Archives of Virology

, Volume 157, Issue 6, pp 1211–1215 | Cite as

Characterization and analysis of the full-length genome of a strain of the European QX-like genotype of infectious bronchitis virus

  • Shahid Hussain Abro
  • Lena H. M. Renström
  • Karin Ullman
  • Sándor Belák
  • Claudia Baule
Annotated Sequence Record


In recent years, strains of infectious bronchitis virus belonging to the QX-like genotype have been causing huge economic losses in commercial chicken flocks in different countries in Europe. In order to expand the knowledge of the molecular features of these viruses, we have sequenced and characterized the complete genome of European QX-like IBV strain CK/SWE/0658946/10, which was isolated in 2010 in Sweden. The genome is 27664 nucleotides in length, comprising six genes and 5′ and 3′ untranslated regions. The ORF1a, spike and nucleocapsid genes were under strong positive selective pressure that resulted in genetic diversity in relation to classical IBV isolates. The full-length genome of the CK/SWE/0658946/10 strain has the highest nucleotide sequence identity (93.18%) to ITA/90254/2005 and the lowest nucleotide identity (89.10%) to strain CQ04-1. Phylogenetic analysis of partial S1 gene sequences of IBV strains showed that the European QX-like genotype comprises strains that have been predominantly circulating in this continent for the past decade.


Infectious Bronchitis Virus Infectious Bronchitis Virus Strain Replicase Gene Chicken Flock Infectious Bronchitis Virus Isolate 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



This study was funded by Grant 70031/2009 of the National Veterinary Institute (SVA) Research Fund. We are also grateful to Ulla Berglöf and Karin von Schantz (SVA) for providing specific-pathogen-free eggs.

Supplementary material

705_2012_1284_MOESM1_ESM.doc (42 kb)
ESM 1 List of complete genome of IBV strains downloaded from GenBank used in this study (DOC 42 kb)
705_2012_1284_MOESM2_ESM.doc (126 kb)
ESM 2 List of reference strains of IBV of which sequences were downloaded from GenBank for the phylogenetic analysis of the partial S1 gene. (DOC 125 kb)
705_2012_1284_MOESM3_ESM.eps (1.4 mb)
ESM 3 The selective pressure analysis in ORF1a and ORF1b. The diagram indicates that ORF1a of the spike glycoprotein was mostly subject to positive selective pressure. In ORF1b, showing regions with mostly negative selective pressure were found. The strong selective pressures in the regions of ORFs are indicated by circles. (EPS 1398 kb)
705_2012_1284_MOESM4_ESM.eps (1 mb)
ESM 4 Consensus phylogenetic trees constructed with the (a) M gene and (b) N gene of IBV strains downloaded from GenBank. The IBV European QX-like strain used in the present study is indicated by ♦ (EPS 1044 kb)


  1. 1.
    Gonzalez JM, Gomez-Puertas P, Cavanagh D, Gorbalenya AE, Enjuanes L (2003) A comparative sequence analysis to revise the current taxonomy of the family Coronaviridae. Arch Virol 148:2207–2235PubMedCrossRefGoogle Scholar
  2. 2.
    Enjuanes L, Brian D, Cavanagh D, Holmes K, Lai MMC, Laude H, Masters P, Rottier P, Siddell S et al (2000) Coronaviridae. In: Van Regenmortel MHV, Fauquet CM, Bishop DHL, Carstens EB, Lemon SM, Mayo MA, McGeoch DJ, Pringle CR, Wickner RB (eds) Virus taxonomy: seventh report of the international committee on taxonomy of viruses. Academic Press, New York, pp 835–849Google Scholar
  3. 3.
    Cavanagh D (2007) Coronavirus avian infectious bronchitis virus. Vet Res 38:281–297PubMedCrossRefGoogle Scholar
  4. 4.
    Lai MM, Cavanagh D (1997) The molecular biology of coronaviruses. Adv Virus Res 48:1–100PubMedCrossRefGoogle Scholar
  5. 5.
    Pasternak AO, Spaan WJ, Snijder EJ (2006) Nidovirus transcription: how to make sense…? J Gen Virol 87:1403–1421PubMedCrossRefGoogle Scholar
  6. 6.
    Sjaak de Wit JJ, Cook JK, van der Heijden HM (2011) Infectious bronchitis virus variants: a review of the history, current situation and control measures. Avian Pathol 40:223–235PubMedCrossRefGoogle Scholar
  7. 7.
    Ignjatovic J, Gould G, Sapats S (2006) Isolation of a variant infectious bronchitis virus in Australia that further illustrates diversity among emerging strains. Arch Virol 151:1567–1585PubMedCrossRefGoogle Scholar
  8. 8.
    Liu XL, Su JL, Zhao JX, Zhang GZ (2009) Complete genome sequence analysis of a predominant infectious bronchitis virus (IBV) strain in China. Virus Genes 38:56–65PubMedCrossRefGoogle Scholar
  9. 9.
    Yu L, Jiang Y, Low S, Wang Z, Nam SJ, Liu W, Kwangac J (2001) Characterization of three infectious bronchitis virus isolates from China associated with proventriculus in vaccinated chickens. Avian Dis 45:416–424PubMedCrossRefGoogle Scholar
  10. 10.
    Abro SH, Renstrom LH, Ullman K, Isaksson M, Zohari S, Jansson DS, Belak S, Baule C (2011) Emergence of novel strains of avian infectious bronchitis virus in Sweden. Vet microbiol 55(1):155–161Google Scholar
  11. 11.
    Bochkov YA, Batchenko GV, Shcherbakova LO, Borisov AV, Drygin VV (2006) Molecular epizootiology of avian infectious bronchitis in Russia. Avian Pathol 35:379–393PubMedCrossRefGoogle Scholar
  12. 12.
    Gough RE, Cox WJ, de BWD, De Worthington KJ, Jones RC (2008) Chinese QX strain of infectious bronchitis virus isolated in the UK. Vet Rec 162:99–100PubMedCrossRefGoogle Scholar
  13. 13.
    Benyeda Z, Mato T, Suveges T, Szabo E, Kardi V, Abonyi-Toth Z, Rusvai M, Palya V (2009) Comparison of the pathogenicity of QX-like, M41 and 793/B infectious bronchitis strains from different pathological conditions. Avian Pathol 38:449–456PubMedCrossRefGoogle Scholar
  14. 14.
    Domanska-Blicharz K, Minta Z, Smietanka K, Porwan T (2006) New variant of IBV in Poland. Vet Rec 158:808PubMedCrossRefGoogle Scholar
  15. 15.
    Krapez U, Slavec B, Rojs OZ (2011) Circulation of infectious bronchitis virus strains from Italy 02 and QX genotypes in Slovenia between 2007 and 2009. Avian Dis 55:155–161PubMedCrossRefGoogle Scholar
  16. 16.
    Valastro V, Monne I, Fasolato M, Cecchettin K, Parker D, Terregino C, Cattoli G (2010) QX-type infectious bronchitis virus in commercial flocks in the UK. Vet Rec 167:865–866PubMedCrossRefGoogle Scholar
  17. 17.
    Worthington KJ, Currie RJ, Jones RC (2008) A reverse transcriptase-polymerase chain reaction survey of infectious bronchitis virus genotypes in Western Europe from 2002 to 2006. Avian Pathol 37:247–257PubMedCrossRefGoogle Scholar
  18. 18.
    Worthington KJ, Jones RC (2006) New genotype of infectious bronchitis virus in chickens in Scotland. Vet Rec 159:291–292PubMedCrossRefGoogle Scholar
  19. 19.
    Korber B, Muldoon M, Theiler J, Gao F, Gupta R, Lapedes A, Hahn BH, Wolinsky S, Bhattacharya T (2000) Timing the ancestor of the HIV-1 pandemic strains. Science 288:1789–1796PubMedCrossRefGoogle Scholar
  20. 20.
    Kosakovsky Pond SL, Posada D, Gravenor MB, Woelk CH, Frost SD (2006) GARD: a genetic algorithm for recombination detection. Bioinformatics 22:3096–3098PubMedCrossRefGoogle Scholar
  21. 21.
    Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599PubMedCrossRefGoogle Scholar
  22. 22.
    Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574PubMedCrossRefGoogle Scholar
  23. 23.
    Ducatez MF, Martin AM, Owoade AA, Olatoye IO, Alkali BR, Maikano I, Snoeck CJ, Sausy A, Cordioli P, Muller CP (2009) Characterization of a new genotype and serotype of infectious bronchitis virus in Western Africa. J Gen Virol 90:2679–2685PubMedCrossRefGoogle Scholar
  24. 24.
    Zhang Y, Wang HN, Wang T, Fan WQ, Zhang AY, Wei K, Tian GB, Yang X (2010) Complete genome sequence and recombination analysis of infectious bronchitis virus attenuated vaccine strain H120. Virus Genes 41:377–388PubMedCrossRefGoogle Scholar
  25. 25.
    Ammayappan A, Upadhyay C, Gelb J Jr, Vakharia VN (2008) Complete genomic sequence analysis of infectious bronchitis virus Ark DPI strain and its evolution by recombination. Virol J 5:157PubMedCrossRefGoogle Scholar
  26. 26.
    Mardani K, Noormohammadi AH, Hooper P, Ignjatovic J, Browning GF (2008) Infectious bronchitis viruses with a novel genomic organization. J Virol 82:2013–2024PubMedCrossRefGoogle Scholar
  27. 27.
    Adzhar A, Gough RE, Haydon D, Shaw K, Britton P, Cavanagh D (1997) Molecular analysis of the 793/B serotype of infectious bronchitis virus in Great Britain. Avian Pathol J WVPA 26:625–640CrossRefGoogle Scholar
  28. 28.
    Kingham BF, Keeler CL Jr, Nix WA, Ladman BS, Gelb J Jr (2000) Identification of avian infectious bronchitis virus by direct automated cycle sequencing of the S-1 gene. Avian Dis 44:325–335PubMedCrossRefGoogle Scholar
  29. 29.
    Lee SK, Sung HW, Kwon HM (2004) S1 glycoprotein gene analysis of infectious bronchitis viruses isolated in Korea. Arch Virol 149:481–494PubMedCrossRefGoogle Scholar
  30. 30.
    Mondal SP, Cardona CJ (2004) Comparison of four regions in the replicase gene of heterologous infectious bronchitis virus strains. Virology 324:238–248PubMedCrossRefGoogle Scholar
  31. 31.
    Kuo SM, Wang CH, Hou MH, Huang YP, Kao HW, Su HL (2010) Evolution of infectious bronchitis virus in Taiwan: characterisation of RNA recombination in the nucleocapsid gene. Vet Microbiol 144:293–302PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  • Shahid Hussain Abro
    • 1
    • 2
  • Lena H. M. Renström
    • 2
  • Karin Ullman
    • 2
  • Sándor Belák
    • 1
    • 2
  • Claudia Baule
    • 2
  1. 1.Department of Biomedical Sciences and Veterinary Public HealthSection of Virology, The Swedish University of Agricultural SciencesUppsalaSweden
  2. 2.Department of Virology, Immunobiology and ParasitologyThe National Veterinary InstituteUppsalaSweden

Personalised recommendations