Genetic characterization of the Belgian nephropathogenic infectious bronchitis virus (NIBV) reference strain B1648

Viruses

Volumn 7, Issue 8, 2015, Pages 4488-4506

  Reddy, Vishwanatha R A P ^a   Theuns, Sebastiaan ^a   Roukaerts, Inge D M ^a   Zeller, Mark ^b   Matthijnssens, Jelle ^b   Nauwynck, Hans J ^a  

^a GHENT UNIVERSITY   (Belgium)

^b REGA INSTITUTE FOR MEDICAL RESEARCH   (Belgium)

Author keywords

B1648; Chicken; IBV; Nephropathogenic; Nonstructural protein

Indexed keywords

M PROTEIN; RNA DIRECTED RNA POLYMERASE; TRANSCRIPTASE; VIRUS SPIKE PROTEIN; VIRUS RNA;

ARTICLE; AVIAN INFECTIOUS BRONCHITIS VIRUS; CHICKEN; EGG; EMBRYO; GENE; GENOME ANALYSIS; NEXT GENERATION SEQUENCING; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHYLOGENY; RNA SEQUENCE; S1 GENE; SEQUENCE ANALYSIS; VIRUS GENOME; ANIMAL; BELGIUM; BIRD DISEASE; CLASSIFICATION; CLUSTER ANALYSIS; CORONAVIRUS INFECTION; DNA SEQUENCE; GENETIC VARIATION; GENETICS; HIGH THROUGHPUT SEQUENCING; ISOLATION AND PURIFICATION; MOLECULAR EVOLUTION; MOLECULAR GENETICS; SEQUENCE HOMOLOGY; VETERINARY; VIROLOGY;

ANIMALS; BELGIUM; CHICKENS; CLUSTER ANALYSIS; CORONAVIRUS INFECTIONS; EVOLUTION, MOLECULAR; GENETIC VARIATION; GENOME, VIRAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; INFECTIOUS BRONCHITIS VIRUS; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PHYLOGENY; POULTRY DISEASES; RNA, VIRAL; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY;

EID: 84941129150     PISSN: None     EISSN: 19994915     Source Type: Journal    
DOI: 10.3390/v7082827     Document Type: Article

References (57)

1. Cavanagh, D. Coronaviruses in poultry and other birds. Avian Pathol. 2005, 34, 439-448. [CrossRef] [PubMed]
2. Woo, P.C.; Lau, S.K.; Lam, C.S.; Tsang, A.K.; Hui, S.W.; Fan, R.Y.; Martelli, P.; Yuen, K.Y. Discovery of a novel bottlenose dolphin coronavirus reveals a distinct species of marine mammal coronavirus in Gammacoronavirus. J. Virol. 2014, 88, 1318-1331. [CrossRef] [PubMed]
3. Cavanagh, D. Coronavirus avian infectious bronchitis virus. Vet. Res. 2007, 38, 281-297. [CrossRef] [PubMed]
4. Kottier, S.A.; Cavanagh, D.; Britton, P. Experimental evidence of recombination in coronavirus infectious bronchitis virus. Virology 1995, 213, 569-580. [CrossRef] [PubMed]
5. Thor, S.W.; Hilt, D.A.; Kissinger, J.C.; Paterson, A.H.; Jackwood, M.W. Recombination in avian gamma-coronavirus infectious bronchitis virus. Viruses 2011, 3, 1777-1799. [CrossRef] [PubMed]
6. Cook, J.K.; Jackwood, M.; Jones, R.C. The long view: 40 years of infectious bronchitis research. Avian Pathol. 2012, 41, 239-250. [CrossRef] [PubMed]
7. Meulemans, G.; Carlier, M.C.; Gonze, M.; Petit, P.; Vandenbroeck, M. Incidence, characterisation and prophylaxis of nephropathogenic avian infectious bronchitis viruses. Vet. Rec. 1987, 120, 205-206. [CrossRef] [PubMed]
8. Winterfield, R.W.; Hitchner, S.B. Etiology of an infectious nephritis-nephrosis syndrome of chickens. Am. J. Vet. Res. 1962, 23, 1273-1279. [PubMed]
9. Cumming, R.B. Infectious avian nephrosis (uraemia) in Australia. Aust. Vet. J. 1963, 39, 145-147. [CrossRef]
10. Wang, C.H.; Hsieh, M.C.; Chang, P.C. Isolation, pathogenicity, and H120 protection efficacy of infectious bronchitis viruses isolated in Taiwan. Avian Dis. 1996, 40, 620-625. [CrossRef] [PubMed]
11. Song, C.S.; Lee, Y.J.; Kim, J.H.; Sung, H.W.; Lee, C.W.; Izumiya, Y.; Miyazawa, T.; Jang, H.K.; Mikami, T. Epidemiological classification of infectious bronchitis virus isolated in Korea between 1986 and 1997. Avian Pathol. 1998, 27, 409-416. [CrossRef] [PubMed]
12. Lim, T.H.; Lee, H.J.; Lee, D.H.; Lee, Y.N.; Park, J.K.; Youn, H.N.; Kim, M.S.; Lee, J.B.; Park, S.Y.; Choi, I.S.; et al. An emerging recombinant cluster of nephropathogenic strains of avian infectious bronchitis virus in Korea. Infect. Genet. Evol. 2011, 11, 678-685. [CrossRef] [PubMed]
13. Meir, R.; Rosenblut, E.; Perl, S.; Kass, N.; Ayali, G.; Perk, S.; Hemsani, E. Identification of a novel nephropathogenic infectious bronchitis virus in Israel. Avian Dis. 2004, 48, 635-641. [CrossRef] [PubMed]
14. Mahmood, Z.H.; Sleman, R.R.; Uthman, A.U. Isolation and molecular characterization of Sul/01/09 avian infectious bronchitis virus, indicates the emergence of a new genotype in the Middle East. Vet. Microbiol. 2011, 150, 21-27. [CrossRef] [PubMed]
15. Abdel-Moneim, A.S.; El-Kady, M.F.; Ladman, B.S.; Gelb, J. S1 gene sequence analysis of a nephropathogenic strain of avian infectious bronchitis virus in Egypt. Virol. J. 2006, 3, e78. [CrossRef] [PubMed]
16. Bayry, J.; Goudar, M.S.; Nighot, P.K.; Kshirsagar, S.G.; Ladman, B.S.; Gelb, J.; Ghalsasi, G.R.; Kolte, G.N. Emergence of a nephropathogenic avian infectious bronchitis virus with a novel genotype in India. J. Clin. Microbiol. 2005, 43, 916-918. [CrossRef] [PubMed]
17. Pensaert, M.; Lambrechts, C. Vaccination of chickens against a Belgian nephropathogenic strain of infectious bronchitis virus B1648 using attenuated homologous and heterologous strains. Avian Pathol. 1994, 23, 631-641. [CrossRef] [PubMed]
18. Bochkov, Y.A.; Batchenko, G.V.; Shcherbakova, L.O.; Borisov, A.V.; Drygin, V.V. Molecular epizootiology of avian infectious bronchitis in Russia. Avian Pathol. 2006, 35, 379-393. [CrossRef] [PubMed]
19. Ducatez, M.F.; Martin, A.M.; Owoade, A.A.; Olatoye, I.O.; Alkali, B.R.; Maikano, I.; Snoeck, C.J.; Sausy, A.; Cordioli, P.; Muller, C.P. Characterization of a new genotype and serotype of infectious bronchitis virus in Western Africa. J. Gen. Virol. 2009, 90, 2679-2685. [CrossRef] [PubMed]
20. Krapež, U.; Slavec, B.; Barlič-Maganja, D.; Rojs, O.Z. Molecular analysis of infectious bronchitis viruses isolated in Slovenia between 1990 and 2005: A retrospective study. Virus Genes 2010, 41, 414-416. [CrossRef] [PubMed]
21. Tosi, G.; Taddei, R.; Barbieri, I.; Fiorentini, L.; Massi, P. Caratterizzazione molecolare dei ceppi di virus della bronchite infettiva aviare isolati in Italia nel periodo 2007-2009 e nel primo bimestre del 2010. In Proceedings of the 49th Annual Conference of Acts Italian society of Avian Pathology (SIPA), Forli, Italy, 29-30 April 2010; pp. 217-224.
22. Bourogaa, H.; Hellal, I.; Hassen, J.; Fathallah, I.; Ghram, A. S1 gene sequence analysis of new variant isolates of avian infectious bronchitis virus in Tunisia. Vet. Med. 2012, 3, 41-48. [CrossRef]
23. Toffan, A.; Bonci, M.; Bano, L.; Valastro, V.; Vascellari, M.; Capua, I.; Terregino, C. Diagnostic and clinical observation on the infectious bronchitis virus strain Q1 in Italy. Vet. Ital. 2013, 49, 347-355. [PubMed]
24. Shaw, K.; Britton, P.; Cavanagh, D. Sequence of the spike protein of the Belgian B164S isolate of nephropathogenic infectious bronchitis virus. Avian Pathol. 1996, 25, 607-611. [CrossRef] [PubMed]
25. Bankevich, A.; Nurk, S.; Antipov, D.; Gurevich, A.A.; Dvorkin, M.; Kulikov, A.S.; Lesin, V.M.; Nikolenko, S.I.; Pham, S.; Prjibelski, A.D.; et al. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 2012, 19, 455-477. [CrossRef] [PubMed]
26. Altschul, S.F.; Gish, W.; Miller, W.; Myers, E.W.; Lipman, D.J. Basic local alignment search tool. J. Mol. Biol. 1990, 215, 403-410. [CrossRef]
27. Huang, Y.; Lau, S.K.; Woo, P.C.; Yuen, K.Y. CoVDB: A comprehensive database for comparative analysis of coronavirus genes and genomes. Nucleic Acids Res. 2008, 36, D504-D511. [CrossRef] [PubMed]
28. Wang, S.; Sundaram, J.P.; Spiro, D. VIGOR, an annotation program for small viral genomes. BMC Bioinform. 2010, 11, e451. [CrossRef] [PubMed]
29. Lambrechts, C.; Pensaert, M.; Ducatelle, R. 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. Avian Pathol. 1993, 22, 577-590. [CrossRef] [PubMed]
30. Cook, J.K.; Chesher, J.; Baxendale, W.; Greenwood, N.; Huggins, M.B.; Orbell, S.J. Protection of chickens against renal damage caused by a nephropathogenic infectious bronchitis virus. Avian Pathol. 2001, 30, 423-426. [CrossRef] [PubMed]
31. Hewson, K.A.; Ignjatovic, J.; Browning, G.F.; Devlin, J.M.; Noormohammadi, A.H. Infectious bronchitis viruses with naturally occurring genomic rearrangement and gene deletion. Arch. Virol. 2011, 156, 245-252. [CrossRef] [PubMed]
32. Xue, Y.; Xie, Q.; Yan, Z.; Ji, J.; Chen, F.; Qin, J.; Sun, B.; Ma, J.; Bi, Y. Complete genome sequence of a recombinant nephropathogenic infectious bronchitis virus strain in China. J. Virol. 2012, 86, 13812-13813. [CrossRef] [PubMed]
33. Abolnik, C. Genomic and single nucleotide polymorphism analysis of infectious bronchitis coronavirus. Infect. Genet. Evol. 2015, 32, 416-424. [CrossRef] [PubMed]
34. Cao, J.; Wu, C.C.; Lin, T.L. Complete nucleotide sequence of polyprotein gene 1 and genome organization of turkey coronavirus. Virus Res. 2008, 136, 43-49. [CrossRef] [PubMed]
35. Bentley, K.; Keep, S.M.; Armesto, M.; Britton, P. Identification of a noncanonically transcribed subgenomic mRNA of infectious bronchitis virus and other gammacoronaviruses. J. Virol. 2013, 87, 2128-2136. [CrossRef] [PubMed]
36. Yang, Y.; Zhang, L.; Geng, H.; Deng, Y.; Huang, B.; Guo, Y.; Zhao, Z.; Tan, W. The structural and accessory proteins M, ORF 4a, ORF 4b, and ORF 5 of Middle East respiratory syndrome coronavirus (MERS-CoV) are potent interferon antagonists. Protein Cell 2013, 4, 951-961. [CrossRef] [PubMed]
37. Ye, Z.; Wong, C.K.; Li, P.; Xie, Y. A SARS-CoV protein, ORF-6, induces caspase-3 mediated, ER stress and JNK-dependent apoptosis. Biochim. Biophys. Acta 2008, 1780, 1383-1387. [CrossRef] [PubMed]
38. Gough, R.E.; Cox, W.J.; de B.; Welchman, D.; Worthington, K.J.; Jones, R.C. Chinese QX strain of infectious bronchitis virus isolated in the UK. Vet. Rec. 2008, 162, 99-100. [CrossRef] [PubMed]
39. Abro, S.H.; Renström, L.H.; Ullman, K.; Isaksson, M.; Zohari, S.; Jansson, D.S.; Belák, S.; Baule, C. Emergence of novel strains of avian infectious bronchitis virus in Sweden. Vet. Microbiol. 2012, 155, 237-246. [CrossRef] [PubMed]
40. Benyeda, Z.; Mató, T.; Süveges, T.; Szabó, E.; Kardi, V.; Abonyi-Tóth, Z.; Rusvai, M.; Palya, V. Comparison of the pathogenicity of QX-like, M41 and 793/B infectious bronchitis strains from different pathological conditions. Avian Pathol. 2009, 38, 449-456. [CrossRef] [PubMed]
41. Domanska-Blicharz, K.; Minta, Z.; Smietanka, K.; Porwan, T. New variant of IBV in Poland. Vet. Rec. 2006, 158, e808. [CrossRef]
42. Krapez, U.; Slavec, B.; Rojs, O.Z. Circulation of infectious bronchitis virus strains from Italy 02 and QX genotypes in Slovenia between 2007 and 2009. Avian Dis. 2011, 55, 155-161. [CrossRef] [PubMed]
43. Valastro, V.; Monne, I.; Fasolato, M.; Cecchettin, K.; Parker, D.; Terregino, C.; Cattoli, G. QX-type infectious bronchitis virus in commercial flocks in the UK. Vet. Rec. 2010, 167, 865-866. [CrossRef] [PubMed]
44. Worthington, K.J.; Currie, R.J.; Jones, R.C. A reverse transcriptase-polymerase chain reaction survey of infectious bronchitis virus genotypes inWestern Europe from 2002 to 2006. Avian Pathol. 2008, 37, 247-257. [CrossRef] [PubMed]
45. Yu, L.; Jiang, Y.; Low, S.; Wang, Z.; Nam, S.J.; Liu, W.; Kwangac, J. Characterization of three infectious bronchitis virus isolates from China associated with proventriculus in vaccinated chickens. Avian Dis. 2001, 45, 416-424. [CrossRef] [PubMed]
46. Hughes, A.L. Recombinational histories of avian infectious bronchitis virus and turkey coronavirus. Arch. Virol. 2011, 156, 1823-1829. [CrossRef] [PubMed]
47. Ammayappan, A.; Upadhyay, C.; Gelb, J.; Vakharia, V.N. Identification of sequence changes responsible for the attenuation of avian infectious bronchitis virus strain Arkansas DPI. Arch. Virol. 2009, 154, 495-499. [CrossRef] [PubMed]
48. Armesto, M.; Cavanagh, D.; Britton, P. The replicase gene of avian coronavirus infectious bronchitis virus is a determinant of pathogenicity. PLoS ONE 2009, 4, e7384. [CrossRef] [PubMed]
49. Phillips, J.E.; Jackwood, M.W.; McKinley, E.T.; Thor, S.W.; Hilt, D.A.; Acevedol, N.D.; Williams, S.M.; Kissinger, J.C.; Paterson, A.H.; Robertson, J.S.; et al. Changes in nonstructural protein 3 are associated with attenuation in avian coronavirus infectious bronchitis virus. Virus Genes 2012, 44, 63-74. [CrossRef] [PubMed]
50. Züst, R.; Cervantes-Barragán, L.; Kuri, T.; Blakqori, G.; Weber, F.; Ludewig, B.; Thiel, V. Coronavirus non-structural protein 1 is a major pathogenicity factor: Implications for the rational design of coronavirus vaccines. PLoS Pathog. 2007, 3, e109. [CrossRef] [PubMed]
51. Eriksson, K.K.; Cervantes-Barragán, L.; Ludewig, B.; Thiel, V. Mouse hepatitis virus liver pathology is dependent on ADP-ribose-1ʺ-phosphatase, a viral function conserved in the alpha-like supergroup. J. Virol. 2008, 82, 12325-12334. [CrossRef] [PubMed]
52. Sperry, S.M.; Kazi, L.; Graham, R.L.; Baric, R.S.; Weiss, S.R.; Denison, M.R. Single-amino-acid substitutions in open reading frame (ORF) 1b-nsp14 and ORF 2a proteins of the coronavirus mouse hepatitis virus are attenuating in mice. J. Virol. 2005, 79, 3391-3400. [CrossRef] [PubMed]
53. Rimondi, A.; Craig, M.I.; Vagnozzi, A.; König, G.; Delamer, M.; Pereda, A. Molecular characterization of avian infectious bronchitis virus strains from outbreaks in Argentina (2001-2008). Avian Pathol. 2009, 38, 149-153. [CrossRef] [PubMed]
54. Abdel-Moneim, A.S. Middle East respiratory syndrome coronavirus (MERS-CoV): Evidence and speculations. Arch. Virol. 2014, 159, 1575-1584. [CrossRef] [PubMed]
55. Chastel, C. Middle East respiratory syndrome (MERS): Bats or dromedary, which of them is responsible? Bull. Soc. Pathol. Exot. 2014, 107, 69-73. [CrossRef] [PubMed]
56. Kim, H.R.; Oem, J.K. Surveillance of avian coronaviruses in wild bird populations of Korea. J. Wildl. Dis. 2014, 50, 964-968. [CrossRef] [PubMed]
57. Muradrasoli, S.; Bálint, A.; Wahlgren, J.; Waldenström, J.; Belák, S.; Blomberg, J.; Olsen, B. Prevalence and phylogeny of coronaviruses in wild birds from the Bering Strait area (Beringia). PLoS ONE 2010, 5, e13640. [CrossRef] [PubMed]