Springer Nature is making SARS-CoV-2 and COVID-19 research free. View research | View latest news | Sign up for updates

A recombinant infectious bronchitis virus from a chicken with a spike gene closely related to that of a turkey coronavirus


Using viral metagenomics, the complete genome sequence of an infectious bronchitis virus (IBV) strain (named ahysx-1) from a fecal sample from a healthy chicken in Anhui province, China, was determined. The genome sequence of ahysx-1 was found to be very similar to that of IBV strain ck/CH/LLN/131040 (KX252787), except for the spike gene region, which is similar to that of a turkey coronavirus strain (EU022526), suggesting that ahysx-1 is a recombinant. Recombination analysis and phylogenetic analysis based on the genomic sequences of ahysx-1 and other related strains confirmed that ahysx-1 appears to be a recombinant resulting from a recombination event that occurred between a chicken coronavirus and a turkey coronavirus. Further studies need to be performed to determine whether this recombinant IBV strain is pathogenic and whether it is transmitted between chickens and turkeys.

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

Fig. 1


  1. 1.

    Perlman S, Netland J (2009) Coronaviruses post-SARS: update on replication and pathogenesis. Nat Rev Microbiol 7:439–450. https://doi.org/10.1038/nrmicro2147

  2. 2.

    Menachery VD, Graham RL, Baric RS (2017) Jumping species—a mechanism for coronavirus persistence and survival. Curr Opin Virol 23:1–7. https://doi.org/10.1016/j.coviro.2017.01.002

  3. 3.

    Woo PCY, Lau SKP, Lam CSF et al (2012) Discovery of Seven Novel Mammalian and Avian Coronaviruses in the Genus Deltacoronavirus Supports Bat Coronaviruses as the Gene Source of Alphacoronavirus and Betacoronavirus and Avian Coronaviruses as the Gene Source of Gammacoronavirus and Deltacoronavirus. J Virol 86:3995–4008. https://doi.org/10.1128/JVI.06540-11

  4. 4.

    Ziebuhr J, Thiel V, Gorbalenya AE (2001) The autocatalytic release of a putative RNA virus transcription factor from its polyprotein precursor involves two paralogous papain-like proteases that cleave the same peptide bond. J Biol Chem 276:33220–33232. https://doi.org/10.1074/jbc.M104097200

  5. 5.

    Bickerton E, Maier HJ, Stevenson-Leggett P et al (2018) The S2 Subunit of infectious bronchitis virus beaudette is a determinant of cellular tropism. J Virol 92:e01044–18. https://doi.org/10.1128/JVI.01044-18

  6. 6.

    Shan D, Fang S, Han Z et al (2018) Effects of hypervariable regions in spike protein on pathogenicity, tropism, and serotypes of infectious bronchitis virus. Virus Res 250:104–113. https://doi.org/10.1016/j.virusres.2018.04.013

  7. 7.

    Goebel SJ, Hsue B, Dombrowski TF, Masters PS (2004) Characterization of the RNA components of a putative molecular switch in the 3’ untranslated region of the murine coronavirus genome. J Virol 78:669–682

  8. 8.

    Zhang W, Li L, Deng X et al (2016) Viral nucleic acids in human plasma pools. Transfusion 56:2248–2255. https://doi.org/10.1111/trf.13692

  9. 9.

    Deng X, Naccache SN, Ng T et al (2015) An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data. Nucleic Acids Res. https://doi.org/10.1093/nar/gkv002

  10. 10.

    Zhang W, Yang S, Shan T et al (2017) Virome comparisons in wild-diseased and healthy captive giant pandas. Microbiome 5:90. https://doi.org/10.1186/s40168-017-0308-0

  11. 11.

    Skewes-Cox P, Sharpton TJ, Pollard KS, DeRisi JL (2014) Profile hidden Markov models for the detection of viruses within metagenomic sequence data. PLoS One 9:e105067. https://doi.org/10.1371/journal.pone.0105067

  12. 12.

    Johnson LS, Eddy SR, Portugaly E (2010) Hidden Markov model speed heuristic and iterative HMM search procedure. BMC Bioinformatics 11:431. https://doi.org/10.1186/1471-2105-11-431

  13. 13.

    Eddy SR (2009) A new generation of homology search tools based on probabilistic inference. Genome Inform 23:205–211

  14. 14.

    Finn RD, Clements J, Eddy SR (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 39:W29–W37. https://doi.org/10.1093/nar/gkr367

  15. 15.

    Cao J, Wu C-C, Lin TL (2008) Complete nucleotide sequence of polyprotein gene 1 and genome organization of turkey coronavirus. Virus Res 136:43–49. https://doi.org/10.1016/j.virusres.2008.04.015

  16. 16.

    Larkin MA, Blackshields G, Brown NP et al (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948. https://doi.org/10.1093/bioinformatics/btm404

  17. 17.

    Martin DP, Murrell B, Golden M et al (2015) RDP4: detection and analysis of recombination patterns in virus genomes. Virus Evol 1:vev003. https://doi.org/10.1093/ve/vev003

  18. 18.

    Tamura K, Peterson D, Peterson N et al (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739. https://doi.org/10.1093/molbev/msr121

  19. 19.

    Lin S-Y, Chen H-W (2017) Infectious bronchitis virus variants: molecular analysis and pathogenicity investigation. Int J Mol Sci 18:2030. https://doi.org/10.3390/ijms18102030

  20. 20.

    Jackwood MW, Boynton TO, Hilt DA et al (2010) Emergence of a group 3 coronavirus through recombination. Virology 398:98–108. https://doi.org/10.1016/j.virol.2009.11.044

Download references


This work was partly supported by the National Key Research and Development Programs of China (no. 2017YFC1200201), Jiangsu Provincial Key Research and Development Projects (no. BE2017693), Jiangsu Social Development Project (no. BE2016663), National Natural Science Foundation of China (no. 81741062), Student’s Platform for Innovation and Entrepreneurship Training Program (no. 201810299587 W), and the Blood Systems Research Institute.

Author information

Correspondence to Yu Li or Wen Zhang.

Ethics declarations

Competing interests

All authors declare that they have no competing interests.

Ethical approval

This article does not contain any studies with animals performed by any of the authors.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Handling Editor: Diego G. Diel.

Electronic supplementary material

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Wang, Y., Cui, X., Chen, X. et al. A recombinant infectious bronchitis virus from a chicken with a spike gene closely related to that of a turkey coronavirus. Arch Virol 165, 703–707 (2020). https://doi.org/10.1007/s00705-019-04488-3

Download citation


  • Viral metagenomics
  • Coronavirus
  • Infectious bronchitis virus
  • Genome recombination