Virus Genes

, Volume 52, Issue 4, pp 509–520 | Cite as

Genome sequence and origin analyses of the recombinant novel IBV virulent isolate SAIBK2

  • Xuan Wu
  • Xin Yang
  • Pengwei Xu
  • Long Zhou
  • Zhikun Zhang
  • Hongning WangEmail author


Recombination between infectious bronchitis viruses (IBVs), together with point mutations, insertions, and deletions, is thought to be responsible for the emergence of new IBV variants. SAIBK2 is a nephropathogenic strain isolated from layer flocks vaccinated with live attenuated H120 vaccine in Sichuan province, China in 2011. SAIBK2 causes severe kidney lesions and results in 50 % mortality in 30-day-old specific-pathogen-free chickens (with a dose of 105 EID50/0.1 mL SAIBK2 per chicken). The complete genome of SAIBK2 consists of 27669 nucleotides, excluding the poly-A tail at the 3′ end. SAIBK2 has the highest identity to YX10 in terms of complete genome. Phylogenetic analysis of complete sequence showed that SAIBK2 belongs to the most dominant genotype in China. Comparison and recombination analyses with other IBV strains revealed that SAIBK2 may originate from recombination events among a YX10-, a YN-, and a Mass-like strain. Furthermore, whole gene 5 and parts of nsp 3, nsp 4, nsp 16, and N genes are involved in the recombination events, and the uptake of these regions from YN and Mass strains by SAIBK2 may increase its replication efficiency and be responsible for its increased virulence in specific-pathogen-free chickens.


Infectious bronchitis virus Complete genome Virulent strain Recombination event 



The study was supported by the earmarked fund for Modern Agro-industry Technology Research System (CARS-41-K09), Project for Science and Technology Support Program of Sichuan province (2014NZ0020), and Natural Science Foundation of China (31302094).


  1. 1.
    I. Brierley, M.E. Boursnell, M.M. Binns, B. Bilimoria, V.C. Blok, T.D. Brown, S.C. Inglis, EMBO J. 6, 3779 (1987)PubMedPubMedCentralGoogle Scholar
  2. 2.
    J. Ziebuhr, V. Thiel, A.E. Gorbalenya, J. Biol. Chem. 276, 33220–33232 (2001)CrossRefPubMedGoogle Scholar
  3. 3.
    M. Armesto, D. Cavanagh, P. Britton, PLoS ONE 4, e7384 (2009)CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    T. Hodgson, R. Casais, B. Dove, P. Britton, D. Cavanagh, J. Virol. 78, 13804–13811 (2004)CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    R. Casais, B. Dove, D. Cavanagh, P. Britton, J. Virol. 77, 9084–9089 (2003)CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    D. Cavanagh, P.J. Davis, J.K. Cook, D. Li, A. Kant, G. Koch, Avian Pathol. 21, 33–43 (1992)CrossRefPubMedGoogle Scholar
  7. 7.
    R.L. Parr, E.W. Collissor, Arch. Virol. 133, 369–383 (1993)CrossRefPubMedGoogle Scholar
  8. 8.
    T. Hodgson, P. Britton, D. Cavanagh, J. Virol. 80, 296–305 (2006)CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    R. Casais, M. Davies, D. Cavanagh, P. Britton, J. Virol. 79, 8065–8078 (2005)CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Y. Zhang, H. Wang, T. Wang, W. Fan, A. Zhang, K. Wei, G. Tian, X. Yang, Virus Genes 41, 377–388 (2010)CrossRefPubMedGoogle Scholar
  11. 11.
    T. Zhang, Z. Han, Q. Xu, Q. Wang, M. Gao, W. Wu, Y. Shao, H. Li, X. Kong, S. Liu, Infect. Genet. Evol. 32, 377–387 (2015)CrossRefPubMedGoogle Scholar
  12. 12.
    P.S. Masters, Adv. Virus Res. 66, 193–292 (2006)CrossRefPubMedGoogle Scholar
  13. 13.
    X. Liu, H. Ma, Q. Xu, N. Sun, Z. Han, C. Sun, H. Guo, Y. Shao, X. Kong, S. Liu, Vet. Microbiol. 162, 429–436 (2013)CrossRefPubMedGoogle Scholar
  14. 14.
    S. Liu, Q. Xu, Z. Han, X. Liu, H. Li, H. Guo, N. Sun, Y. Shao, X. Kong, Infect. Genet. Evol. 23, 189–195 (2014)CrossRefPubMedGoogle Scholar
  15. 15.
    S.W. Thor, D.A. Hilt, J.C. Kissinger, A.H. Paterson, M.W. Jackwood, Viruses 3, 1777–1799 (2011)CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    M.W. Jackwood, T.O. Boynton, D.A. Hilt, E.T. McKinley, J.C. Kissinger, A.H. Paterson, J. Robertson, C. Lemke, A.W. McCall, S.M. Williams, J.W. Jackwood, L.A. Byrd, Virology 398, 98–108 (2010)CrossRefPubMedGoogle Scholar
  17. 17.
    Y. Xue, Q. Xie, Z. Yan, J. Ji, F. Chen, J. Qin, B. Sun, J. Ma, Y. Bi, J. Virol. 86, 13812–13813 (2012)CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    J. Feng, Y. Hu, Z. Ma, Q. Yu, J. Zhao, X. Liu, G. Zhang, Emerg. Infect. Dis. 18, 1994–2001 (2012)CrossRefPubMedPubMedCentralGoogle Scholar
  19. 19.
    M. Oostra, M.C. Hagemeijer, M. van Gent, C.P.J. Bekker, E.G. Te Lintelo, P.J.M. Rottier, C.A.M. de Haan, J. Virol. 82, 12392–12405 (2008)CrossRefPubMedPubMedCentralGoogle Scholar
  20. 20.
    A. Kanjanahaluethai, Z. Chen, D. Jukneliene, S.C. Baker, Virology 361, 391–401 (2007)CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    S.H. van den Worm, K. Knoops, J.C. Zevenhoven-Dobbe, C. Beugeling, Y. van der Meer, A.M. Mommaas, E.J. Snijder, J. Virol. 85, 5669–5673 (2011)CrossRefPubMedPubMedCentralGoogle Scholar
  22. 22.
    M.M. Lai, R.S. Baric, P.R. Brayton, S.A. Stohlman, Proc. Natl. Acad. Sci. U.S.A. 81, 3626–3630 (1984)CrossRefPubMedPubMedCentralGoogle Scholar
  23. 23.
    Y. Chen, C. Su, M. Ke, X. Jin, L. Xu, Z. Zhang, A. Wu, Y. Sun, Z. Yang, P. Tien, T. Ahola, Y. Liang, X. Liu, D. Guo, PLoS Pathog. 7, e1002294 (2011)CrossRefPubMedPubMedCentralGoogle Scholar
  24. 24.
    J.D. Lewis, E. Izaurralde, Eur. J. Biochem. 247, 461–469 (1997)CrossRefPubMedGoogle Scholar
  25. 25.
    B. Schwer, X. Mao, S. Shuman, Nucleic Acids Res. 26, 2050–2057 (1998)CrossRefPubMedPubMedCentralGoogle Scholar
  26. 26.
    S. Kuo, H. Kao, M. Hou, C. Wang, S. Lin, H. Su, Vet. Microbiol. 162, 408–418 (2013)CrossRefPubMedGoogle Scholar
  27. 27.
    H. Jayaram, H. Fan, B.R. Bowman, A. Ooi, J. Jayaram, E.W. Collisson, J. Lescar, B.V.V. Prasad, J. Virol. 80, 6612–6620 (2006)CrossRefPubMedPubMedCentralGoogle Scholar
  28. 28.
    K.R. Hurst, R. Ye, S.J. Goebel, P. Jayaraman, P.S. Masters, J. Virol. 84, 10276–10288 (2010)CrossRefPubMedPubMedCentralGoogle Scholar
  29. 29.
    N.E. Grossoehme, L. Li, S.C. Keane, P. Liu, C.E. Dann, J.L. Leibowitz, D.P. Giedroc, J. Mol. Biol. 394, 544–557 (2009)CrossRefPubMedPubMedCentralGoogle Scholar
  30. 30.
    S.A. Kopecky-Bromberg, L. Martinez-Sobrido, M. Frieman, R.A. Baric, P. Palese, J. Virol. 81, 548–557 (2006)CrossRefPubMedPubMedCentralGoogle Scholar
  31. 31.
    K. Feng, Y. Xue, J. Wang, W. Chen, F. Chen, Y. Bi, Q. Xie, Vaccine 33, 1113–1120 (2015)CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Xuan Wu
    • 1
  • Xin Yang
    • 1
  • Pengwei Xu
    • 2
  • Long Zhou
    • 1
  • Zhikun Zhang
    • 1
  • Hongning Wang
    • 1
    Email author
  1. 1.School of Life Science, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, “985 Project” Science Innovative Platform for Resource and Environment Protection of Southwestern, Key Laboratory of Bio-resources and Eco-environmentMinistry of EducationChengduChina
  2. 2.School of Public HealthXinxiang Medical UniversityXinxiangChina

Personalised recommendations