New insights on epidemiology of infectious bronchitis virus in Iran by comparing two genotyping methods

Abstract

Different genotypes of infectious bronchitis virus (IBV) in poultry are circulating worldwide. The most efficient classification system for IBV genotypes is based on the complete sequencing of S1 gene, and the target organ can be trachea, kidney, oviduct, lung, esophagus, proventriculus, intestine, liver, spleen, bursa, cecal tonsils, cloaca, and testis. In Iran, IBV genotyping is usually performed by partial sequencing of S1 gene, and the trachea is often selected for sampling. This study applies a different genotyping method, and compares the results with the routine method of genotyping. Samples were collected from the trachea and kidneys of 50 broiler flocks with respiratory symptoms. The presence of IBV was confirmed by a real-time RT-PCR analysis targeting the 5'UTR region of the genome. Genotype of positive samples was determined by two methods of partial S1 gene sequencing and genotype-specific primers. In the real-time RT-PCR test, 88% and 90% of tracheal and kidney samples showed positive results, respectively. When the S gene was sequenced, Variant 2 (GI-23) (68.18%), 793/B (GI-13) (22.73%), Massachusetts (GI-1) (6.82%), and QX (GI-19) (2.27%) were detected in the tracheal samples, whereas QX (GI-19) and Massachusetts (GI-1) were not diagnosed in the kidney samples. In the genotypespecific method, IBV genotypes Variant 2, 793/B, Massachusetts, and QX were detected in both tracheal and kidney samples. The results of genotype-specific method also demonstrated that 70% of tracheal samples and 62% of kidney samples were infected with a single IBV genotype, while 30% of tracheal samples and 38% of kidney samples were coinfected with different IBV types. When comparing two genotyping methods, the use of genotype-specific primers was superior to partial S1 gene sequencing, not only in detecting different IBV types, but also in efficiently applying them in both trachea and kidney.