背景:关于鸟类的病毒学研究,包括鸡相对稀缺,特别是来自非洲大陆。尽管RNA病毒不断进化,家禽因季节性病毒爆发而遭受严重损失,RNA病毒组成的信息由于其高度不稳定的性质而变得更加贫乏,遗传多样性,以及与表征相关的困难。此外,有关可能调节鸟类中某些病毒发生的因素的信息有限,特别是对驯养的鸟类。病毒宏基因组学通过测序技术的进步,已经能够使用各种样品表征不同宿主物种的整个病毒体。
方法:测定了在两个独立季节的3个时间点收集的来自南非农场的27个无症状鸡的粪便样品中存在的复杂RNA病毒成分,进一步研究了鸡的年龄和采集季节对病毒丰度和多样性的影响。这项研究利用了非侵入性粪便取样方法,mRNA病毒靶向富集步骤,一个完整的转录组扩增策略,Illumina测序,和生物信息学工具。
结果:获得的结果显示,共有48种病毒,跨越11个订单,15科21属。病毒RNA家族,如冠状病毒,小导航科,呼肠孤病毒科,星状病毒科,杯状病毒科,Picorbirnaviridae和逆转录病毒科丰富,其中小核糖核酸病毒,在所调查的27个粪便样本中,三个年龄组(2、4和7周)和两个季节(夏季和冬季)的患病率为100%。对所调查的不同鸡群之间的变异程度的进一步调查表明,鸡群之间的病毒多样性和丰度受年龄(P=0.01099)和季节(P=0.00099)的显着影响。而对于年龄(P=0.146)和季节(P=0.242)的一组(α多样性)样品中的病毒脱落没有影响。
结论:存在非常不同的鸡RNA病毒,包括鸟类,哺乳动物,真菌,和饮食相关的病毒,强调了理解因果关系所固有的复杂性,动力学,和RNA病毒在所研究的鸡群内的种间传播。因此,鸡,即使没有明显的症状,可以携带可能表现出机会主义的病毒,共生,或致病特征。
BACKGROUND: Virome studies on birds, including chickens are relatively scarce, particularly from the African continent. Despite the continuous evolution of RNA viruses and severe losses recorded in poultry from seasonal viral outbreaks, the information on RNA virome composition is even scantier as a result of their highly unstable nature, genetic diversity, and difficulties associated with characterization. Also, information on factors that may modulate the occurrence of some viruses in birds is limited, particularly for domesticated birds. Viral metagenomics through advancements in sequencing technologies, has enabled the characterization of the entire virome of diverse host species using various samples.
METHODS: The complex RNA viral constituents present in 27 faecal samples of asymptomatic chickens from a South African farm collected at 3-time points from two independent seasons were determined, and the impact of the chicken\'s age and collection season on viral abundance and diversity was further investigated. The study utilized the non-invasive faecal sampling method, mRNA viral targeted enrichment steps, a whole transcriptome amplification strategy, Illumina sequencing, and bioinformatics tools.
RESULTS: The results obtained revealed a total of 48 viral species spanning across 11 orders, 15 families and 21 genera. Viral RNA families such as Coronaviridae, Picornaviridae, Reoviridae, Astroviridae, Caliciviridae, Picorbirnaviridae and Retroviridae were abundant, among which picornaviruses, demonstrated a 100% prevalence across the three age groups (2, 4 and 7 weeks) and two seasons (summer and winter) of the 27 faecal samples investigated. A further probe into the extent of variation between the different chicken groups investigated indicated that viral diversity and abundance were significantly influenced by age (P = 0.01099) and season (P = 0.00099) between chicken groups, while there was no effect on viral shedding within samples in a group (alpha diversity) for age (P = 0.146) and season (P = 0.242).
CONCLUSIONS: The presence of an exceedingly varied chicken RNA virome, encompassing avian, mammalian, fungal, and dietary-associated viruses, underscores the complexities inherent in comprehending the causation, dynamics, and interspecies transmission of RNA viruses within the investigated chicken population. Hence, chickens, even in the absence of discernible symptoms, can harbour viruses that may exhibit opportunistic, commensal, or pathogenic characteristics.