Skip to main content
SpringerLink
Log in

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

  • Annotated Sequence Record
  • Published:
Archives of Virology Aims and scope Submit manuscript

Abstract

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

References

  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 148:2207–2235

    Article  PubMed  CAS  Google Scholar 

  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 835–849

    Google Scholar 

  3. Cavanagh D (2007) Coronavirus avian infectious bronchitis virus. Vet Res 38:281–297

    Article  PubMed  CAS  Google Scholar 

  4. Lai MM, Cavanagh D (1997) The molecular biology of coronaviruses. Adv Virus Res 48:1–100

    Article  PubMed  CAS  Google Scholar 

  5. Pasternak AO, Spaan WJ, Snijder EJ (2006) Nidovirus transcription: how to make sense…? J Gen Virol 87:1403–1421

    Article  PubMed  CAS  Google Scholar 

  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 40:223–235

    Article  PubMed  CAS  Google Scholar 

  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 151:1567–1585

    Article  PubMed  CAS  Google Scholar 

  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 38:56–65

    Article  PubMed  Google Scholar 

  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 45:416–424

    Article  PubMed  CAS  Google Scholar 

  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):155–161

    Google Scholar 

  11. Bochkov YA, Batchenko GV, Shcherbakova LO, Borisov AV, Drygin VV (2006) Molecular epizootiology of avian infectious bronchitis in Russia. Avian Pathol 35:379–393

    Article  PubMed  CAS  Google Scholar 

  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 162:99–100

    Article  PubMed  CAS  Google Scholar 

  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 38:449–456

    Article  PubMed  CAS  Google Scholar 

  14. Domanska-Blicharz K, Minta Z, Smietanka K, Porwan T (2006) New variant of IBV in Poland. Vet Rec 158:808

    Article  PubMed  CAS  Google Scholar 

  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 55:155–161

    Article  PubMed  Google Scholar 

  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 167:865–866

    Article  PubMed  CAS  Google Scholar 

  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 37:247–257

    Article  PubMed  CAS  Google Scholar 

  18. Worthington KJ, Jones RC (2006) New genotype of infectious bronchitis virus in chickens in Scotland. Vet Rec 159:291–292

    Article  PubMed  Google Scholar 

  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 288:1789–1796

    Article  PubMed  CAS  Google Scholar 

  20. Kosakovsky Pond SL, Posada D, Gravenor MB, Woelk CH, Frost SD (2006) GARD: a genetic algorithm for recombination detection. Bioinformatics 22:3096–3098

    Article  PubMed  Google Scholar 

  21. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599

    Article  PubMed  CAS  Google Scholar 

  22. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574

    Article  PubMed  CAS  Google Scholar 

  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 90:2679–2685

    Article  PubMed  CAS  Google Scholar 

  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 41:377–388

    Article  PubMed  CAS  Google Scholar 

  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 5:157

    Article  PubMed  Google Scholar 

  26. Mardani K, Noormohammadi AH, Hooper P, Ignjatovic J, Browning GF (2008) Infectious bronchitis viruses with a novel genomic organization. J Virol 82:2013–2024

    Article  PubMed  CAS  Google Scholar 

  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 26:625–640

    Article  CAS  Google Scholar 

  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 44:325–335

    Article  PubMed  CAS  Google Scholar 

  29. Lee SK, Sung HW, Kwon HM (2004) S1 glycoprotein gene analysis of infectious bronchitis viruses isolated in Korea. Arch Virol 149:481–494

    Article  PubMed  CAS  Google Scholar 

  30. Mondal SP, Cardona CJ (2004) Comparison of four regions in the replicase gene of heterologous infectious bronchitis virus strains. Virology 324:238–248

    Article  PubMed  CAS  Google Scholar 

  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 144:293–302

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgements

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.

Author information

Authors and Affiliations

  1. Department of Biomedical Sciences and Veterinary Public Health, Section of Virology, The Swedish University of Agricultural Sciences, Ulls Väg 2B, 751 89, Uppsala, Sweden

    Shahid Hussain Abro & Sándor Belák

  2. Department of Virology, Immunobiology and Parasitology, The National Veterinary Institute, Ulls Väg 2B, 751 89, Uppsala, Sweden

    Shahid Hussain Abro, Lena H. M. Renström, Karin Ullman, Sándor Belák & Claudia Baule

Authors
  1. Shahid Hussain Abro
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Lena H. M. Renström
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Karin Ullman
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Sándor Belák
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Claudia Baule
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Shahid Hussain Abro.

Electronic supplementary material

Below is the link to the electronic supplementary material.

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

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

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

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)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Abro, S.H., Renström, L.H.M., Ullman, K. et al. Characterization and analysis of the full-length genome of a strain of the European QX-like genotype of infectious bronchitis virus. Arch Virol 157, 1211–1215 (2012). https://doi.org/10.1007/s00705-012-1284-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00705-012-1284-0

Keywords

Search

Navigation