apoptotic drift and cellular innate immune responses. In turn, the maneuverability margins of such hijacking appear to be so narrow that the modulation of the autophagy, regardless of whether using inducers or inhibitors (many of which are FDA-approved for the treatment of other diseases), is usually detrimental to viral replication, including SARS-CoV-2. Recent discoveries indicate that these interactions stretch into the still poorly explored noncanonical autophagy pathway, which might play a substantial role in coronavirus replication. Still, some potential therapeutic targets within this pathway, such as RAB9 and its interacting proteins, look promising considering current knowledge. Thus, the combinatory treatment of COVID-19 with drugs affecting both canonical and noncanonical autophagy pathways may be a turning point in the fight against this and other viral infections, which may also imply beneficial prospects of long-term protection.


id: cord-299428-gon6bzat
title: Sequence analysis of infectious bronchitis virus isolates from the 1960s in the United States
author: Mondal, Shankar
date: 2012-10-11
txt: ./txt/cord-299428-gon6bzat.txt
cache: ./cache/cord-299428-gon6bzat.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1007/s00705-012-1500-y
doi: 10.1007/s00705-012-1500-y
summary:
  To better understand the molecular epidemiology of infectious bronchitis virus (IBV) in the United States following the introduction of commercial IBV vaccines, we sequenced the S1 and N structural protein genes of thirteen IBV field isolates collected in the 1960s. Analysis of the S1 sequence showed that seven isolates were of the Massachusetts (Mass) genotype, five were SE17, and one was of the Connecticut (Conn) genotype, suggesting that these three IBVs were circulating in commercial poultry raised in different regions in the United States during the 1960s. In addition, the Mass-type isolates had high levels of sequence identity in the S1 gene compared with widely used modified live vaccines (Mass41, Ma5 and H120) and modern field strains from the USA and other countries, suggesting a common ancestor.

abstract:
  To better understand the molecular epidemiology of infectious bronchitis virus (IBV) in the United States following the introduction of commercial IBV vaccines, we sequenced the S1 and N structural protein genes of thirteen IBV field isolates collected in the 1960s. Analysis of the S1 sequence showed that seven isolates were of the Massachusetts (Mass) genotype, five were SE17, and one was of the Connecticut (Conn) genotype, suggesting that these three IBVs were circulating in commercial poultry raised in different regions in the United States during the 1960s. The S1 genes of Mass-type isolates had high levels of sequence variation, representing 81.3-81.9 % nucleotide (nt) and 77.3-78.7 % amino acid (aa) identity when compared to those of the SE17-type isolates. In contrast, the N genes from the same isolates were less variable (>92 % nt and >93 % aa identity) when compared to those of the SE17-type isolates. Phylogenetic analysis based on the S1 gene indicated that one isolate (L748) was more closely related to the Mass type. In contrast, phylogenetic analysis based on the N gene showed that L748 was more closely related to the SE17 type, indicating that there had been exchange of S1 genetic materials between Mass- and SE17-like viruses. In addition, the Mass-type isolates had high levels of sequence identity in the S1 gene compared with widely used modified live vaccines (Mass41, Ma5 and H120) and modern field strains from the USA and other countries, suggesting a common ancestor. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00705-012-1500-y) contains supplementary material, which is available to authorized users.


id: cord-300104-855iw9wi
title: The Preparation of Chicken Kidney Cell Cultures for Virus Propagation
author: Hennion, Ruth M.
date: 2014-12-18
txt: ./txt/cord-300104-855iw9wi.txt
cache: ./cache/cord-300104-855iw9wi.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/25720471/
doi: 10.1007/978-1-4939-2438-7_6
summary:
  Chicken kidney (CK) cell cultures have historically proved useful for the assay of a number of viruses including coronaviruses. A technique for the preparation of such cell cultures, using a combination of manual and trypsin disaggregation of kidneys dissected from 2to 3-week-old birds is described. When all the kidneys required have been removed from the birds, agitate them in the beaker and discard the PBSa. Repeat this process until the wash PBSa looks clear ( see Note 6 ). 5. Dilute cell suspension in growth medium to the cell concentration required, seed culture fl asks and place in incubator until intact monolayer forms ( see Note 10 ). 6. Whilst some kidney cells may be lost in this process, it is an effective way of removing many of the red blood cells that are still present at this stage of the preparation.

abstract:
  Chicken kidney (CK) cell cultures have historically proved useful for the assay of a number of viruses including coronaviruses. A technique for the preparation of such cell cultures, using a combination of manual and trypsin disaggregation of kidneys dissected from 2- to 3-week-old birds is described. This technique routinely gives high cell yield together with high viability and the resultant adherent primary cultures can be used for virus growth and plaque formation.


id: cord-301720-majpfxqn
author: Saadat, Yousef
date: 2017-09-15
txt: ./txt/cord-301720-majpfxqn.txt
cache: ./cache/cord-301720-majpfxqn.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/29085606/
doi: nan
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

title:
  Molecular characterization of infectious bronchitis viruses isolated from broiler flocks in Bushehr province, Iran: 2014 - 2015

abstract:
  The aim of this study was to provide information on the molecular characteristic and the phylogenic relationship of infectious bronchitis viruses (IBV) strains in Bushehr province in comparison to other strains reported in the Middle East. Samples were collected from broiler flocks in Bushehr province during 2014 - 2015. These flocks had respiratory problems such as gasping, sneezing and bronchial rales. A number of 135 tracheal swabs were taken from fifteen flocks (nine swabs per flock). Each three swabs collected from each flock were pooled in one tube (finally, we had three tubes for each flock). The samples were subjected to reverse transcription polymerase chain reaction (RT-PCR). The PCR products of positive samples were analyzed by sequencing of a (392 bp) segment of the spike gene and the related results were compared with the other IBV sequences in GenBank database. Samples from twelve farms (80.0%) were found to be positive. The viruses from seven farms (46.6%) were identified as field viruses closely related to variant 2. The viruses from three farms (20.0%) were characterized as Mass type and were related to vaccine strains. Two different IB viruses (variant 2 and Mass) were detected in samples from two farms (13.3%). The variant 2 genotype detected in Bushehr had high similarity to variant 2 reported from the Middle East. These variants displayed homologies ranging from 72.9% to 76.5%, and 78.8% to 80.0% with H120 and 4/91, respectively. It is necessary to design vaccination program of poultry farms using IBV strains circulating in the region.


id: cord-301810-vtgdqart
title: Effect of Pullet Vaccination on Development and Longevity of Immunity
author: Aston, Emily J.
date: 2019-02-02
txt: ./txt/cord-301810-vtgdqart.txt
cache: ./cache/cord-301810-vtgdqart.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3390/v11020135
doi: 10.3390/v11020135
summary:
  Because of the need to protect long-lived poultry against respiratory tract pathogens from an early age, vaccination programs for pullets typically involve serial administration of a variety of vaccines, including infectious bronchitis virus (IBV), Newcastle disease virus (NDV), and infectious laryngotracheitis virus (ILTV). At 5 days following challenge with IBV GA98, vaccinated/challenged birds had significantly lower RNA loads compared to positive controls at all collection times and in all tissue samples, with the exception of cecal tonsil at 24 WOA (Table 1 ). ILTV-specific IgG titers in serum collected 5 days post-challenge were significantly higher in vaccinated birds from both challenged and non-challenged groups, compared to the positive and negative controls ( Figure 6 ). ILTV-specific IgG titers in serum collected 5 days post-challenge were significantly higher in vaccinated birds from both challenged and non-challenged groups, compared to the positive and negative controls ( Figure 6 ).

abstract:
  Avian respiratory disease causes significant economic losses in commercial poultry. Because of the need to protect long-lived poultry against respiratory tract pathogens from an early age, vaccination programs for pullets typically involve serial administration of a variety of vaccines, including infectious bronchitis virus (IBV), Newcastle disease virus (NDV), and infectious laryngotracheitis virus (ILTV). Often the interval between vaccinations is only a matter of weeks, yet it is unknown whether the development of immunity and protection against challenge when vaccines are given in short succession occurs in these birds, something known as viral interference. Our objective was to determine whether serially administered, live attenuated vaccines against IBV, NDV, and ILTV influence the development and longevity of immunity and protection against challenge in long-lived birds. Based on a typical pullet vaccination program, specific-pathogen-free white leghorns were administered multiple live attenuated vaccines against IBV, NDV, and ILTV until 16 weeks of age (WOA), after which certain groups were challenged with IBV, NDV, or ILTV at 20, 24, 28, 32, and 36 WOA. Five days post-challenge, viral load, clinical signs, ciliostasis, tracheal histopathology, and antibody titers in serum and tears were evaluated. We demonstrate that pullets serially administered live attenuated vaccines against IBV, NDV, and ILTV were protected against homologous challenge with IBV, NDV, or ILTV for at least 36 weeks, and conclude that the interval between vaccinations used in this study (at least 2 weeks) did not interfere with protection. This information is important because it shows that a typical pullet vaccination program consisting of serially administered live attenuated vaccines against multiple respiratory pathogens can result in the development of protective immunity against each disease agent.


id: cord-303393-9zs3qqo4
title: Infectious bronchitis virus from chickens in Al-Hasa, Saudi Arabia 2015-2016
author: Alsultan, Musaed Abdulaziz
date: 2019-03-19
txt: ./txt/cord-303393-9zs3qqo4.txt
cache: ./cache/cord-303393-9zs3qqo4.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/31089313/
doi: 10.14202/vetworld.2019.424-433
summary:
  AIM: This study aimed to isolate some of the currently circulating infectious bronchitis virus (IBV) strains from some broiler chicken farms in Al-Hasa and to do some molecular characteristics of these strains. MATERIALS AND METHODS: We collected 300 tissue specimens, including the trachea, bronchi, lungs, and kidneys from some four commercial chicken farms showing respiratory manifestations. We used three tissue suspensions (trachea, lungs, and kidneys) from three specimens representing three different IBV outbreaks in some chicken farms from Al-Hasa region. Some of these farms were reporting IBV outbreaks based on Figure-4: Phylogenetic analysis based on the partial S1 gene for the circulating infectious bronchitis virus (IBV) strains from some chicken farms in Al-Hasa region 2015-2016. Table-5: Pairwise distance analysis of partial S1 gene for the circulating IBV strains in some chicken farms in Al-Hasa region

abstract:
  AIM: This study aimed to isolate some of the currently circulating infectious bronchitis virus (IBV) strains from some broiler chicken farms in Al-Hasa and to do some molecular characteristics of these strains. MATERIALS AND METHODS: We collected 300 tissue specimens, including the trachea, bronchi, lungs, and kidneys from some four commercial chicken farms showing respiratory manifestations. We tested these tissue specimens by the real-time polymerase chain reaction (RT-PCR) and gel-based PCR. We selected some PCR positive samples for isolation in the embryonated chicken eggs (ECE). We sequenced some PCR-positive samples and conducted phylogenetic analysis based on the obtained sequences. RESULTS: Our molecular surveillance revealed that 31.6% of the tested specimens were IBV positive by PCR. We selected some positive specimens showing low Ct values by the qRT-PCR for virus isolation by the ECE. The infected eggs showed hemorrhage, dwarfing, and death in some cases after three passages in the ECE. We sequenced some of the positive PCR specimens and used the obtained sequences to draw the phylogenetic tree based on the partial IBV-ORF-1a, N, and S1 gene sequences. The phylogenetic trees based on the IBV-N and S1 gene sequences showed that the circulating IBV strains in Al-Hasa during 2016 was showing a high degree of identity to some strains from Taiwan and Italy. Meanwhile, the grouping of these strains based on the IBV-S1 sequences revealed that the currently circulating IBV strains in Al-Hasa belonged to Gr.I.7 along with strains from Taiwan. CONCLUSION: Our results confirmed the continuous circulation of the IBV among the chicken population in Al-Hasa despite the intensive application of vaccines against this virus.


id: cord-303588-bwllypvq
title: High-resolution melting curve analysis for infectious bronchitis virus strain differentiation
author: Ababneh, Mustafa
date: 2020-03-03
txt: ./txt/cord-303588-bwllypvq.txt
cache: ./cache/cord-303588-bwllypvq.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.14202/vetworld.2020.400-406
doi: 10.14202/vetworld.2020.400-406
summary:
  MATERIALS AND METHODS: In this study, qRT-PCR was conducted on a partial fragment S1 gene followed by a high resolution melting curve analysis (qRT-PCR/HRM) on 23 IBV-positive samples in Jordan. Although the third cluster contained the highest number of samples, it displayed no similarity to any of the reference vaccine strains, and, after comparing them with the sequencing results, we found that the samples in the third cluster were similar to the variant II-like (IS-1494-06) IBV field strain. CONCLUSION: Our developed qRT-PCR/HRM curve analysis was able to detect and rapidly identify novel and vaccine-related IBV strains as confirmed by S1 gene nucleotide sequences, making it a rapid and cost-effective tool. High-resolution melting (HRM) curve analysis is a newly established PCR-based technique that has been used to differentiate related strains of the same animal or avian virus [16] [17] [18] [19] . Those 22 samples, along with the five IBV vaccine reference strains, were subjected to qRT-PCR targeting the S1 gene followed with HRM curve analysis.

abstract:
  BACKGROUND AND AIM: Belonging to the Coronaviridae family, avian infectious bronchitis virus (IBV) causes respiratory, reproductive, and renal diseases in poultry. Preventative measures lie mainly in vaccination, while the gold standard for IBV classification and differentiation is based on the sequence analysis of the spike 1 (S1) gene. In this study, we tested a new assay for IBV strain classification that is less expensive and requires reduced time and effort to perform. We carried out a quantitative real-time polymerase chain reaction followed by high-resolution melting (qRT-PCR/HRM) curve analysis. MATERIALS AND METHODS: In this study, qRT-PCR was conducted on a partial fragment S1 gene followed by a high resolution melting curve analysis (qRT-PCR/HRM) on 23 IBV-positive samples in Jordan. For this assay, we utilized the most common IBV vaccine strains (Mass and 4/91) as a reference in the HRM assay. To evaluate the discrimination power of the qRT-PCR/HRM, we did the sequencing of the partial S1 gene. RESULTS: It was shown that HRM was able to classify IBV samples into four clusters based on the degree of similarity between their melting points: The first cluster exhibited the highest similarity to the 4/91 strain, while the second was similar to the Mass-related IBV strain. Although the third cluster contained the highest number of samples, it displayed no similarity to any of the reference vaccine strains, and, after comparing them with the sequencing results, we found that the samples in the third cluster were similar to the variant II-like (IS-1494-06) IBV field strain. Finally, the fourth cluster comprised one unique sample that was found to belong to the Q1 IBV strain. CONCLUSION: Our developed qRT-PCR/HRM curve analysis was able to detect and rapidly identify novel and vaccine-related IBV strains as confirmed by S1 gene nucleotide sequences, making it a rapid and cost-effective tool.


id: cord-303794-fn3jkiil
author: Hassan, Kareem E.
date: 2017-06-30
txt: ./txt/cord-303794-fn3jkiil.txt
cache: ./cache/cord-303794-fn3jkiil.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S003452881730022X
doi: 10.1016/j.rvsc.2017.06.024
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.

title:
  Experimental co-infection of infectious bronchitis and low pathogenic avian influenza H9N2 viruses in commercial broiler chickens

abstract:
  In this study, commercial broilers were experimentally infected with single (classical IBV, variant IBV or AIV-H9N2) or mixed AIV-H9N2 with classical, variant or vaccine strains of IBV. Birds were monitored for clinical and pathological outcomes and virus shedding for 10 days post infection (DPI). Clinical signs were limited to the respiratory tract in all challenged groups and varied from mild to moderate mouth breathing to severe respiratory signs with snorting sound and extended head. Mortalities were only recorded in mixed AIV-H9N2/variant IBV challenge group. AIV-H9N2 challenge caused tracheal petechial hemorrhage that progressed to tracheal congestion and caseation. In mixed AIV-H9N2/IBV vaccine challenge, severe tracheitis with bronchial cast formation was observed. In mixed AIV-H9N2/variant IBV challenge severe congestion of the tracheal mucosa and excessive exudates with a tendency to form tubular casts were observed. Kidney ureate deposition was only observed in variant IBV challenge group. Histopathologically, tracheal congestion, severe degeneration, and deciliation were noticed in all groups of mixed infection. Interestingly, hemorrhage and atrophy were observed in thymus gland of birds challenged with single AIV-H9N2 or mixed AIV-H9N2/IBV. There was no difference in the tracheal shedding level of variant IBV between single and mixed infected groups while classical IBV shedding increased in mixed infection group. Interestingly, the AIV-H9N2 showed constantly high shedding titers till 7DPI with variant or vaccine IBV co-infection. In conclusion, co-infection of IBV and AIV-H9N2 induced severe clinical outcome and high mortality. Also, IBV co-infection increased the shedding of AIV-H9N2 in experimentally infected birds.


id: cord-304278-0qy1nngs
title: Infectious bronchitis virus: immunopathogenesis of infection in the chicken
author: Raj, G. Dhinakar
date: 2007-11-12
txt: ./txt/cord-304278-0qy1nngs.txt
cache: ./cache/cord-304278-0qy1nngs.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/18483939/
doi: 10.1080/03079459708419246
summary:
  While infectious bronchitis (IB) is considered primarily a disease of the respiratory system, different IBV strains may show variable tissue tropisms and also affect the oviduct and the kidneys, with serious consequences. Nevertheless, the lack of correlation between antibodies and resistance, discrepancies between in vitro strain differentiation by VN tests and in vivo cross-protection results (Darbyshire, 1985) and re-excretion of virus in the presence of high titres of circulating antibodies (Jones & Ambali, 1987) all suggest that while humoral antibodies play a role in recovery from IBV infection, other immunological mechanisms are involved. Comparison of the susceptibility of chicks of different ages to infection with nephrosis-nephritis causing strain of infectious bronchitis virus Challenge experiments to evaluate cross-protection induced at the trachea and kidney level by vaccine strains and Belgian nephropathogenic isolates of avian infectious bronchitis virus Effects of avian infectious bronchitis virus (Arkansas strain) on vaccinated laying chickens

abstract:
  The immunopathogenesis of infectious bronchitis virus (IBV) infection in the chicken is reviewed. While infectious bronchitis (IB) is considered primarily a disease of the respiratory system, different IBV strains may show variable tissue tropisms and also affect the oviduct and the kidneys, with serious consequences. Some strains replicate in the intestine but apparently without pathological changes. Pectoral myopathy has been associated with an important recent variant. Several factors can influence the course of infection with IBV, including the age, breed and nutrition of the chicken, the environment and intercurrent infection with other infectious agents. Immunogenic components of the virus include the S (spike) proteins and the N nucleoprotein. The humoral, local and cellular responses of the chicken to IBV are reviewed, together with genetic resistance of the chicken. In long-term persistence of IBV, the caecal tonsil or kidney have been proposed as the sites of persistence. Antigenic variation among IBV strains is related to relatively small differences in amino acid sequences in the S1 spike protein. However, antigenic studies alone do not adequately define immunological relationships between strains and cross-immunisation studies have been used to classify IBV isolates into ‘protectotypes’. It has been speculated that changes in the S1 protein may be related to differences in tissue tropisms shown by different strains. Perhaps in the future, new strains of IBV may arise which affect organs or systems not normally associated with IB.


id: cord-304322-k9egxskw
author: Promkuntod, N.
date: 2015-06-30
txt: ./txt/cord-304322-k9egxskw.txt
cache: ./cache/cord-304322-k9egxskw.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S003452881500123X
doi: 10.1016/j.rvsc.2015.05.002
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

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:
  Abstract The new variants of the avian infectious bronchitis virus (IBV) produce a range of symptoms and cause global economic losses to the poultry industry. We investigated the S1 glycoprotein of 24 recent IBV isolates from chickens and demonstrated that two predominant genetic groups were circulating in southern Thailand between 2008 and 2013. Seven IBV variants, isolated from 2008 to 2009, were clustered in the Thailand THA001 group I while 15 IBV variants, isolated from 2009 to 2013, were classified into the QX-like group II. Moreover, a single isolate from a broiler was categorized into the Massachusetts-type, and an isolate from a layer belonged to the 4/91 type virus. Interestingly, both the IBV groups I and II were isolated from native chickens (62.5%) and caused a range of symptoms. Our results indicate that the QX-like viruses were predominant after 2009, replacing the THA001 type viruses. Furthermore, native chickens may contribute to the epidemiology of IB.


id: cord-305079-foifc8ch
author: Zhou, Ying Shun
date: 2013-02-22
txt: ./txt/cord-305079-foifc8ch.txt
cache: ./cache/cord-305079-foifc8ch.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0378113512004646
doi: 10.1016/j.vetmic.2012.08.013
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.

title:
  Establishment of reverse genetics system for infectious bronchitis virus attenuated vaccine strain H120

abstract:
  Infectious bronchitis virus (IBV) strain H120 was successfully rescued as infectious clone by reverse genetics. Thirteen 1.5–2.8 kb fragments contiguously spanning the virus genome were amplified and cloned into pMD19-T. Transcription grade complete length cDNA was acquired by a modified “No See’m” ligation strategy, which employed restriction enzyme Bsa I and BsmB I and ligated more than two fragments in one T4 ligase reaction. The full-length genomic cDNA was transcribed and its transcript was transfected by electroporation into BHK-21 together with the transcript of nucleocapsid gene. At 48 h post transfection, the medium to culture the transfected BHK-21 cells was harvested and inoculated into 10-days old SPF embryonated chicken eggs (ECE) to replicate the rescued virus. After passage of the virus in ECE five times, the rescued H120 virus (R-H120) was successfully recovered. R-H120 was subsequently identified to possess the introduced silent mutation site in its genome. Some biological characteristics of R-H120 such as growth curve, EID50 and HA titers, were tested and all of them were very similar to its parent strain H120. In addition, both R-H120 and H120 induced a comparable titer of HA inhibition (HI) antibody in immunized chickens and also provided up to 85% of immune protection to the chickens that were challenged with Mass41 IBV strain. The present study demonstrated that construction of infectious clone from IBV vaccine strain H120 is possible and IBV-H120 can be use as a vaccine vector for the development of novel vaccines through molecular recombination and the modified reverse genetics approach.


id: cord-305684-ipeup5mp
author: Chen, Yuqiu
date: 2016-12-16
txt: ./txt/cord-305684-ipeup5mp.txt
cache: ./cache/cord-305684-ipeup5mp.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/28062000/
doi: 10.1016/j.vetmic.2016.12.017
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) .

title:
  Identification and molecular characterization of a novel serotype infectious bronchitis virus (GI-28) in China

abstract:
  Avian infectious bronchitis coronavirus (IBV) is a major poultry pathogen. A characteristic feature of IBV is the occurrence of many different strains belonging to different serotypes, which renders complete control of the disease by vaccination a challenging task due to the poor cross-protection between different serotypes. In this study, based on the results of S1 sequence analysis and virus cross-neutralization tests, IBV strain ck/CH/LGX/111119 was found to be genetically and antigenically different from other known IBV types, representing not only a novel genotype, but also a novel serotype (designated as GI-28). Viruses belonging to this novel serotype have been isolated from several regions in China in recent years, suggesting endemic circulation of the serotype in various geographic locations in China. Further studies by complete genomic analysis showed that strain ck/CH/LGX/111119 may have originated from recombination events involving LX4 genotype IBVs and an as-yet-unidentified IBV donating a S1 gene, or from the result of accumulation of mutations and selections, especially in the S1 gene, from a LX4 genotype virus. ck/CH/LGX/111119 is a nephropathogenic strain, although it had broader tissue tropism (respiratory, digestive, urinary, and reproductive tracts) among chickens challenged at one day old. Infection of the oviducts with ck/CH/LGX/111119 found in this study may have severe implications because the virus will likely induce the occurrence of false layers.


id: cord-306380-msk9p1yy
title: Evidence of genetic diversity generated by recombination among avian coronavirus IBV
author: Lee, C.-W.
date: 2000
txt: ./txt/cord-306380-msk9p1yy.txt
cache: ./cache/cord-306380-msk9p1yy.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/11087096/
doi: 10.1007/s007050070044
summary:
  Phylogenetic analysis of selected regions of the genome of the DE072 serotype field isolates further support those results and indicate that isolates within the same serotype may have different amounts of nucleotide sequence similarity with each other in individual genes other than the S gene. Further, we conducted sequence analysis of six isolates of the DE072 serotype in order to determine if recombination is frequently occurring in this region in field isolates of IBV. We conducted phylogenetic analysis by dividing 3.8 kb of the 3 end of the genome among five IBV strains at the IG sequences. However, these 6 isolates had a much different level of nucleotide sequence similarity with each other in gene 3 and gene 4, and clustered randomly with other serotypes of IBV (Fig. 3) . Sequence analysis of gene 3, gene 4 and gene 5 of avian infectious bronchitis virus strain CU-T2 Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus

abstract:
  Previously, we demonstrated that the DE072 strain of IBV is a recombinant which has an IBV strain D1466-like sequence in the S gene. Herein, we analyzed the remaining 3.8 kb 3′ end of the genome, which includes Gene 3, Gene 4, Gene 5, Gene 6, and the 3′ non-coding region of the DE072 and D1466 strains. Those two viruses had high nucleotide similarity in Gene 4. However, the other individual genes had a much different level of sequence similarity with the same gene of the other IBV strains. The genome of five IBV strains, of which the complete sequence of the 3′ end of the genome has been determined, were divided at an intergenic (IG) consensus sequence (CTGAACAA or CTTAACAA) and compared phylogenetically. Phylogenetic trees of different topology indicated that the consensus IG sequences and the highly conserved sequence around this regions may serve as recombination ‘hot spots’. Phylogenetic analysis of selected regions of the genome of the DE072 serotype field isolates further support those results and indicate that isolates within the same serotype may have different amounts of nucleotide sequence similarity with each other in individual genes other than the S gene. Presumably this occurs because the consensus IG sequence serves as the template switching site for the viral encoded polymerase.


id: cord-306976-p2521bl4
author: Gao, Mengying
date: 2016-08-15
txt: ./txt/cord-306976-p2521bl4.txt
cache: ./cache/cord-306976-p2521bl4.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.vetmic.2016.05.018
doi: 10.1016/j.vetmic.2016.05.018
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.

title:
  Serotype, antigenicity, and pathogenicity of a naturally recombinant TW I genotype infectious bronchitis coronavirus in China

abstract:
  Since 2009, strains of the naturally recombinant TW I genotype of infectious bronchitis virus (IBV) have caused considerable damage to the Chinese poultry industry. To better understand the antigenicity and pathogenesis of this genotype, the characteristics of the ck/CH/LDL/140520 strain were compared to those of four commercial IB vaccine strains that are used commonly in China, as well as four attenuated viruses that represent two types of IBV strains, which are believed to have originated in China and are the predominant IBV types circulating in chicken flocks in China and many other parts of the world. The results showed that all eight strains were genetically and serotypically different from the strain ck/CH/LDL/140520. Furthermore, neither the vaccine strains nor the attenuated viruses could provide complete respiratory protection of chickens against a challenge with the ck/CH/LDL/140520 strain, indicating that it is necessary to develop new live vaccines or to evaluate the use of established vaccines in combination to control naturally recombinant TW I-type IBV strains in the future. Our results showed that strain ck/CH/LDL/140520 is very pathogenic, and that it is able to cause cystic oviducts in a high percentage of birds, as well as mortality due to nephritis and respiratory distress with complete tracheal ciliostasis, especially in chickens infected at 1 day of age.


id: cord-307304-irji8owi
author: Britton, Paul
date: 2004-11-05
txt: ./txt/cord-307304-irji8owi.txt
cache: ./cache/cord-307304-irji8owi.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/15620403/
doi: 10.1016/j.jviromet.2004.09.017
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) .

title:
  Generation of a recombinant avian coronavirus infectious bronchitis virus using transient dominant selection

abstract:
  A reverse genetics system for the avian coronavirus infectious bronchitis virus (IBV) has been described in which a full-length cDNA, corresponding to the IBV (Beaudette-CK) genome, was inserted into the vaccinia virus genome following in vitro assembly of three contiguous cDNAs [Casais, R., Thiel, V., Siddell, S.G., Cavanagh, D., Britton, P., 2001. Reverse genetics system for the avian coronavirus infectious bronchitis virus. J. Virol. 75, 12359–12369]. The method has subsequently been used to generate a recombinant IBV expressing a chimaeric S gene [Casais, R., Dove, B., Cavanagh, D., Britton, P., 2003. Recombinant avian infectious bronchitis virus expressing a heterologous spike gene demonstrates that the spike protein is a determinant of cell tropism. J. Virol. 77, 9084–9089]. Use of vaccinia virus as a vector for the full-length cDNA of the IBV genome has the advantage that modifications can be made to the IBV cDNA using homologous recombination, a method frequently used to insert and delete sequences from the vaccinia virus genome. We describe the use of homologous recombination as a method for modifying the Beaudette full-length cDNA, within the vaccinia virus genome, without the requirement for in vitro assembly of the IBV cDNA. To demonstrate the feasibility of the method we exchanged the ectodomain of the Beaudette spike gene for the corresponding region from IBV M41 and generated two recombinant infectious bronchitis viruses (rIBVs) expressing the chimaeric S protein, validating the method as an alternative way for generating rIBVs.


id: cord-308591-cs8os2f5
author: Tawakol, Maram M.
date: 2019-11-29
txt: ./txt/cord-308591-cs8os2f5.txt
cache: ./cache/cord-308591-cs8os2f5.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1080/20008686.2019.1686822
doi: 10.1080/20008686.2019.1686822
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.

title:
  Evaluation of bacteriophage efficacy in reducing the impact of single and mixed infections with Escherichia coli and infectious bronchitis in chickens

abstract:
  Infectious bronchitis virus (IBV) represents a major threat to poultry production worldwide particularly when complicated with bacterial infection. In the present study samples were collected from forty broiler farms with respiratory manifestations to characterize IBV and E. coli. Bacteriophages were isolated and enriched from sampled farms to study its efficacy to control single and mixed infections with E. coli and IBV in vivo. Twelve out of forty farms were positive for IBV. Phylogenetic analysis of partial spike protein revealed that all positive cases clustered within the GI-23 genotype. Eight out of forty farms were positive for E. coli serogroups O26, O78, O86, O114, O119, with O125 found on three farms. Bacteriophage treatment delayed the onset and reduced the severity of clinical signs, and prevented the mortality associated with single and mixed infection with IBV and E. coli. Furthermore, in mixed infections, bacteriophage treatment significantly reduced E. coli as well as IBV shedding. Groups treated with bacteriophages showed a significant reduction of E. coli shedding that gradually decreased over time, in contrast to higher and gradually increasing shedding without bacteriophage treatment. In conclusion, bacteriophage treatment significantly reduced the pathogenicity and shedding of IBVand E. coli in mixed infections.


id: cord-308950-bl83r4v3
title: The role of feline aminopeptidase N as a receptor for infectious bronchitis virus : Brief Review
author: Miguel, B.
date: 2002
txt: ./txt/cord-308950-bl83r4v3.txt
cache: ./cache/cord-308950-bl83r4v3.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/12417943/
doi: 10.1007/s00705-002-0888-1
summary:
  Our objective was to determine if fAPN can serve as a receptor for infectious bronchitis virus (IBV). Feline kidney cells that express fAPN and hamster kidney fibroblasts that do not express fAPN were inoculated with IBV and monitored for replication by indirect fluorescent assay and confocal microscopy and in chicken embryonated eggs. To evaluate the permissiveness of cells to IBV, monolayers of transfected (pBK-fAPN and pBK-CMV) BHK-21, non-transfected BHK-21 and FEK on coverslips were infected with a 10 3.2 EID 50 of Ark/IBV virus. To test the hypothesis that the feline APN had a role in permissiveness of FEK cells to Ark/IBV, BHK-21 cells were transfected with pBK-CMV plasmid or pBK-fAPN. The BHK-21 cells transfected with pBK-fAPN were shown to express the fAPN receptor on the cell surface (Fig. 3) , and were permissive to Ark/IBV (Figs.

abstract:
  Feline aminopeptidase N (fAPN) has been shown to serve as a receptor for feline, canine, porcine and human coronaviruses. Our objective was to determine if fAPN can serve as a receptor for infectious bronchitis virus (IBV). Feline kidney cells that express fAPN and hamster kidney fibroblasts that do not express fAPN were inoculated with IBV and monitored for replication by indirect fluorescent assay and confocal microscopy and in chicken embryonated eggs. The results showed that the feline cells were permissive to IBV but the hamster cells were not. The hamster cells became permissive to IBV after transfection with a fAPN cDNA suggesting that the feline APN molecule plays a role in IBV entry.


id: cord-309469-2naxn580
author: An, Hongliu
date: 2019-01-05
txt: ./txt/cord-309469-2naxn580.txt
cache: ./cache/cord-309469-2naxn580.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.virol.2018.12.019
doi: 10.1016/j.virol.2018.12.019
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.

title:
  Identification and formation mechanism of a novel noncoding RNA produced by avian infectious bronchitis virus

abstract:
  Viral noncoding (nc) RNAs have been shown to play important roles in viral life cycle. Many viruses employ different mechanism to produce ncRNAs. Here, we report that coronavirus infectious bronchitis virus (IBV) produces a novel ncRNA in virus-infected cells. This ncRNA consists of 563 nucleotides excluding a poly(A) tail, is mainly derived from the 3′-untranslated region of IBV genome, and contains a 63-nt-long of terminal leader sequence derived from the 5′ end of the viral genome. Using mutagenesis and reverse genetics, we reveal that this ncRNA is a subgenomic RNA generated by discontinuous transcription mechanism.


id: cord-309623-2ngr682l
author: Han, Xiaoxiao
date: 2017-07-26
txt: ./txt/cord-309623-2ngr682l.txt
cache: ./cache/cord-309623-2ngr682l.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/28933760/
doi: 10.3390/v9080198
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.

title:
  Infectious Bronchitis Virus Infection Induces Apoptosis during Replication in Chicken Macrophage HD11 Cells

abstract:
  Avian infectious bronchitis has caused huge economic losses in the poultry industry. Previous studies have reported that infectious bronchitis virus (IBV) infection can produce cytopathic effects (CPE) and apoptosis in some mammalian cells and primary cells. However, there is little research on IBV-induced immune cell apoptosis. In this study, chicken macrophage HD11 cells were established as a cellular model that is permissive to IBV infection. Then, IBV-induced apoptosis was observed through a cell viability assay, morphological changes, and flow cytometry. The activity of caspases, the inhibitory efficacy of caspase-inhibitors and the expression of apoptotic genes further suggested the activation of apoptosis through both intrinsic and extrinsic pathways in IBV-infected HD11 cells. Additionally, ammonium chloride (NH(4)Cl) pretreated HD11 cells blocked IBV from entering cells and inhibited IBV-induced apoptosis. UV-inactivated IBV also lost the ability of apoptosis induction. IBV replication was increased by blocking caspase activation. This study presents a chicken macrophage cell line that will enable further analysis of IBV infection and offers novel insights into the mechanisms of IBV-induced apoptosis in immune cells.


id: cord-310372-qc6941pm
author: Ji, Jun
date: 2011-04-22
txt: ./txt/cord-310372-qc6941pm.txt
cache: ./cache/cord-310372-qc6941pm.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/1743-422x-8-184
doi: 10.1186/1743-422x-8-184
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

title:
  Phylogenetic distribution and predominant genotype of the avian infectious bronchitis virus in China during 2008-2009

abstract:
  BACKGROUND: The nephropathogenic avian infectious bronchitis (IB) caused unprecedented economic losses to the commercial chicken industry of China in 2008-2009. To investigate the prevalence of nephropathogenic IB in China, eighty IBV isolates from different provinces during 2008-2009 were identified by dwarf embryo test and RT-PCR. RESULTS: The strains were mostly isolated in winter and spring with a wide age range of IB outbreaks, from 4 to 69 days. By the virus recovery trials, 70/80 of the strains resulted in the deaths or distresses of birds from nephritis. To learn more about the molecular evolutionary characteristics of the circulating field strains, the coding region of major spike 1 (S1) protein gene of these strains was RT-PCR amplified and sequenced. Compared to the published representative strains, nucleotides and amino acids sequence analysis indicated that the S1 genes of these strains and the reference strains displayed homologies ranging from 75.1% to 99.8% and from 73.1% to 99.8% respectively. S1 protein of the major pandemic strains contained 540 or 542 amino acids with the cleavage site of HRRRR or RRFRR. Phylogenetic analysis revealed that recent field isolates of IBV in China were mostly belonged to A2-branch (QXIBV-branch) and HN08-branch, only one isolate was belonged to Gray-branch and M41-branch respectively. Most of the 80 strains showed evolutionarily distant from vaccine strains. CONCLUSIONS: The results of this study suggested that nephropathogenic IBVs were mainly A2-like strains in China during 2008-2009.


id: cord-310536-u30cufg7
author: Finger, Paula Fonseca
date: 2018-12-12
txt: ./txt/cord-310536-u30cufg7.txt
cache: ./cache/cord-310536-u30cufg7.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/s12985-018-1096-2
doi: 10.1186/s12985-018-1096-2
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

title:
  Combined use of ELISA and Western blot with recombinant N protein is a powerful tool for the immunodiagnosis of avian infectious bronchitis

abstract:
  BACKGROUND: The avian infectious bronchitis virus (IBV) remains a significant source of loss in the poultry industry and early diagnosis is required to prevent the disease from spreading. This study examined the combined use of an ELISA and Western blot (WB) to detect antibodies against the nucleocapsid protein (N) of IBV. The coding sequence for N was amplified by RT-PCR and expressed in Escherichia coli. A soluble recombinant N protein (rN) of approximately 50 kDa was obtained. A total of 389 sera were tested against the rN in ELISA and the results were compared with those of the commercial IDEXX IBV Ab test. ELISA-rN achieved a 90.34% sensitivity and 90.16% specificity. WB confirmed all false negative sera in ELISA-rN or IDEXX test as truly positive. The current study indicate that the combined use of rN in ELISA and WB is a powerful tool for the immunodiagnosis of avian infectious bronchitis. METHODS: Constructed recombinant pAE/n expression vectors were used to transform E. coli BL21(DE3) Star competent cells (Invitrogen). The rN of infectious bronchitis virus was purified by affinity chromatography using HisTrap HP 1 mL columns pre-packed with pre-charged Ni Sepharose in the ÄKTAprime Automated Liquid Chromatography system (GE Healthcare). A total of 389 serum samples from chickens were used to develop and evaluate the ELISA-rN test. To standardize the indirect ELISA development, serum dilutions (1:100, 1:200 and 1:400) and different concentrations of purified rN antigen (50, 100 and 200 ng/well) were tested. Positive and negative sera for IBV were used as controls. The results were compared with those obtained from a commercial kit. Serum samples scored as negative with the commercial kit but as positive with the ELISA-rN were further analysed by Western blot analyses using the rN protein as an antigen. The results of the ELISA-rN were compared to the commercial kit results using receiver-operating characteristics curves, area under the curve, and confidence intervals with the software GraphPad Prism version 6.0 for Windows (GraphPad Software, USA). RESULTS: The expected cDNA fragment of approximately 1240 bp was successfully amplified by PCR using primers designed to select for the coding region of the N protein. The rN was expressed as a soluble protein to avoid the refolding steps and, after purification a yield of 10 mg/L of rN was obtained. The SDS-PAGE results demonstrated the presence of two distinct bands that had a molecular mass of approximately 45 and 50 KDa. Out of 244 sera that scored positive in the commercial ELISA IDEXX IBV Ab Test, 220 were also positive in the ELISA-rN, yielding an ELISA-rN test sensitivity of 90.16%. Out of 145 sera that scored negative in the IDEXX IBV Ab Test, 131 also scored negative in the ELISA-rN, indicating a specificity of 90.34%. Sera that tested negative in the ELISA-rN and positive in the commercial test also reacted with the rN protein in Western blot. CONCLUSIONS: The association between the ELISA and Western blot techniques developed in this study with a subunit of IBV (rN) were able to detect antibodies that the commercial ELISA did not detect suggesting that the ELISA-rN has greater sensitivity.


id: cord-312489-ywep0c08
title: Decreased neutralizing antigenicity in IBV S1 protein expressed from mammalian cells
author: Andoh, Kiyohiko
date: 2015-10-02
txt: ./txt/cord-312489-ywep0c08.txt
cache: ./cache/cord-312489-ywep0c08.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0168170215002841
doi: 10.1016/j.virusres.2015.06.019
summary:
  We evaluated the antigenicity of recombinant infectious bronchitis virus (IBV) S1 protein expressed in mammalian cells. Native S1 ELISA detected similar titers in the sera of animals immunized with recombinant S1 protein compared to those in sera of chickens immunized with inactivated virus (Fig. 6b ) (Control experiments (data not shown) demonstrated that mock and unvaccinated control groups did not differ from each other in VN and ELISA tests of anti-S1 activity.) These results indicated that while recombinant S1 protein retained antigenicity (the ability to induce antibodies against S1 protein), the resulting antibodies was decreased its neutralizing activity, in contrast to those induced by inactivated virus. The S1 glycoprotein but not the N or M proteins of avian infectious bronchitis virus induces protection in vaccinated chickens Induction of protective immunity in chickens vaccinated with infectious bronchitis virus S1 glycoprotein expressed by a recombinant baculovirus

abstract:
  We evaluated the antigenicity of recombinant infectious bronchitis virus (IBV) S1 protein expressed in mammalian cells. Recombinant S1 was expressed as a secreted protein fused with a trimerization motif peptide, then purified using Ni Sepharose. The purified protein was analyzed by Western blotting, mixed with oil adjuvant, and administered to 29-day-old specific-pathogen-free chickens. Six weeks after immunization, anti-IBV neutralizing titer and anti-S1 ELISA titer were determined; immunized chickens then were inoculated with IBV via the trachea and ciliary activity was observed. Results showed that the recombinant S1 protein was highly glycosylated, and the neutralizing antigenicity of recombinant S1 protein was lower than that of inactivated virus. However, anti-S1 ELISA indicated that the recombinant S1 protein induced antibodies against S1. These results suggest that the recombinant S1 may retain non-neutralizing epitopes but have unnatural glycosylation pattern and conformation, resulting in lacking neutralizing conformational epitopes. In conclusion, the neutralizing antigenicity of recombinant S1 protein expressed from mammalian cells was decreased, and was not sufficient to induce neutralizing antibodies.


id: cord-313676-6rebpe57
title: Enteric Virus Diversity Examined by Molecular Methods in Brazilian Poultry Flocks
author: De la Torre, David I.
date: 2018-03-29
txt: ./txt/cord-313676-6rebpe57.txt
cache: ./cache/cord-313676-6rebpe57.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3390/vetsci5020038
doi: 10.3390/vetsci5020038
summary:
  The most common enteric viruses affecting commercial flocks in Brazil include Fowl Adenovirus of group I (FAdV-I), Chicken Parvovirus (ChPV), Chicken Astrovirus (CAstV), Avian Nephritis Virus (ANV), Infectious Bronchitis Virus (IBV), Avian Reovirus (AReo), and Avian Rotavirus (ARtV). The main enteric viruses reported to cause enteric diseases are found in single and multiple infections and include the Fowl Adenovirus of group I (FAdV-I); Chicken Parvovirus (ChPV); two viruses from the Astroviridae family: Chicken Astrovirus (CAstV) and Avian Nephritis Virus (ANV); two viruses from the Reoviridae family: Avian Reovirus (AReo) and Avian Rotavirus (ARtV); and a member of the Coronaviridae family, Infectious Bronchitis Virus (IBV) [4, [6] [7] [8] [9] . The association of enteric virus with the age of broilers, breeders, and layers (Tables 4 and 5) showed that molecular diagnosis of these viruses can be performed at different stages of production, which can be useful in the control of vertical infections.

abstract:
  Enteric viruses play an important role in the Brazilian poultry industry due to the economic impact of resulting low yields of broilers, layers, and breeders. The most common enteric viruses affecting commercial flocks in Brazil include Fowl Adenovirus of group I (FAdV-I), Chicken Parvovirus (ChPV), Chicken Astrovirus (CAstV), Avian Nephritis Virus (ANV), Infectious Bronchitis Virus (IBV), Avian Reovirus (AReo), and Avian Rotavirus (ARtV). The aim of this study was to identify single and multiple infections using data obtained from 270 samples from eleven Brazilian states, corresponding to the period between 2010 and 2017. This was accompanied by an analysis of the relationship between the age of birds, clinical signs, and geographical distribution, using Polymerase Chain Reaction (PCR) and Reverse Transcription-PCR (RT-PCR) techniques. Twenty-five profiles of virus combinations were detected. Single infections were encountered in 86.3% of samples, and multiple infections were present in the remaining 13.7%. Both single and multiple infections affected all kinds of commercial chickens with digestive problems, stunting syndrome, decreases in egg and meat production, increased mortality, and respiratory signs. FAdV-I, ChPV, CAstV, ANV, and ARtV were mostly detected in young broilers, in contrast with IBV, which was detected in hens from one to greater than 51 weeks of age. These results exhibit the complexity of enteric diseases and the still poorly understood role of each pathogen as a unique etiological agent.


id: cord-316153-wet0go35
author: Jia, W.
date: 1995
txt: ./txt/cord-316153-wet0go35.txt
cache: ./cache/cord-316153-wet0go35.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/7710354/
doi: 10.1007/bf01309861
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

title:
  A novel variant of avian infectious bronchitis virus resulting from recombination among three different strains

abstract:
  An antigenic variant of avian infectious bronchitis virus (IBV), a coronavirus, was isolated and characterized. This strain, CU-T2, possesses a number of unusual features, which have not been previously observed in IBV. The S1 glycoprotein of CU-T2 carries virus-neutralizing and serotype-specific epitopes of two IBV serotypes, Arkansas (Ark) and Massachusetts (Mass). Sequence analysis revealed that the virus, originally an Ark serotype, has acquired the Mass-specific epitope by mutation(s). This provides evidence that point mutations may lead to generation of IBV antigenic variants in the field. It was further observed that two independent recombination events involving three different IBV strains had occurred in the S2 glycoprotein gene and N protein gene of CU-T2, indicating that genomic RNA recombination in IBV may occur in multiple genes in nature. It was especially significant that a sequence of Holland 52 (a vaccine strain) had replaced half of the N gene of CU-T2. This proves that recombination among vaccine strains is contributing to the generation of IBV variants in the field. Based on these observations it is predicted that every IBV field isolate could have unique genetic nature. Therefore, several recently reported diagnostic and serotyping methods of IBV which are based on dot-blot hybridization, restriction fragment length polymorphism (RFLP), and polymerase chain reaction (PCR), may not reveal the true antigenic and/or genetic nature of IBV isolates, and may in fact yield misleading information.


id: cord-316234-vtjsfi2c
title: New oligonucleotide microarray for rapid diagnosis of avian viral diseases
author: Sultankulova, Kulyaisan T.
date: 2017-04-05
txt: ./txt/cord-316234-vtjsfi2c.txt
cache: ./cache/cord-316234-vtjsfi2c.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1186/s12985-017-0738-0
doi: 10.1186/s12985-017-0738-0
summary:
  BACKGROUND: We developed a new oligonucleotide microarray comprising 16 identical subarrays for simultaneous rapid detection of avian viruses: avian influenza virus (AIV), Newcastle disease virus (NDV), infection bronchitis virus (IBV), and infectious bursal disease virus (IBDV) in singleand mixed-virus infections. METHODS AND RESULTS: The paper describes the technique for rapid and simultaneous diagnosis of avian diseases such as avian influenza, Newcastle disease, infectious bronchitis and infectious bursal disease with use of oligonucleotide microarray, conditions for hybridization of fluorescent-labelled viral cDNA on the microarray and its specificity tested with use of AIV, NDV, IBV, IBDV strains as well as biomaterials from poultry. The paper describes the technique for rapid and simultaneous diagnosis of avian diseases such as avian influenza, Newcastle disease, infectious bronchitis and infectious bursal disease with use of oligonucleotide microarray, conditions for hybridization of fluorescentlabelled viral cDNA on the microarray and its specificity tested with use of AIV, NDV, IBV, IBDV strains as well as biomaterials from poultry.

abstract:
  BACKGROUND: We developed a new oligonucleotide microarray comprising 16 identical subarrays for simultaneous rapid detection of avian viruses: avian influenza virus (AIV), Newcastle disease virus (NDV), infection bronchitis virus (IBV), and infectious bursal disease virus (IBDV) in single- and mixed-virus infections. The objective of the study was to develop an oligonucleotide microarray for rapid diagnosis of avian diseases that would be used in the course of mass analysis for routine epidemiological surveillance owing to its ability to test one specimen for several infections. METHODS AND RESULTS: The paper describes the technique for rapid and simultaneous diagnosis of avian diseases such as avian influenza, Newcastle disease, infectious bronchitis and infectious bursal disease with use of oligonucleotide microarray, conditions for hybridization of fluorescent-labelled viral cDNA on the microarray and its specificity tested with use of AIV, NDV, IBV, IBDV strains as well as biomaterials from poultry. Sensitivity and specificity of the developed microarray was evaluated with use of 122 specimens of biological material: 44 cloacal swabs from sick birds and 78 tissue specimens from dead wild and domestic birds, as well as with use of 15 AIV, NDV, IBV and IBDV strains, different in their origin, epidemiological and biological characteristics (RIBSP Microbial Collection). This microarray demonstrates high diagnostic sensitivity (99.16% within 95% CI limits 97.36–100%) and specificity (100%). Specificity of the developed technique was confirmed by direct sequencing of NP and M (AIV), VP2 (IBDV), S1 (IBV), NP (NDV) gene fragments. CONCLUSION: Diagnostic effectiveness of the developed DNA microarray is 99.18% and therefore it can be used in mass survey for specific detection of AIV, NDV, IBV and IBDV circulating in the region in the course of epidemiological surveillance. Rather simple method for rapid diagnosis of avian viral diseases that several times shortens duration of assay versus classical diagnostic methods is proposed.


id: cord-316525-uadfehr6
title: Testing the hypothesis of a recombinant origin of the SARS-associated coronavirus
author: Zhang, X. W.
date: 2004-10-11
txt: ./txt/cord-316525-uadfehr6.txt
cache: ./cache/cord-316525-uadfehr6.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/15480857/
doi: 10.1007/s00705-004-0413-9
summary:
  Surprisingly, we found that 7 putative recombination regions, located in Replicase 1ab and Spike protein, exist between SARS-CoV and other 6 coronaviruses: porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), bovine coronavirus (BCoV), human coronavirus 229E (HCoV), murine hepatitis virus (MHV), and avian infectious bronchitis virus (IBV). After potential recombination events were identified by at least 3 methods above, separate neighbor joining trees were constructed for each putative recombination region to better evaluate the evidence for conflicting evolutionary histories of different sequence regions. Two regions (13151-13299 and 16051-16449, position in alignment) are identified as putative recombination regions and all 6 coronaviruses are potential parents with SARS-CoV as potential daughter. In this study, seven recombination detection methods and phylogenetic analyses were performed on SARS-CoV and the six coronaviruses identified by BLAST (IBV, BCoV, HCoV, MHV, PEDV and TGEV).

abstract:
  The origin of severe acute respiratory syndrome-associated corona-virus (SARS-CoV) is still a matter of speculation, although more than one year has passed since the onset of the SARS outbreak. In this study, we implemented a 3-step strategy to test the intriguing hypothesis that SARS-CoV might have been derived from a recombinant virus. First, we blasted the whole SARS-CoV genome against a virus database to search viruses of interest. Second, we employed 7 recombination detection techniques well documented in successfully detecting recombination events to explore the presence of recombination in SARS-CoV genome. Finally, we conducted phylogenetic analyses to further explore whether recombination has indeed occurred in the course of coronaviruses history predating the emergence of SARS-CoV. Surprisingly, we found that 7 putative recombination regions, located in Replicase 1ab and Spike protein, exist between SARS-CoV and other 6 coronaviruses: porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), bovine coronavirus (BCoV), human coronavirus 229E (HCoV), murine hepatitis virus (MHV), and avian infectious bronchitis virus (IBV). Thus, our analyses substantiate the presence of recombination events in history that led to the SARS-CoV genome. Like the other coronaviruses used in the analysis, SARS-CoV is also a mosaic structure.


id: cord-317347-by8albr9
title: Age-dependent immune responses and immune protection after avian coronavirus vaccination
author: van Ginkel, Frederik W.
date: 2015-05-28
txt: ./txt/cord-317347-by8albr9.txt
cache: ./cache/cord-317347-by8albr9.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0264410X1500479X
doi: 10.1016/j.vaccine.2015.04.026
summary:
  The delayed and/or lower antibody response combined with lower IgG avidity indices coincided with increased tracheal inflammation and depletion of tracheal epithelia cells and goblet cells upon IBV field strain challenge. Therefore, the ability of SPF chickens of different age to induce an IBV-specific antibody response and protect against challenge with an IBV field strain was measured. In order to measure IgG (IgY), IgA and IgM antibody levels in plasma and tears of chicken, an IBV-specific enzyme-linked immunosorbent assay (ELISA) was developed as previously described [20] . These data are consistent with a delay in the IgA plasma response to IBV in birds vaccinated at a younger age and a non-significant decline in mean IgA titers in the 1-day-old group. This would be consistent with a drop of presumably natural maternal IBV-specific IgM antibodies in these SPF chickens in the day 7 control age group.

abstract:
  Infectious bronchitis virus (IBV) is an endemic disease of chickens and a major contributor to economic losses for the poultry industry despite vaccination. Recent observations indicated that chicks may have an immature immune system immediately after hatching when vaccinated for IBV. Therefore we hypothesized that early IBV vaccination will generate an immature, poorly protective IBV-specific immune response contributing to immune escape and persistence of IBV. To test this hypothesis the IBV-specific immune response and immune protection were measured in chicks vaccinated at different ages. This demonstrated a delayed production of IgG and IgA plasma antibodies in the 1, 7 and 14-day-old vaccination groups and also lower IgA antibody levels were observed in plasma of the 1-day-old group. Similar observations were made for antibodies in tears. In addition, IgG antibodies from the 1-day-old group had lower avidity indices than day 28 vaccinated birds. The delayed and/or lower antibody response combined with lower IgG avidity indices coincided with increased tracheal inflammation and depletion of tracheal epithelia cells and goblet cells upon IBV field strain challenge. The lack of vaccine-mediated protection was most pronounced in the 1-day-old vaccination group and to a lesser extent the 7-day-old group, while the 14-day-old and older chickens were protected. These data strongly support IBV vaccination after day 7 post hatch.


id: cord-317587-rrx2r4n2
author: Fan, Wensheng
date: 2019-09-26
txt: ./txt/cord-317587-rrx2r4n2.txt
cache: ./cache/cord-317587-rrx2r4n2.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/31561498/
doi: 10.3390/v11100898
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

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

abstract:
  The high mutation rates of infectious bronchitis virus (IBV) pose economic threats to the poultry industry. In order to track the genetic evolutionary of IBV isolates circulating in yellow chickens, we continued to conduct the genetic analyses of the structural genes S1, E, M, and N from 64 IBV isolates in southern China during 2009–2017. The results showed that the dominant genotypes based on the four genes had changed when compared with those during 1985–2008. Based on the S1 gene phylogenetic tree, LX4-type (GI-19) was the most dominant genotype, which was different from that during 1985–2008. The second most dominant genotype was LDT3-A-type, but this genotype disappeared after 2012. New-type 1 (GVI-1) isolates showed increasing tendency and there were four aa (QKEP) located in the hypervariable region (HVR) III and one aa (S) insertion in all the New-type 1 isolates. Both the analyses of amino acid entropy and molecular evolutionary rate revealed that the variations from large to small were S1, E, M, and N. Purifying selection was detected in the S1, E, M, and N gene proteins, which was different from the positive selection during 1985–2008. Six isolates were confirmed to be recombinants, possibly generated from a vaccine virus of the 4/91-type or LDT3-A-type and a circulating virus. The estimated times for the most recent common ancestors based on the S1, E, M, and N genes were the years of 1744, 1893, 1940, and 1945, respectively. Bayesian skyline analysis revealed a sharp decrease in genetic diversity of all the four structural genes after 2010 and since late 2015, the viral population rapidly rose. In conclusion, the IBVs circulating in southern China over the past decade have experienced a remarkable change in genetic diversity, dominant genotypes, and selection pressure, indicating the importance of permanent monitoring of circulating strains and the urgency for developing new vaccines to counteract the emerging LX4-type and New-type IBVs.


id: cord-318400-l9kwxsq7
author: Chhabra, Rajesh
date: 2016-01-15
txt: ./txt/cord-318400-l9kwxsq7.txt
cache: ./cache/cord-318400-l9kwxsq7.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/26655241/
doi: 10.1016/j.virol.2015.11.011
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.

title:
  Pathogenicity and tissue tropism of infectious bronchitis virus is associated with elevated apoptosis and innate immune responses

abstract:
  To establish a characteristic host response to predict the pathogenicity and tissue tropism of infectious bronchitis viruses (IBV), we investigated innate immune responses (IIR) and apoptosis in chicken embryo kidney cells (CEKC) and tracheal organ cultures (TOC) infected with three IBV strains. Results showed nephropathogenic IBV strains 885 and QX induced greater apoptosis in CEKC than M41, which induced greater apoptosis in TOCs compared to 885 and QX. Elevated IIR is associated with tissue tropism of different IBV strains. Compared to M41, 885 and QX caused greater induction of toll like receptor 3 (TLR3), melanoma differentiation associated protein 5 (MDA5) and interferon beta (IFN-β) in CEKC. In contrast, M41 infection caused greater expression of these genes than 885 or QX in TOCs. In summary, greater levels of apoptosis and elevated levels of TLR3, MDA5 and IFN-β expression are associated with increased pathogenicity of IBV strains in renal and tracheal tissues.


id: cord-319168-i23pqiwx
title: Emergence of novel strains of avian infectious bronchitis virus in Sweden
author: Abro, Shahid Hussain
date: 2012-03-23
txt: ./txt/cord-319168-i23pqiwx.txt
cache: ./cache/cord-319168-i23pqiwx.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.vetmic.2011.09.022
doi: 10.1016/j.vetmic.2011.09.022
summary:
  Nucleotide and amino acid sequence comparisons have shown that the recent isolates bear 98.97% genetic similarity with strains of the QX-like genotype. Twenty Swedish IBV isolates from different outbreaks were selected for comprehensive study of the complete spike gene of the virus. Analysis of the nucleotide sequences of spike glycoprotein of Swedish isolates from 1995 to 2010 showed that they comprise distinct sets of IBV variants; differing among themselves along that timeline (Table 3 ). The phylogenetic studies, based on the partial S1 gene regions, showed that Swedish IBV isolates from 1995 to 1999 were related to the Massachusetts genotype. Taken together, the complete spike sequence data revealed different isolates of IBV of the Massachusetts type and European D388/QX-like strains circulating over a time-line in Sweden. Complete genome sequence analysis of a predominant infectious bronchitis virus (IBV) strain in China

abstract:
  Infectious bronchitis virus (IBV) causes avian infectious bronchitis, an important disease that produces severe economic losses in the poultry industry worldwide. Recent IBV infections in Sweden have been associated with poor growth in broilers, drop in egg production and thin egg shells in layers. The complete spike gene of selected isolates from IBV cases was amplified and sequenced using conventional RT-PCR. Nucleotide and amino acid sequence comparisons have shown that the recent isolates bear 98.97% genetic similarity with strains of the QX-like genotype. The phylogenetic analysis revealed that strains predominant in the nineties, which were of the Massachusetts type, have been replaced by D388/QX-like strains, however the evolutionary link could not be established. The homology between the two genotypes was 79 and 81%. Remarkably, a strong positive selection pressure was determined, mostly involving the S1 subunit of the S gene. This strong selective pressure resulted in recombination events, insertions and deletions in the S gene. Two new isolates generated from recombination were found with nucleotide sequence diverging 1.7–2.4% from the D388/QX-like branch, indicating the emergence of a new lineage. The study demonstrates a constant evolution of IBV that might be in relation to increased poultry farming, trade and vaccine pressure. The findings underscore the importance of continuous monitoring to control spread of infections, as well as to timely adjust diagnostic methods, molecular epidemiological studies, development and use of vaccines that are adapted to the changing disease scenario.


id: cord-319253-8bssrn9o
author: OKINO, Cintia Hiromi
date: 2018-02-27
txt: ./txt/cord-319253-8bssrn9o.txt
cache: ./cache/cord-319253-8bssrn9o.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/29491226/
doi: 10.1292/jvms.17-0566
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

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

abstract:
  A method based on Melting Temperature analysis of Hypervariable regions (HVR) of S1 gene within a RT-qPCR was developed to detect different genotypes of avian infectious bronchitis virus (IBV) and identify the Mass genotype. The method was able to rapidly identify the Mass genotype among IBV field isolates, vaccine attenuated strains and reference M41 strain in allantoic liquid and also directly in tissues. The RT-qPCR developed detected the virus in both tracheal and pulmonary samples from M41-infected or H120-infected birds, in a larger post-infection period compared to detection by standard method of virus isolation. RT-qPCR method tested provided a sensitivity and rapid approach for screening on IBV detection and Mass genotyping from IBV isolates.


id: cord-321261-3lp54mmu
author: Kuo, Shu-Ming
date: 2010-08-26
txt: ./txt/cord-321261-3lp54mmu.txt
cache: ./cache/cord-321261-3lp54mmu.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/20299165/
doi: 10.1016/j.vetmic.2010.02.027
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

title:
  Evolution of infectious bronchitis virus in Taiwan: Characterisation of RNA recombination in the nucleocapsid gene

abstract:
  Avian infectious bronchitis virus (IBV) belongs to the Coronaviridae family and causes significant economic loss in Taiwan (TW), even in flocks that have been extensively immunised with Massachusetts (Mass)-serotype vaccines. Phylogenetic analysis of all non-structural and most structural genes shows that TW IBV is genetically distinct from the US strain and more similar to Chinese (CH) IBV. In contrast, the nucleocapsid (N) gene of TW IBV presents phylogenetic incongruence. RNA recombination at the 5′ end of the N gene between TW and US IBV is shown to be responsible for this discordance. Surprisingly, the recombinant N gene is found in all of tested TW IBV isolates, suggesting that a recombination event gave origin to a founder lineage. Our data indicate that RNA recombination in the recombinant 5′ end of the N gene may have caused the emergence of the current IBV population in Taiwan.


id: cord-321545-3gzj09mr
author: Pohuang, Tawatchai
date: 2009-09-07
txt: ./txt/cord-321545-3gzj09mr.txt
cache: ./cache/cord-321545-3gzj09mr.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/19687622/
doi: 10.4142/jvs.2009.10.3.219
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

title:
  Detection and molecular characterization of infectious bronchitis virus isolated from recent outbreaks in broiler flocks in Thailand

abstract:
  Thirteen field isolates of infectious bronchitis virus (IBV) were isolated from broiler flocks in Thailand between January and June 2008. The 878-bp of the S1 gene covering a hypervariable region was amplified and sequenced. Phylogenetic analysis based on that region revealed that these viruses were separated into two groups (I and II). IBV isolates in group I were not related to other IBV strains published in the GenBank database. Group 1 nucleotide sequence identities were less than 85% and amino acid sequence identities less than 84% in common with IBVs published in the GenBank database. This group likely represents the strains indigenous to Thailand. The isolates in group II showed a close relationship with Chinese IBVs. They had nucleotide sequence identities of 97-98% and amino acid sequence identities 96-98% in common with Chinese IBVs (strain A2, SH and QXIBV). This finding indicated that the recent Thai IBVs evolved separately and at least two groups of viruses are circulating in Thailand.


id: cord-321602-88b2h06y
author: Lv, Chenfei
date: 2020-08-19
txt: ./txt/cord-321602-88b2h06y.txt
cache: ./cache/cord-321602-88b2h06y.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32813067/
doi: 10.1007/s00253-020-10834-2
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).

title:
  Construction of an infectious bronchitis virus vaccine strain carrying chimeric S1 gene of a virulent isolate and its pathogenicity analysis

abstract:
  ABSTRACT: Infectious bronchitis virus (IBV) is a member of genus gamma-coronavirus in the family Coronaviridae, causing serious economic losses to the poultry industry. Reverse genetics is a common technique to study the biological characteristics of viruses. So far, there is no BAC reverse genetic system available for rescue of IBV infectious clone. In the present study, a new strategy for the construction of IBV infectious cDNA clone was established. The full-length genomic cDNA of IBV vaccine strain H120 was constructed in pBAC vector from four IBV fragment subcloning vectors by homologous recombination, which contained the CMV promoter at the 5′ end and the hepatitis D virus ribozyme (HDVR) sequence and bovine growth hormone polyadenylation (BGH) sequence after the polyA tail at the 3′ end of the full-length cDNA. Subsequently, using the same technique, another plasmid pBAC-H120/SCS1 was also constructed, in which S1 gene from IBV H120 strain was replaced with that of a virulent SC021202 strain. Recombinant virus rH120 and rH120/SCS1 were rescued by transfecting the plasmids into BHK cells and passaged in embryonated chicken eggs. Finally, the pathogenicity of both the recombinant virus strains rH120 and rH120/SCS1 was evaluated in SPF chickens. The results showed that the chimeric rH120/SCS1 strain was not pathogenic compared with the wild-type IBV SC021202 strain and the chickens inoculated with rH120/SCS1 could resist challenge infection by IBV SC021202. Taken together, our results indicate that BAC reverse genetic system could be used to rescue IBV in vitro and IBV S1 protein alone might not be the key factor for IBV pathogenicity. KEY POINTS: • BAC vector was used to construct IBV full-length cDNA by homologous recombination. • Based on four subcloning vectors, a recombinant chimeric IBV H120/SCS1 was constructed and rescued. • Pathogenicity of H120/SCS1 was similar to that of H120, but different to that of SC021202.


id: cord-322410-k23engcx
author: Naguib, Mahmoud M.
date: 2017-03-21
txt: ./txt/cord-322410-k23engcx.txt
cache: ./cache/cord-322410-k23engcx.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/28336367/
doi: 10.1016/j.jviromet.2017.02.018
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).

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

abstract:
  In Egypt, currently two geographically restricted genotypes of the infectious bronchitis coronavirus (IBV) are circulating with detrimental effects for poultry industry. A sensitive real-time RT-PCR assay targeting the IBV nucleocapsid gene (N) was developed to screen clinical samples for presence of IBV. Conventional RT-PCRs amplifying hypervariable regions (HVRs 1–2 and 3) of the IBV S1 gene were developed and amplificates used for nucleotide sequence-based typing of IBV field strains in Egyptian chickens directly from clinical samples.


id: cord-322516-wekvet6f
author: Maceyka, Michael
date: 1997-12-15
txt: ./txt/cord-322516-wekvet6f.txt
cache: ./cache/cord-322516-wekvet6f.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/9396747/
doi: nan
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.

title:
  Ceramide Accumulation Uncovers a Cycling Pathway for the cis-Golgi Network Marker, Infectious Bronchitis Virus M Protein

abstract:
  The M glycoprotein from the avian coronavirus, infectious bronchitis virus (IBV), contains information for localization to the cis-Golgi network in its first transmembrane domain. We hypothesize that localization to the Golgi complex may depend in part on specific interactions between protein transmembrane domains and membrane lipids. Because the site of sphingolipid synthesis overlaps the localization of IBV M, we asked whether perturbation of sphingolipids affected localization of IBV M. Short-term treatment with two inhibitors of sphingolipid synthesis had no effect on localization of IBV M or other Golgi markers. Thus, ongoing synthesis of these lipids was not required for proper localization. Surprisingly, a third inhibitor, d,l-threo-1-phenyl-2-decanoylamino-3-morpholino- 1-propanol (PDMP), shifted the steady-state distribution of IBV M from the Golgi complex to the ER. This effect was rapid and reversible and was also observed for ERGIC-53 but not for Golgi stack proteins. At the concentration of PDMP used, conversion of ceramide into both glucosylceramide and sphingomyelin was inhibited. Pretreatment with upstream inhibitors partially reversed the effects of PDMP, suggesting that ceramide accumulation mediates the PDMP-induced alterations. Indeed, an increase in cellular ceramide was measured in PDMP-treated cells. We propose that IBV M is at least in part localized by retrieval mechanisms. Further, ceramide accumulation reveals this cycle by upsetting the balance of anterograde and retrograde traffic and/ or disrupting retention by altering bilayer dynamics.


id: cord-323568-s0wmll4q
author: Shang, Jian
date: 2018-04-23
txt: ./txt/cord-323568-s0wmll4q.txt
cache: ./cache/cord-323568-s0wmll4q.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1371/journal.ppat.1007009
doi: 10.1371/journal.ppat.1007009
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.

title:
  Cryo-EM structure of infectious bronchitis coronavirus spike protein reveals structural and functional evolution of coronavirus spike proteins

abstract:
  As cell-invading molecular machinery, coronavirus spike proteins pose an evolutionary conundrum due to their high divergence. In this study, we determined the cryo-EM structure of avian infectious bronchitis coronavirus (IBV) spike protein from the γ-genus. The trimeric IBV spike ectodomain contains three receptor-binding S1 heads and a trimeric membrane-fusion S2 stalk. While IBV S2 is structurally similar to those from the other genera, IBV S1 possesses structural features that are unique to different other genera, thereby bridging these diverse spikes into an evolutionary spectrum. Specifically, among different genera, the two domains of S1, the N-terminal domain (S1-NTD) and C-terminal domain (S1-CTD), diverge from simpler tertiary structures and quaternary packing to more complex ones, leading to different functions of the spikes in receptor usage and membrane fusion. Based on the above structural and functional comparisons, we propose that the evolutionary spectrum of coronavirus spikes follows the order of α-, δ-, γ-, and β-genus. This study has provided insight into the evolutionary relationships among coronavirus spikes and deepened our understanding of their structural and functional diversity.


id: cord-324324-8ybfiz8f
title: Novel human coronavirus (SARS-CoV-2): A lesson from animal coronaviruses
author: Decaro, Nicola
date: 2020-04-14
txt: ./txt/cord-324324-8ybfiz8f.txt
cache: ./cache/cord-324324-8ybfiz8f.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0378113520302935
doi: 10.1016/j.vetmic.2020.108693
summary:
  In addition, the close contact between human beings and different animal species sold at the wet markets of East Asia represents the optimal situation for the host species jump and adaptation to humans of potentially zoonotic agents like CoVs. It is not a coincidence that two of the most severe zoonoses of the last two decades (highly pathogenic H5N1 avian influenza and SARS) have emerged in the same Chinese province of Guangdong where the contact between humans and animals is closer (Lorusso et al., 2020) . All these viruses as well as analogous IBV-like CoVs detected in other birds including penguins, pigeons, peafowl, parrots, waterfowl, teal, quail, duck and whooper swan (Cavanagh et al., 2002; Circella et al., 2007; Domanska-Blicharz et al., 2014; Torres et al., 2013; Hughes et al., 2009; Liu et al., 2005; Wille et al., 2016; Jordan et al., 2015; Bande et al., 2016; Suryaman et al., 2019) have been assigned to the same viral species known as Avian coronavirus (ACoV) within the subgenus Igacovirus of genus Gammacoronavirus.

abstract:
  The recent pandemic caused by the novel human coronavirus, referrred to as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), not only is having a great impact on the health care systems and economies in all continents but it is also causing radical changes of common habits and life styles. The novel coronavirus (CoV) recognises, with high probability, a zoonotic origin but the role of animals in the SARS-CoV-2 epidemiology is still largely unknown. However, CoVs have been known in animals since several decades, so that veterinary coronavirologists have a great expertise on how to face CoV infections in animals, which could represent a model for SARS-CoV-2 infection in humans. In the present paper, we provide an up-to-date review of the literature currently available on animal CoVs, focusing on the molecular mechanisms that are responsible for the emergence of novel CoV strains with different antigenic, biologic and/or pathogenetic features. A full comprehension of the mechanisms driving the evolution of animal CoVs will help better understand the emergence, spreading, and evolution of SARS-CoV-2.


id: cord-326319-3538jmqd
author: Yuan, Yuan
date: 2018-06-27
txt: ./txt/cord-326319-3538jmqd.txt
cache: ./cache/cord-326319-3538jmqd.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3390/v10070347
doi: 10.3390/v10070347
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

title:
  Protection against Virulent Infectious Bronchitis Virus Challenge Conferred by a Recombinant Baculovirus Co-Expressing S1 and N Proteins

abstract:
  Avian infectious bronchitis virus (IBV) is the causative agent of infectious bronchitis, which results in considerable economic losses. It is imperative to develop safe and efficient candidate vaccines to control IBV infection. In the current study, recombinant baculoviruses co-expressing the S1 and N proteins and mono-expressing S1 or N proteins of the GX-YL5 strain of IBV were constructed and prepared into subunit vaccines rHBM-S1-N, rHBM-S1 and rHBM-N. The levels of immune protection of these subunit vaccines were evaluated by inoculating specific pathogen-free (SPF) chickens at 14 days of age, giving them a booster with the same dose 14 days later and challenging them with a virulent GX-YL5 strain of IBV 14 days post-booster (dpb). The commercial vaccine strain H120 was used as a control. The IBV-specific antibody levels, as well as the percentages of CD4+ and CD8+ T lymphocytes, were detected within 28 days post-vaccination (dpv). The morbidity, mortality and re-isolation of the virus from the tracheas and kidneys of challenged birds were evaluated at five days post-challenge (dpc). The results showed that the IBV-specific antibody levels and the percentages of CD4+ and CD8+ T lymphocytes were higher in the rHBM-S1-N vaccinated birds compared to birds vaccinated with the rHBM-S1 and rHBM-N vaccines. At 5 dpc, the mortality, morbidity and virus re-isolation rate of the birds vaccinated with the rHBM-S1-N vaccine were slightly higher than those vaccinated with the H120 control vaccine but were lower than those vaccinated with the rHBM-S1 and rHBM-N vaccines. The present study demonstrated that the protection of the recombinant baculovirus co-expressing S1 and N proteins was better than that of recombinant baculoviruses mono-expressing the S1 or N protein. Thus, the recombinant baculovirus co-expressing S1 and N proteins could serve as a potential IBV vaccine and this demonstrates that the bivalent subunit vaccine including the S1 and N proteins might be a strategy for the development of an IBV subunit vaccine.


id: cord-328046-5us4se5o
author: Xu, H. Y.
date: 2001-09-30
txt: ./txt/cord-328046-5us4se5o.txt
cache: ./cache/cord-328046-5us4se5o.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S0042682201910980
doi: 10.1006/viro.2001.1098
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 .

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

abstract:
  Abstract The coronavirus 3C-like proteinase is one of the viral proteinases responsible for processing of the 1a and 1a/1b polyproteins to multiple mature products. In cells infected with avian coronavirus infectious bronchitis virus (IBV), three proteins of 100, 39, and 35 kDa, respectively, were previously identified as mature cleavage products released from the 1b region of the 1a/1b polyprotein by the 3C-like proteinase. In this report, we show the identification of two more cleavage products of 68 and 58 kDa released from the same region of the polyprotein. In addition, two stable intermediate cleavage products with molecular masses of 160 and 132 kDa, respectively, were identified in IBV-infected cells. The 160-kDa protein was shown to be an intermediate cleavage product covering the 100- and 68-kDa proteins, and the 132-kDa protein to be an intermediate cleavage product covering the 58-, 39-, and 35-kDa proteins. Immunofluorescent staining of IBV-infected cells and cells expressing individual cleavage products showed that the 100-, 68-, and 58-kDa proteins were associated with the membranes of the endoplasmic reticulum, and the 39- and 35-kDa proteins displayed diffuse distribution patterns.


id: cord-329245-6tj2k1yn
title: The cytoplasmic tails of infectious bronchitis virus E and M proteins mediate their interaction
author: Corse, Emily
date: 2003-07-20
txt: ./txt/cord-329245-6tj2k1yn.txt
cache: ./cache/cord-329245-6tj2k1yn.txt
extension: .txt
mime: text/plain
url: https://www.sciencedirect.com/science/article/pii/S0042682203001752
doi: 10.1016/s0042-6822(03)00175-2
summary:
  Indeed, it has been shown that both the MHV E and the infectious bronchitis virus (IBV) E proteins are sufficient for formation of the virus-like particles (VLPs) described above (Corse and Machamer, 2000; Maeda et al., 1999) , although the efficiency probably varies with cell type and protein expression system. (B) IBV-infected Vero cells were labeled with [ 35 S]methionine-cysteine at 45 h postinfection, treated with DSP as indicated, lysed, and immunoprecipitated with anti-E or anti-M antibodies as described under Materials and methods. The E and M proteins of several coronaviruses are released from cotransfected cells in membrane-bound particles that are morphologically similar to virions (VLPs), suggesting that interactions between these proteins are an integral part of coronavirus assembly (Baudoux et al., 1998; Corse and Machamer, 2000; Godeke et al., 2000; Vennema et al., 1996) .

abstract:
  Abstract Virus-like particle (VLP) formation by the coronavirus E and M proteins suggests that interactions between these proteins play a critical role in coronavirus assembly. We studied interactions between the infectious bronchitis virus (IBV) E and M proteins using in vivo crosslinking and VLP assembly assays. We show that IBV E and M can be crosslinked to each other in IBV-infected and transfected cells, indicating that they interact. The cytoplasmic tails of both proteins are important for this interaction. We also examined the ability of the mutant and chimeric E and M proteins to form VLPs. IBV M proteins that are missing portions of their cytoplasmic tails or transmembrane regions were not able to support VLP formation, regardless of their ability to be crosslinked to IBV E. Interactions between the E and M proteins and the membrane bilayer are likely to play an important role in VLP formation and virus budding.


id: cord-329429-ur8g68vp
title: Coronaviruses in Avian Species – Review with Focus on Epidemiology and Diagnosis in Wild Birds
author: Miłek, Justyna
date: 2018-12-10
txt: ./txt/cord-329429-ur8g68vp.txt
cache: ./cache/cord-329429-ur8g68vp.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/30584600/
doi: 10.2478/jvetres-2018-0035
summary:
  Within the gamma-CoVs the main representative is avian coronavirus, a taxonomic name which includes the highly contagious infectious bronchitis viruses (IBVs) in chickens and similar viruses infecting other domestic birds such as turkeys, guinea fowls, or quails. The methods adopted in monitoring studies of CoVs in different avian species are mainly based on detection of conservative regions within the viral replicase, nucleocapsid genes, and 3''UTR or 5''UTR. The purpose of this review is to summarise recent discoveries in the areas of epidemiology and diagnosis of CoVs in avian species and to understand the role of wild birds in the virus distribution. This taxonomic name includes IBV which causes a highly contagious disease of chickens, and genetically similar viruses isolated from other domestic galliformes: turkey coronavirus (TCoV), responsible for turkey enteritis, and the more recently detected guinea fowl coronavirus (GfCoV), the aetiological factor of fulminating disease in this species (2, 6, 27) .

abstract:
  Coronaviruses (CoVs) are a large group of enveloped viruses with a single-strand RNA genome, which continuously circulate in mammals and birds and pose a threat to livestock, companion animals, and humans. CoVs harboured by avian species are classified to the genera gamma- and deltacoronaviruses. Within the gamma-CoVs the main representative is avian coronavirus, a taxonomic name which includes the highly contagious infectious bronchitis viruses (IBVs) in chickens and similar viruses infecting other domestic birds such as turkeys, guinea fowls, or quails. Additionally, IBVs have been detected in healthy wild birds, demonstrating that they may act as the vector between domestic and free-living birds. Moreover, CoVs other than IBVs, are identified in wild birds, which suggests that wild birds play a key role in the epidemiology of other gammaCoVs and deltaCoVs. Development of molecular techniques has significantly improved knowledge of the prevalence of CoVs in avian species. The methods adopted in monitoring studies of CoVs in different avian species are mainly based on detection of conservative regions within the viral replicase, nucleocapsid genes, and 3’UTR or 5’UTR. The purpose of this review is to summarise recent discoveries in the areas of epidemiology and diagnosis of CoVs in avian species and to understand the role of wild birds in the virus distribution.


id: cord-329468-vjsurl60
author: Okino, Cintia Hiromi
date: 2017-02-15
txt: ./txt/cord-329468-vjsurl60.txt
cache: ./cache/cord-329468-vjsurl60.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/28199419/
doi: 10.1371/journal.pone.0172275
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).

title:
  Early immune responses and development of pathogenesis of avian infectious bronchitis viruses with different virulence profiles

abstract:
  Avian infectious bronchitis virus (IBV) primarily replicates in epithelial cells of the upper respiratory tract of chickens, inducing both morphological and immune modulatory changes. However, the association between the local immune responses induced by IBV and the mechanisms of pathogenesis has not yet been completely elucidated. This study compared the expression profile of genes related to immune responses in tracheal samples after challenge with two Brazilian field isolates (A and B) of IBV from the same genotype, associating these responses with viral replication and with pathological changes in trachea and kidney. We detected a suppressive effect on the early activation of TLR7 pathway, followed by lower expression levels of inflammatory related genes induced by challenge with the IBV B isolate when compared to the challenge with to the IBV A isolate. Cell-mediated immune (CMI) related genes presented also lower levels of expression in tracheal samples from birds challenged with B isolate at 1dpi. Increased viral load and a higher percentage of birds with relevant lesions were observed in both tracheal and renal samples from chickens exposed to challenge with IBV B isolate. This differential pattern of early immune responses developed after challenge with IBV B isolate, related to the downregulation of TLR7, leading to insufficient pro-inflammatory response and lower CMI responses, seem to have an association with a most severe renal lesion and an enhanced capability of replication of this isolate in chicken.


id: cord-329497-3jow4xbn
title: Dynamics of avian coronavirus circulation in commercial and non-commercial birds in Asia – a review
author: Promkuntod, Naruepol
date: 2015-12-28
txt: ./txt/cord-329497-3jow4xbn.txt
cache: ./cache/cord-329497-3jow4xbn.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1080/01652176.2015.1126868
doi: 10.1080/01652176.2015.1126868
summary:
  It is essential to understand the latest situation regarding avian coronaviruses (ACoVs), commonly referred to as the well-known avian infectious bronchitis virus (IBV), given that new and diverse types of IBV are continually being identified worldwide, particularly ones that are isolated from commercial poultry and associated with a wide range of disease conditions. Vaccines against IBVs are generally effective, but new strains continue to emerge causing clinical diseases and production problems in vaccinated flocks, eventually having an economic impact on the global poultry industry Liu et al. In addition, the production of a new generation of vaccines, genetically related to the circulating IBV local strains, is economically beneficial for control of infectious bronchitis (IB) in global geographic regions. Isolation and genetic analysis revealed no predominant new strains of avian infectious bronchitis virus circulating in south China during

abstract:
  It is essential to understand the latest situation regarding avian coronaviruses (ACoVs), commonly referred to as the well-known avian infectious bronchitis virus (IBV), given that new and diverse types of IBV are continually being identified worldwide, particularly ones that are isolated from commercial poultry and associated with a wide range of disease conditions. The existing IBVs continue to evolve in various geographic areas in Asia, which results in the recombination and co-circulation between IBV types. This makes it increasingly difficult to prevent and control IBV infections, despite routine vaccination. Some ACoVs have also been identified in other avian species and they may pose a threat of cross-transmission to commercial sectors. The present review provides an overview of IBV circulation and the dynamic emergence of new variants found throughout Asia via the recombination of IBV strains. In addition to commercial poultry, backyard poultry and free-ranging birds may serve as a ‘hub’ for ACoV transmission within a particular area. These birds may be capable of spreading viruses, either to areas of close proximity, or to remote places via migration and trade.


id: cord-330057-3vucm0s1
author: Franzo, Giovanni
date: 2020-04-29
txt: ./txt/cord-330057-3vucm0s1.txt
cache: ./cache/cord-330057-3vucm0s1.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1038/s41598-020-64477-4
doi: 10.1038/s41598-020-64477-4
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.

title:
  Phylodynamic analysis and evaluation of the balance between anthropic and environmental factors affecting IBV spreading among Italian poultry farms

abstract:
  Infectious bronchitis virus (IBV) control is mainly based on wide vaccine administration. Although effective, its efficacy is not absolute, the viral circulation is not prevented and some side effects cannot be denied. Despite this, the determinants of IBV epidemiology and the factors affecting its circulation are still largely unknown and poorly investigated. In the present study, 361 IBV QX (the most relevant field genotype in Italy) sequences were obtained between 2012 and 2016 from the two main Italian integrated poultry companies. Several biostatistical and bioinformatics approaches were used to reconstruct the history of the QX genotype in Italy and to assess the effect of different environmental, climatic and social factors on its spreading patterns. Moreover, two structured coalescent models were considered in order to investigate if an actual compartmentalization occurs between the two integrated poultry companies and the role of a third “ghost” deme, representative of minor industrial poultry companies and the rural sector. The obtained results suggest that the integration of the poultry companies is an effective barrier against IBV spreading, since the strains sampled from the two companies formed two essentially-independent clades. Remarkably, the only exceptions were represented by farms located in the high densely populated poultry area of Northern Italy. The inclusion of a third deme in the model revealed the likely role of other poultry companies and rural farms (particularly concentrated in Northern Italy) as sources of strain introduction into one of the major poultry companies, whose farms are mainly located in the high densely populated poultry area of Northern Italy. Accordingly, when the effect of different environmental and urban parameters on IBV geographic spreading was investigated, no factor seems to contribute to IBV dispersal velocity, being poultry population density the only exception. Finally, the different viral population pattern observed in the two companies over the same time period supports the pivotal role of management and control strategies on IBV epidemiology. Overall, the present study results stress the crucial relevance of human action rather than environmental factors, highlighting the direct benefits that could derive from improved management and organization of the poultry sector on a larger scale.


id: cord-330260-xuw31zfn
title: Identification of Taiwan and China-like recombinant avian infectious bronchitis viruses in Taiwan
author: Chen, Hui-Wen
date: 2009-01-20
txt: ./txt/cord-330260-xuw31zfn.txt
cache: ./cache/cord-330260-xuw31zfn.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/19100792/
doi: 10.1016/j.virusres.2008.11.012
summary:
  All of the recombinants showed chimeric IBV genome arrangements originated from Taiwan and China-like parental strains. Phylogenetic analyses were performed based on the nucleotide sequence alignment using each ORF from the S to N genes among eight Taiwan and reference strains (Fig. 1) . Phylogenetic analysis of partial S1 and N gene sequences of infectious bronchitis virus isolates from Italy revealed genetic diversity and recombination Recombinant avian infectious bronchitis virus expressing a heterologous spike gene demonstrates that the spike protein is a determinant of cell tropism A novel variant of avian infectious bronchitis virus resulting from recombination among three different strains Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus Genetic diversity of avian infectious bronchitis coronavirus strains isolated in China between Genetic grouping for the isolates of avian infectious bronchitis virus in Taiwan

abstract:
  Infectious bronchitis virus (IBV) infections in poultry cause great economic losses to the poultry industry worldwide. The emergence of viral variants complicates disease control. The IBV strains in Taiwan were clustered into two groups, Taiwan group I and Taiwan group II, based on the S1 gene. A variant was previously identified and showed a distinct S1 gene homology with other local strains. This study investigated the 3′ 7.3 kb genome of eight Taiwan strains isolated from 1992 to 2007. The genes of interest were directly sequenced. Sequence analyses were performed to detect any recombination event among IBVs. The results demonstrated that all of the examined viruses maintained the typical IBV genome organization as 5′-S-3a-3b-E-M-5a-5b-N-UTR-3′. In the phylogenetic analyses, various genes from one strain were clustered into separate groups. Moreover, frequent recombination events were identified in the Simplot analyses among the Taiwan and China CK/CH/LDL/97I-type strains. Putative crossover sites were located in the S1, S2, 3b, M genes and the intergenic region between the M and 5a genes. All of the recombinants showed chimeric IBV genome arrangements originated from Taiwan and China-like parental strains. Field IBVs in Taiwan undergo genetic recombination and evolution.


id: cord-331020-lyxje82u
author: M. Najimudeen, Shahnas
date: 2020-09-24
txt: ./txt/cord-331020-lyxje82u.txt
cache: ./cache/cord-331020-lyxje82u.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.3390/pathogens9100779
doi: 10.3390/pathogens9100779
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] .

title:
  Infectious Bronchitis Coronavirus Infection in Chickens: Multiple System Disease with Immune Suppression

abstract:
  In the early 1930s, infectious bronchitis (IB) was first characterized as a respiratory disease in young chickens; later, the disease was also described in older chickens. The etiology of IB was confirmed later as being due to a coronavirus: the infectious bronchitis virus (IBV). Being a coronavirus, IBV is subject to constant genome change due to mutation and recombination, with the consequence of changing clinical and pathological manifestations. The potential use of live attenuated vaccines for the control of IBV infection was demonstrated in the early 1950s, but vaccine breaks occurred due to the emergence of new IBV serotypes. Over the years, various IBV genotypes associated with reproductive, renal, gastrointestinal, muscular and immunosuppressive manifestations have emerged. IBV causes considerable economic impacts on global poultry production due to its pathogenesis involving multiple body systems and immune suppression; hence, there is a need to better understand the pathogenesis of infection and the immune response in order to help developing better management strategies. The evolution of new strains of IBV during the last nine decades against vaccine-induced immune response and changing clinical and pathological manifestations emphasize the necessity of the rational development of intervention strategies based on a thorough understanding of IBV interaction with the host.


id: cord-331740-yjt3q9ph
author: Jones, R. M.
date: 2011-04-07
txt: ./txt/cord-331740-yjt3q9ph.txt
cache: ./cache/cord-331740-yjt3q9ph.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1111/j.1865-1682.2011.01222.x
doi: 10.1111/j.1865-1682.2011.01222.x
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.

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

abstract:
  Two tests were developed that allow the detection and genotyping of infectious bronchitis virus (IBV) and other closely related gammacoronaviruses. The first test employs a one‐step, reverse transcription‐polymerase chain reaction (RT‐PCR) assay in which the amplification is monitored in real time using a TaqMan(®) probe. This real‐time RT‐PCR test was used to examine a panel of field samples and its performance compared to virus isolation in embryonated fowls’ eggs. A total of 323 field samples were tested; 176 samples were positive using the real‐time RT‐PCR method, but only three were positive by virus isolation. Sequencing was used to confirm the positive real‐time RT‐PCR results for a subset of samples. The test is suitable for swabs and post‐mortem samples and has been shown to be highly sensitive and specific. The second test, a genotyping method, was developed for identification of the strain of IBV present in field samples based on nucleotide variations within the gene encoding the S1 subunit of the surface spike (S) glycoprotein. This method was developed to provide a tool to inform vaccination decisions and for ongoing surveillance to detect new and emerging strains of IBV within the UK. The performance of the test was evaluated using laboratory isolates of IBV and field samples. Both tests are suitable for use in a high‐throughput diagnostic laboratory.


id: cord-334090-66d8c75g
title: Genotyping of infectious bronchitis viruses from broiler farms in Iraq during 2014-2015
author: Seger, Waleed
date: 2016-02-18
txt: ./txt/cord-334090-66d8c75g.txt
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extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/26887967/
doi: 10.1007/s00705-016-2790-2
summary:
  Thus, the spread of viral respiratory diseases has become the most commonly reported condition in commercial broiler flocks in Iraq; however, there have been no studies on the detection and genotyping of these viruses using molecular techniques and sequencing. Phylogenetic analysis of the 32 strains (Fig. 2) revealed that Iraqi IBV strains could be classified into four genetic groups or genotypes: group I, variant 2 IS/1494-like viruses, including 15 field isolates (46.87 %); group II, 793/Blike viruses, including 13 field strains (40.62 %); group III, QX-like viruses, including three field strains (9.37); and caused by bacteria and mycoplasmas have already been detected on broiler farms located in the central and southern parts of Iraq. Our result were in line with those of Mahmood et al., who conducted the first study of identification and genotyping of IBV isolates and indicated that the 4/91-like virus is circulating on vaccinated broiler farms of the Kurdistan region of Iraq [21] .

abstract:
  Infectious bronchitis virus (IBV) is one of the most critical pathogens in the poultry industry, causing serious economic losses in all countries including Iraq. IBV has many genotypes that do not confer any cross-protection. This virus has been genotyped by sequence analysis of the S1 glycoprotein gene. A total of 100 tracheal and kidney tissue specimens from different commercial broiler flocks in the middle and south of Iraq were collected from September 2013 to September 2014. Thirty-two IBV-positive samples were selected from among the total and were further characterized by nested PCR. Phylogenetic analysis revealed that isolates belong to four groups (group I, variant 2 [IS/1494-like]; group II, 793/B-like; group III, QX-like; group IV, DY12-2-like). Sequence analysis revealed nucleotide sequence identities within groups I, II, and III of 99.68 %-100 %, 99.36 %-100 %, and 96.42 %-100 %, respectively. Group I (variant 2) was the dominant IBV genotype. One Chinese-like recombinant virus (DY12-2-like) that had not been reported in the Middle East was detected. In addition, the presence of QX on broiler chicken farms in the area studied was confirmed. This is the first comprehensive study on the genotyping of IBV in Iraq with useful information regarding the molecular epidemiology of IBV. The phylogenetic relationship of the strains with respect to different time sequences and geographical regions displayed complexity and diversity. Further studies are needed and should include the isolation and full-length molecular characterization of IBV in this region.


id: cord-335310-61wibso4
author: Chen, Hui-Wen
date: 2016-08-15
txt: ./txt/cord-335310-61wibso4.txt
cache: ./cache/cord-335310-61wibso4.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.biomaterials.2016.08.018
doi: 10.1016/j.biomaterials.2016.08.018
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.

title:
  Synthetic virus-like particles prepared via protein corona formation enable effective vaccination in an avian model of coronavirus infection

abstract:
  The ongoing battle against current and rising viral infectious threats has prompted increasing effort in the development of vaccine technology. A major thrust in vaccine research focuses on developing formulations with virus-like features towards enhancing antigen presentation and immune processing. Herein, a facile approach to formulate synthetic virus-like particles (sVLPs) is demonstrated by exploiting the phenomenon of protein corona formation induced by the high-energy surfaces of synthetic nanoparticles. Using an avian coronavirus spike protein as a model antigen, sVLPs were prepared by incubating 100 nm gold nanoparticles in a solution containing an optimized concentration of viral proteins. Following removal of free proteins, antigen-laden particles were recovered and showed morphological semblance to natural viral particles under nanoparticle tracking analysis and transmission electron microscopy. As compared to inoculation with free proteins, vaccination with the sVLPs showed enhanced lymphatic antigen delivery, stronger antibody titers, increased splenic T-cell response, and reduced infection-associated symptoms in an avian model of coronavirus infection. Comparison to a commercial whole inactivated virus vaccine also showed evidence of superior antiviral protection by the sVLPs. The study demonstrates a simple yet robust method in bridging viral antigens with synthetic nanoparticles for improved vaccine application; it has practical implications in the management of human viral infections as well as in animal agriculture.


