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Phylogenetic analysis of RT-PCR detected infectious bronchitis virus locally infected broiler farms in Diyala Governorate-IRAQ

Background and Aim: One of the primary pathogenic causes linked to economic losses in the chicken business is the infectious bronchitis virus. This virus exploited its S (spike) gene-encoded protein to hook into the host receptor. The biological diversity of the viral S gene may be linked to the chicken industry's vaccination status. Recently, the virus was detected in broilers of six farms located in different districts of Diyala Governorate by the use of RT-PCR. The current study aimed to explore the pattern of biological diversity of infectious bronchitis viruses based on the possibility of genetic variations of the S gene. Materials and Methods: Ten tissue samples were collected from broilers of six farms located in different districts of Diyala Governorate and named R1 to R10. The chickens were recently vaccinated, but naturally infected with infectious bronchitis virus; a particular RT-PCR fragment partially encompassing the coding domains of the S gene was recently obtained. The amplified fragments were immediately submitted to direct sequencing tests to examine the genetic variation pattern in the samples acquired from various chicken sources. Then unique comprehensive trees were generated to validate the correct genotyping of the identified variations and their phylogenetic distribution.