1887

Journal of General Virology header logo

Volume 96, Issue 6

Phylodynamic analysis of avian infectious bronchitis virus in South America Free

Abstract

Infectious bronchitis virus (IBV) is a coronavirus of chickens that causes great economic losses to the global poultry industry. The present study focuses on South American IBVs and their genetic relationships with global strains. We obtained full-length sequences of the S1 coding region and N gene of IBV field isolates from Uruguay and Argentina, and performed Phylodynamic analysis to characterize the strains and estimate the time of the most recent common ancestor. We identified two major South American genotypes, which were here denoted South America I (SAI) and Asia/South America II (A/SAII). The SAI genotype is an exclusive South American lineage that emerged in the 1960s. The A/SAII genotype may have emerged in Asia in approximately 1995 before being introduced into South America. Both SAI and A/SAII genotype strains clearly differ from the Massachusetts strains that are included in the vaccine formulations being used in most South American countries.

  • Received:
  • Accepted:
  • Published Online:
© 2015 The Authors
Loading

Article metrics loading...

/content/journal/jgv/10.1099/vir.0.000077
2015-06-01
2024-04-25
Loading full text...

Full text loading...

/deliver/fulltext/jgv/96/6/1340.html?itemId=/content/journal/jgv/10.1099/vir.0.000077&mimeType=html&fmt=ahah

References

  1. Abro S. H., Renström L. H. M., Ullman K., Isaksson M., Zohari S., Jansson D. S., Belák S., Baule C. 2012; Emergence of novel strains of avian infectious bronchitis virus in Sweden. Vet Microbiol 155:237–246 [View Article][PubMed]
     [Google Scholar]
  2. Adzhar A., Gough R. E., 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 26:625–640 [View Article][PubMed]
     [Google Scholar]
  3. Alvarado I. R., Villegas P., Mossos N., Jackwood M. W. 2005; Molecular characterization of avian infectious bronchitis virus strains isolated in Colombia during 2003. Avian Dis 49:494–499 [View Article][PubMed]
     [Google Scholar]
  4. Brown J. D., Stallknecht D. E., Beck J. R., Suarez D. L., Swayne D. E. 2006; Susceptibility of North American ducks and gulls to H5N1 highly pathogenic avian influenza viruses. Emerg Infect Dis 12:1663–1670 [View Article][PubMed]
     [Google Scholar]
  5. Callison S. A., Hilt D. A., Boynton T. O., Sample B. F., Robison R., Swayne D. E., Jackwood M. W. 2006; Development and evaluation of a real-time Taqman RT-PCR assay for the detection of infectious bronchitis virus from infected chickens. J Virol Methods 138:60–65 [View Article][PubMed]
     [Google Scholar]
  6. Cavanagh D. 2003; Severe acute respiratory syndrome vaccine development: experiences of vaccination against avian infectious bronchitis coronavirus. Avian Pathol 32:567–582 [View Article][PubMed]
     [Google Scholar]
  7. Cavanagh D., Davis P. J., Cook J. K. 1992; Infectious bronchitis virus: evidence for recombination within the Massachusetts serotype. Avian Pathol 21:401–408 [View Article][PubMed]
     [Google Scholar]
  8. Cavanagh D., Mawditt K., Adzhar A., Gough R. E., Picault J. P., Naylor C. J., Haydon D., Shaw K., Britton P. 1998; Does IBV change slowly despite the capacity of the spike protein to vary greatly?. Adv Exp Med Biol 440:729–734 [View Article][PubMed]
     [Google Scholar]
  9. Chacón J. L., Rodrigues J. N., Assayag M. S., Jr, Peloso C., Pedroso A. C., Ferreira A. J. P. 2011; Epidemiological survey and molecular characterization of avian infectious bronchitis virus in Brazil between 2003 and 2009. Avian Pathol 40:153–162 [View Article][PubMed]
     [Google Scholar]
  10. Cobb S. P. 2011; The spread of pathogens through trade in poultry meat: overview and recent developments. Rev Sci Tech 30:149–164[PubMed]
     [Google Scholar]
  11. Collisson E. W., Pei J., Dzielawa J., Seo S. H. 2000; Cytotoxic T lymphocytes are critical in the control of infectious bronchitis virus in poultry. Dev Comp Immunol 24:187–200 [View Article][PubMed]
     [Google Scholar]
  12. de Groot R. 2012; Family Coronaviridae. In Virus Taxonomy, 9th Report of the International Committee on Taxonomy of Viruses. pp. 806–828 Edited by King A. M. Q., Adams M. J., Carstens E. B., Lefkowitz E. J. San Diego, CA: Elsevier Academic Press;
     [Google Scholar]
  13. de Wit J. J. S., Cook J. K. A., van der Heijden H. M. J. F. 2011; Infectious bronchitis virus variants: a review of the history, current situation and control measures. Avian Pathol 40:223–235 [View Article][PubMed]
     [Google Scholar]
  14. Dolz R., Pujols J., Ordóñez G., Porta R., Majó N. 2008; Molecular epidemiology and evolution of avian infectious bronchitis virus in Spain over a fourteen-year period. Virology 374:50–59 [View Article][PubMed]
     [Google Scholar]
  15. Drummond A. J., Suchard M. A., Xie D., Rambaut A. 2012; Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 29:1969–1973 [View Article][PubMed]
     [Google Scholar]
  16. Fan H., Ooi A., Tan Y. W., Wang S., Fang S., Liu D. X., Lescar J. 2005; The nucleocapsid protein of coronavirus infectious bronchitis virus: crystal structure of its N-terminal domain and multimerization properties. Structure 13:1859–1868 [View Article][PubMed]
     [Google Scholar]
  17. Farsang A., Ros C., Renström L. H. M., Baule C., Soós T., Belák S. 2002; Molecular epizootiology of infectious bronchitis virus in Sweden indicating the involvement of a vaccine strain. Avian Pathol 31:229–236 [View Article][PubMed]
     [Google Scholar]
  18. Felippe P. A., da Silva L. H., Santos M. M. A. B., Spilki F. R., Arns C. W. 2010; Genetic diversity of avian infectious bronchitis virus isolated from domestic chicken flocks and coronaviruses from feral pigeons in Brazil between 2003 and 2009. Avian Dis 54:1191–1196 [View Article][PubMed]
     [Google Scholar]
  19. Fu K., Baric R. S. 1992; Evidence for variable rates of recombination in the MHV genome. Virology 189:88–102 [View Article][PubMed]
     [Google Scholar]
  20. Gough R. E., Randall C. J., Dagless M., Alexander D. J., Cox W. J., Pearson D. 1992; A ‘new’ strain of infectious bronchitis virus infecting domestic fowl in Great Britain. Vet Rec 130:493–494 [View Article][PubMed]
     [Google Scholar]
  21. Guindon S., Gascuel O. 2003; A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696–704 [View Article][PubMed]
     [Google Scholar]
  22. Han Z., Sun C., Yan B., Zhang X., Wang Y., Li C., Zhang Q., Ma Y., Shao Y., Liu Q. 2011; A 15-year analysis of molecular epidemiology of avian infectious bronchitis coronavirus in China. Infect Genet Evol 11:190–200 [View Article][PubMed]
     [Google Scholar]
  23. Hernández M., Banda A., Hernández D., Panzera F., Pérez R. 2006; Detection of very virulent strains of infectious bursal disease virus (vvIBDV) in commercial broilers from Uruguay. Avian Dis 50:624–631 [View Article][PubMed]
     [Google Scholar]
  24. Hidalgo H., Gallardo R., Rosende S. 1976; Isolation of infectious bronchitis virus from broiler chickens in Chile. Avian Dis 20:601–603 [View Article][PubMed]
     [Google Scholar]
  25. Hipólito O. 1957; Isolation and identification of the virus of infectious bronchitis of chickens in Brazil. Arq. Esc. Vet. Univ. Minas Gerais 10:131–151 (in Portuguese)
    [Google Scholar]
  26. Hosseini P., Sokolow S. H., Vandegrift K. J., Kilpatrick A. M., Daszak P. 2010; Predictive power of air travel and socio-economic data for early pandemic spread. PLoS ONE 5:e12763 [View Article][PubMed]
     [Google Scholar]
  27. Huang Y.-P., Lee H.-C., Cheng M.-C., Wang C.-H. 2004; S1 and N gene analysis of avian infectious bronchitis viruses in Taiwan. Avian Dis 48:581–589 [View Article][PubMed]
     [Google Scholar]
  28. Ignjatovic J., Galli L. 1994; The S1 glycoprotein but not the N or M proteins of avian infectious bronchitis virus induces protection in vaccinated chickens. Arch Virol 138:117–134 [View Article][PubMed]
     [Google Scholar]
  29. Ignjatović J., Sapats S. 2000; Avian infectious bronchitis virus. Rev Sci Tech 19:493–508[PubMed]
     [Google Scholar]
  30. 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 [View Article][PubMed]
     [Google Scholar]
  31. Jackwood M. W., Hilt D. A., Callison S. A., Lee C. W., Plaza H., Wade E. 2001; Spike glycoprotein cleavage recognition site analysis of infectious bronchitis virus. Avian Dis 45:366–372 [View Article][PubMed]
     [Google Scholar]
  32. Jia W., Karaca K., Parrish C. R., Naqi S. A. 1995; A novel variant of avian infectious bronchitis virus resulting from recombination among three different strains. Arch Virol 140:259–271 [View Article][PubMed]
     [Google Scholar]
  33. Kant A., Koch G., van Roozelaar D. J., Kusters J. G., Poelwijk F. A., van der Zeijst B. A. 1992; Location of antigenic sites defined by neutralizing monoclonal antibodies on the S1 avian infectious bronchitis virus glycopolypeptide. J Gen Virol 73:591–596 [View Article][PubMed]
     [Google Scholar]
  34. Katoh K., Misawa K., Kuma K., Miyata T. 2002; MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30:3059–3066 [View Article][PubMed]
     [Google Scholar]
  35. Kottier S. A., Cavanagh D., Britton P. 1995; Experimental evidence of recombination in coronavirus infectious bronchitis virus. Virology 213:569–580 [View Article][PubMed]
     [Google Scholar]
  36. Lai M. M., Cavanagh D. 1997; The molecular biology of coronaviruses. Adv Virus Res 48:1–100 [View Article][PubMed]
     [Google Scholar]
  37. Lee C. W., Jackwood M. W. 2000; Evidence of genetic diversity generated by recombination among avian coronavirus IBV. Arch Virol 145:2135–2148 [View Article][PubMed]
     [Google Scholar]
  38. Liu S., Kong X. 2004; A new genotype of nephropathogenic infectious bronchitis virus circulating in vaccinated and non-vaccinated flocks in China. Avian Pathol 33:321–327 [View Article][PubMed]
     [Google Scholar]
  39. Liu S. W., Zhang Q. X., Chen J. D., Han Z. X., Liu X., Feng L., Shao Y. H., Rong J. G., Kong X. G., Tong G. Z. 2006; Genetic diversity of avian infectious bronchitis coronavirus strains isolated in China between 1995 and 2004. Arch Virol 151:1133–1148 [View Article][PubMed]
     [Google Scholar]
  40. Liu S., Zhang X., Wang Y., Li C., Han Z., Shao Y., Li H., Kong X. 2009a). Molecular characterization and pathogenicity of infectious bronchitis coronaviruses: complicated evolution and epidemiology in China caused by cocirculation of multiple types of infectious bronchitis coronaviruses. Intervirology 52:223–234 [View Article][PubMed]
     [Google Scholar]
  41. Liu S., Zhang X., Wang Y., Li C., Liu Q., Han Z., Zhang Q., Kong X., Tong G. 2009b). Evaluation of the protection conferred by commercial vaccines and attenuated heterologous isolates in China against the CK/CH/LDL/97I strain of infectious bronchitis coronavirus. Vet J 179:130–136 [View Article][PubMed]
     [Google Scholar]
  42. McKinley E. T., Jackwood M. W., Hilt D. A., Kissinger J. C., Robertson J. S., Lemke C., Paterson A. H. 2011; Attenuated live vaccine usage affects accurate measures of virus diversity and mutation rates in avian coronavirus infectious bronchitis virus. Virus Res 158:225–234 [View Article][PubMed]
     [Google Scholar]
  43. Meulemans G., Boschmans M., Decaesstecker M., van den, Berg T. P., Denis P., Cavanagh D. 2001; Epidemiology of infectious bronchitis virus in Belgian broilers: a retrospective study, 1986 to 1995. Avian Pathol 30:411–421 [View Article][PubMed]
     [Google Scholar]
  44. Posada D. 2008; jModelTest: phylogenetic model averaging. Mol Biol Evol 25:1253–1256 [View Article][PubMed]
     [Google Scholar]
  45. Rimondi A., Craig M. I., Vagnozzi A., König G., Delamer M., Pereda A. 2009; Molecular characterization of avian infectious bronchitis virus strains from outbreaks in Argentina (2001–2008). Avian Pathol 38:149–153 [View Article][PubMed]
     [Google Scholar]
  46. Seo S. H., Wang L., Smith R., Collisson E. W. 1997; The carboxyl-terminal 120-residue polypeptide of infectious bronchitis virus nucleocapsid induces cytotoxic T lymphocytes and protects chickens from acute infection. J Virol 71:7889–7894[PubMed]
     [Google Scholar]
  47. Stern D. F., Sefton B. M. 1982; Coronavirus proteins: biogenesis of avian infectious bronchitis virus virion proteins. J Virol 44:794–803[PubMed]
     [Google Scholar]
  48. Stöver B. C., Müller K. F. 2010; TreeGraph 2: combining and visualizing evidence from different phylogenetic analyses. BMC Bioinformatics 11:7 [View Article][PubMed]
     [Google Scholar]
  49. Toffan A., Bonci M., Bano L., Bano L., Valastro V., Vascellari M., Capua I., Terregino C. 2013; Diagnostic and clinical observation on the infectious bronchitis virus strain Q1 in Italy. Vet Ital 49:347–355[PubMed]
     [Google Scholar]
  50. Toro H., van Santen V. L., Jackwood M. W. 2012; Genetic diversity and selection regulates evolution of infectious bronchitis virus. Avian Dis 56:449–455 [View Article][PubMed]
     [Google Scholar]
  51. USDA (2014). Livestock and poultry: world markets and trade http://www.fas.usda.gov/data/livestock-and-poultry-world-markets-and-trade
  52. Villarreal L. Y., Brandão P. E., Chacón J. L., Saidenberg A. B. S., Assayag M. S., Jones R. C., Ferreira A. J. 2007; Molecular characterization of infectious bronchitis virus strains isolated from the enteric contents of Brazilian laying hens and broilers. Avian Dis 51:974–978 [View Article][PubMed]
     [Google Scholar]
  53. Wang L., Junker D., Collisson E. W. 1993; Evidence of natural recombination within the S1 gene of infectious bronchitis virus. Virology 192:710–716 [View Article][PubMed]
     [Google Scholar]
  54. Yu L., Jiang Y., Low S., Wang Z., Nam S. J., Liu W., Kwang J. 2001; Characterization of three infectious bronchitis virus isolates from China associated with proventriculus in vaccinated chickens. Avian Dis 45:416–424 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/vir.0.000077
Loading
Phylodynamic analysis of avian infectious bronchitis virus in South America
J. Gen. Virol. 96, 1340 (2015); https://doi.org/10.1099/vir.0.000077
/content/journal/jgv/10.1099/vir.0.000077
/content/journal/jgv/10.1099/vir.0.000077
Loading

Data & Media loading...

Supplements

Supplementary Data

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error