Avian Infectious Bronchitis Virus, has become one of the most problematic causes of economic losses in poultry farms. To effectively control the virus, monitoring and surveillance of circulating virus strains in poultry farms is inevitable. Internal organ samples of broilers with clinical signs of infectious bronchitis and two samples of the commonly used vaccine strains (4/91 and H120) in Iranian poultry flocks were used for amplification of a 1.8 kbp fragment including nucleocapsid (N) gene and 3′ untranslated region (UTR) by reverse transcription polymerase chain reaction (RTPCR) method. The amplified fragments were digested with the restriction endonuclease enzyme, AluI. The sequence similarity of the field isolate (Ma1/16) with previous isolates and reference strains of IBV was then investigated. Also, the phylogenetic relationship of Ma1/16 with viruses from other regions was determined based on the sequence of two 600 bp partial sequences of the N gene using Mega7 software. Seven IBVs were classified into two groups based on restriction fragment length polymorphism (RFLP) patterns of the N-3´UTR fragment; all of five field isolates and vaccine strain 4/91 were clustered together. Ma1/16 had the highest similarity with two other Iranian IBV isolates, Ur1/09 and MNS-7861-1 (91.7 % and 90 %, respectively), based on the 600 nucleotides of 5´ end of the N-3' UTR fragment of the isolate. The nucleotide sequence of 600 nucleotides at the 3´ end of the amplified fragment in the Ma1/16 isolate (N-3'UTR) had the highest similarity to the BJ strain (86.4%). Regarding the induction of humoral and cellular immune responses using a vaccine candidate based on T-cell epitope peptides in IBV nucleocapsid protein, the gene sequence data of N-3'UTR fragment can be helpful in monitoring of circulating strains of IBV, designing effective IBV vaccines, and successfully controlling IB disease in Iran.
