Extensive rate of variations in the S1 gene (spike glycoprotein subunit gene) of infectious bronchitis virus (IBV) causes challenges for clinicians in counting variants for differentiation of infected from vaccinated birds and addressing the variants of unknown significance. This study investigated the possibility of using an RNA‐dependent RNA polymerase gene (RdRp) as a target for molecular characterization of IBV strains in Iran. Trachea samples were collected from commercial broiler flocks (n  = 52) showing respiratory syndrome. Specific PCR primers were designed for a variable region located in the RdRp gene flanked by highly conserved regions. Reverse transcriptase PCR followed by sequence analysis identified eight IBV variants, with an overall prevalence of 44.2%. Deduced nucleotide and amino acid sequences were compared with published sequences for IBV strains. Because of the long‐distance similarities, the field samples could be discriminated from vaccine strains. Phylogenetic analysis of RdRp gene sequences resulted in clustering of the IBV strains related to each area. Using RdRp as a genetic marker eliminates the challenges arising from the enormous variations that make it difficult to discriminate between field and vaccine strains as well as affiliate certain variants to various geographical areas.

中文翻译：

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基于 RNA 依赖性 RNA 聚合酶基因的传染性支气管炎病毒的分子特征。

传染性支气管炎病毒 (IBV) 的S1基因（刺突糖蛋白亚基基因）的广泛变异率给临床医生计算变异以区分受感染鸟类和接种疫苗的鸟类和处理未知意义的变异带来了挑战。本研究调查了使用依赖 RNA 的 RNA 聚合酶基因 (RdRp) 作为目标对伊朗 IBV 毒株进行分子表征的可能性。 从显示呼吸综合征的商业肉鸡群 ( n = 52)中收集气管样本。针对位于RdRp中的可变区设计了特异性 PCR 引物基因两侧是高度保守的区域。逆转录酶 PCR 和序列分析确定了八种 IBV 变体，总体流行率为 44.2%。将推导的核苷酸和氨基酸序列与 IBV 毒株的公布序列进行比较。由于长距离相似性，可以将现场样本与疫苗株区分开来。RdRp基因序列的系统发育分析导致与每个区域相关的 IBV 菌株的聚类。使用RdRp作为遗传标记消除了巨大变异所带来的挑战，这些变异使得难以区分田间毒株和疫苗毒株以及将某些变体与不同地理区域相关联。