Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt.
Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YG, UK.
Genes (Basel). 2020 May 29;11(6):605. doi: 10.3390/genes11060605.
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 ( = 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.
在过去的 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冠状病毒，会影响接种和未接种疫苗的鸡群，是造成全球重大经济损失的原因之一。在本研究中，2019 年从沙特阿拉伯的 8 个地区的 4 个不同商业家禽养殖场采集了 58 个样本。基于针对核衣壳（N）基因的实时逆转录 PCR，共有 9 个阳性分离株（9/58；15.5%）被用于进一步的遗传特征和进化分析。部分 S 基因（S1）的遗传特征表明，所报告的分离株聚类为三种不同的基因型，而另外四个分离株被聚类为 4/91 基因型，两个分离株被聚类为 IS/885 基因型，一个分离株与 IS/1494/06 密切相关，两个分离株被聚类为经典血清型（疫苗样株）。系统发育动力学分析表明，四个分离病毒聚类在 GI-13 谱系内，三个分离病毒聚类在 GI-23 谱系内，两个分离病毒聚类在 GI-1 谱系内。结果表明，本研究中鉴定的新 IBV 株与商业上使用的疫苗（GI-1）之间存在较高的进化距离，这表明在沙特阿拉伯流行的 IBV 株处于持续的进化压力下。选择压力生物统计学分析一致显示存在更高的阳性评分，这突出了自然选择的作用，即病毒进化的一种机制，作用于位于蛋白质表面、病毒附着或相关功能相关区域内或附近的位点上。重组分析表明，两个分离株通过重组事件产生了新的重组病毒。综上所述，这些发现提供了对沙特阿拉伯目前流行的 IBV 基因型的遗传和进化的深入了解，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，并确定疾病监测以及对当前使用的疫苗和接种计划进行重新评估的重要性。
