Complete genome sequence and phylogenetic analysis of avian infectious bronchitis virus isolated in India

P  SHILPA; J JOHN KIRUBAHARAN; M  VIDHYA; RANJANI RAJASEKARAN; S RAJALAKSHMI

doi:10.56093/ijans.v92i6.113872

Authors

P SHILPA Department of Animal Husbandry, Kerala
J JOHN KIRUBAHARAN Tamil Nadu Veterinary and Animal Sciences University
M VIDHYA Tamil Nadu Veterinary and Animal Sciences University
RANJANI RAJASEKARAN Tamil Nadu Veterinary and Animal Sciences University
S RAJALAKSHMI Tamil Nadu Veterinary and Animal Sciences University

https://doi.org/10.56093/ijans.v92i6.113872

Keywords:

Infectious bronchitis virus variants, S1 gene, mutation, recombination, Mass 41 genotype, H120 variant

Abstract

Emergence of avian infectious bronchitis virus (IBV) variants with altered tissue tropism and host range has been reported from different parts of the world. Little is known about the different IBV variants existing and emerging in India. To explore the same, an IBV isolate, namely B17 isolated from backyard chicken in Tamil Nadu was used in the present study. The complete genome of B17 was sequenced and its phylogenetic relationship with the existing vaccine strain genotypes was analysed. The phylogenetic analysis of both S1 gene and complete genome sequence grouped B17 under Mass41 genotype comprising of M41, Beaudette, H120 and H120 variant with bootstrap value of 95 â€“ 100%. Further, genomic analysis of B17 revealed the possibilities of emergence of the same from H120 vaccine strain through mutations at various genes.Â

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Author Biographies

P SHILPA, Department of Animal Husbandry, Kerala

Veterinary Surgeon,

Veterinary Dispensary
J JOHN KIRUBAHARAN, Tamil Nadu Veterinary and Animal Sciences University

Professor and Head Department of Veterinary Microbiology Â
M VIDHYA, Tamil Nadu Veterinary and Animal Sciences University

Assistant Professor

Department of Veterinary Microbiology
RANJANI RAJASEKARAN, Tamil Nadu Veterinary and Animal Sciences University

Assistant Professor

Department of Veterinary Microbiology
S RAJALAKSHMI, Tamil Nadu Veterinary and Animal Sciences University

Assistant Professor

Department of Veterinary Microbiology

References

Bayry J, Goudar M S, Nighot P K, Kshirsagar S G, Ladman B S and Gelb J. 2005. Emergence of a nephropathogenic avian infectious bronchitis virus with a novel genotype in India. Journal of Clinical Microbiology 43: 916–18. DOI: https://doi.org/10.1128/JCM.43.2.916-918.2005

Bushnell L D and Brandly C A. 1933. Laryngotracheitis in chicks. Poultry Science 12: 55–60. DOI: https://doi.org/10.3382/ps.0120055

Casais R, Dove B, Cavanagh D and Britton P. 2003. Recombinant avian infectious bronchitis virus expressing a heterologous spike gene demonstrates that the spike protein is a determinant of cell tropism. Journal of Virology 77(16): 9084. DOI: https://doi.org/10.1128/JVI.77.16.9084-9089.2003

Cavanagh D and Naqi S. 2003. Infectious bronchitis, pp 101–119. (Eds) Saif Y M, Barnes H J, Glisson J R, Fadly A M,

McDougald L R and Swayne D E. Diseases of Poultry, 11th edn. Iowa State University Press, Ames, IA.

Cavanagh D. 2007. Coronavirus avian infectious bronchitis virus. Veterinary Research 38(2): 281–97. DOI: https://doi.org/10.1051/vetres:2006055

Chou P Y and Fasman G D. 1974. Prediction of protein conformation. Biochemistry 13: 222-45. DOI: https://doi.org/10.1021/bi00699a002

Dhama K, Singh S D, Barathidasan R, Desingu P A, Chakraborty S, Tiwari R and Kumar M A. Emergence of avian infectious bronchitis virus and its variants need better diagnosis, prevention and control strategies: a global perspective. Pakistan Journal of Biological Sciences 17(6): 751–67. DOI: https://doi.org/10.3923/pjbs.2014.751.767

Elankumaran S, Balachandran C, Chandran N D J, Roy P, Albert A and Manickam R. 1999. Serological evidence for a 793/B related avian infectious bronchitis virus in India. Veterinary Record 144: 299–300.

He K, Li M, Wei P, Mo M L, Wei T C and Li K R. 2012. Complete genome sequence of an infectious bronchitis virus chimera between cocirculating heterotypic strains. Journal of Virology 86(24): 13887. DOI: https://doi.org/10.1128/JVI.02722-12

Jackwood M W, Hilt D A, Callison S A, Lee C W, Plaza H and Wade E. 2001. Spike glycoprotein cleavage recognition site analysis of infectious bronchitis virus. Avian Diseases 1: 366 – 72. DOI: https://doi.org/10.2307/1592976

Kumar S, Stecher G and Tamura K. 2016. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution 33(7): 1870–74. DOI: https://doi.org/10.1093/molbev/msw054

Liu S, Chen J, Chen J, Kong X, Shao Y, Han Z, Feng L, Cai X, Gu S and Liu M. 2005. Isolation of avian infectious bronchitis coronavirus from domestic peafowl (Pavo cristatus) and teal (Anas). Journal of General Virology 86(3) :719–25. DOI: https://doi.org/10.1099/vir.0.80546-0

Liu X L, Su J L, Zhao J X and Zhang G Z. 2009. Complete genome sequence analysis of a predominant infectious bronchitis virus (IBV) strain in China. Virus Genes 38(1): 56 – 65. DOI: https://doi.org/10.1007/s11262-008-0282-5

Martin, D P, Lemey P, Lott M, Moulton V, Posada D and Lefeuvre P. 2010. RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics 26: 2462 – 63. DOI: https://doi.org/10.1093/bioinformatics/btq467

Mousavi F S, Ghalyanchilangeroudi A, Hosseini H, Fasaei B N, Ghafouri S A, Abdollahi H, Fallah-Mehrabadi M H and Sadri N. 2018. Complete genome analysis of Iranian IS-1494 like avian infectious bronchitis virus. Virus Disease 29(3): 390–94. DOI: https://doi.org/10.1007/s13337-018-0462-4

Patel B H, Bhimani M P, Bhanderi B B and Jhala M K. 2015. Isolation and molecular characterization of nephropathic

infectious bronchitis virus isolates of Gujarat state, India. Virus Disease 26(1): 42–47.

Raja A, Raj G D and Kumanan K. 2020. Emergence of variant avian infectious bronchitis virus in India. Iranian Journal of Veterinary Research 21(1): 33.

Schalk A F and Hawn M C. 1931. An apparently new respiratory disease of baby chicks. Journal of American Veterinary

Medical Association 78: 413–22.

Spaan W, Cavanagh D and Horzinek M C. 1988. Coronaviruses: structure and genome expression. Journal of General Virology 69(12): 2939–52. DOI: https://doi.org/10.1099/0022-1317-69-12-2939

Sukumar S and Prabhakar T G. 1993. An outbreak of infectious bronchitis among poultry in Tamil Nadu. Indian Journal of Animal Sciences 63: 820–22.

Sumi V, Singh S D, Dhama K, Gowthaman V, Barathidasan R and Sukumar K. 2012. Isolation and molecular characterization of infectious bronchitis virus from recent outbreaks in broiler flocks reveals emergence of novel strain in India. Tropical Animal Health Production 44: 1791–95. DOI: https://doi.org/10.1007/s11250-012-0140-2

Sutou S, Sato S, Okabe T, Nakai M and Sasaki N. 1988. Cloning and sequencing of genes encoding structural proteins of avian infectious bronchitis virus. Virology 165(2): 589–95. DOI: https://doi.org/10.1016/0042-6822(88)90603-4

Valastro V, Holmes E C, Britton P, Fusaro A, Jackwood M W, Cattoli G and Monne I. 2016. S1 gene-based phylogeny of

infectious bronchitis virus: an attempt to harmonize virus classification. Infection, Genetics and Evolution 39: 349 – 64. DOI: https://doi.org/10.1016/j.meegid.2016.02.015

Wang Y, Wang Y, Zhang Z, Fan G, Jiang Y, Liu X, Ding J and Wang S. 1998. Isolation and identification of glandular

stomach type IBV (QX IBV) in chickens. Chinese Journal of Animal Quarantine 15(1): 1 – 3.

Zhang Y, Wang H N, Wang T, Fan W Q, Zhang A Y, Wei K, Tian G B and Yang X. 2010. Complete genome sequence

and recombination analysis of infectious bronchitis virus attenuated vaccine strain H120. Virus Genesv 41(3): 377–88. DOI: https://doi.org/10.1007/s11262-010-0517-0