In the last 5 years, frequent outbreaks of infectious bronchitis virus (IBV) are observed in both broiler and layer chicken flocks in the Kingdom of Saudi Arabia (KSA) in spite of extensive usage of vaccines. The IBV is a widespread avian coronavirus affecting both vaccinated and unvaccinated chicken flocks and is attributed to significant economic losses, around the globe. In the present study, 58 (n = 58) samples were collected from four different commercial poultry flocks from 8 KSA districts during 2019. A total of nine positive isolates (9/58; 15.5%), based on real-time reverse transcriptase PCR targeting nucleocapsid (N) gene, were used for further genetic characterization and evolutionary analysis. Genetic characterization of the partial spike (S1) gene revealed the clustering of the reported isolates into three different genotypes, whereas four additional isolates were grouped within 4/91 genotype, two isolates within IS/885 genotype, one isolate was closely related to IS/1494/06, and two isolates were grouped within classic serotype (vaccine-like strains). Phylodynamic revealed clustering of four isolated viruses within GI-13 lineage, three isolates within GI-23 lineage, and two isolates within GI-1 lineage. Results indicate that there are high evolutionary distances between the newly identified IBV strains in this study and the commercially used vaccines (GI-1), suggesting that IBV strains circulating in the KSA are under constant evolutionary pressures. Selective pressure biostatistics analyses consistently demonstrate the presence of a higher positive score which highlights the role of natural selection, a mechanism of virus evolution on sites located on the protein surface, within or nearby domains involved in viral attachment or related functions. Recombination analysis revealed emergence of two isolates through recombination events resulting in new recombinant viruses. Taken together, these finding demonstrate the genetic and evolutionary insights into the currently circulating IBV genotypes in KSA, which could help to better understand the origin, spread, and evolution of infectious bronchitis viruses, and to ascertain the importance of disease monitoring as well as re-evaluation for the currently used vaccines and vaccination programs.

中文翻译：

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传染性支气管炎病毒的进化分析揭示了显着的遗传多样性和重组事件

在过去 5 年中，尽管广泛使用了疫苗，但在沙特阿拉伯王国 (KSA) 的肉鸡和蛋鸡群中仍频繁爆发传染性支气管炎病毒 (IBV)。IBV 是一种广泛存在的禽类冠状病毒，可影响已接种疫苗和未接种疫苗的鸡群，并在全球造成重大经济损失。在本研究中，2019 年从 8 个 KSA 区的四个不同商业家禽群中收集了 58 个（n = 58）样本。 基于实时逆转录酶 PCR，共有 9 个阳性分离株（9/58；15.5%）靶向核衣壳 (N) 基因，用于进一步的遗传表征和进化分析。部分刺突 (S1) 基因的遗传特征揭示了报告的分离株聚集成三种不同的基因型，而另外四个分离株被归为 4/91 基因型，两株被归为 IS/885 基因型，一株与 IS/1494/06 密切相关，两株被归为经典血清型（疫苗样菌株）。系统动力学揭示了 GI-13 谱系内的四种分离病毒、GI-23 谱系内的三种分离物和 GI-1 谱系内的两种分离物的聚类。结果表明，本研究中新发现的 IBV 毒株与商业使用的疫苗 (GI-1) 之间存在很高的进化距离，这表明在沙特阿拉伯王国传播的 IBV 毒株处于持续的进化压力之下。选择性压力生物统计学分析一致表明存在更高的正分，这突出了自然选择的作用，位于蛋白质表面的位点上的病毒进化机制，在涉及病毒附着或相关功能的域内或附近。重组分析揭示了通过重组事件产生了两种分离株，从而产生了新的重组病毒。综上所述，这些发现证明了对 KSA 中当前流行的 IBV 基因型的遗传和进化见解，这有助于更好地了解传染性支气管炎病毒的起源、传播和进化，并确定疾病监测和重新评估的重要性。 - 评估当前使用的疫苗和疫苗接种计划。