BACKGROUND Current molecular target-dependent methods are used to detect only known viruses. However, metagenomics based on next-generation sequencing (NGS) technique is a target-independent assay that enables simultaneous detection and genomic characterisation of all microorganisms present in a sample. In this study, we aimed to develop a metagenomics approach using NGS to identify and characterise viruses in stool samples from infants and children with Acute Gastroenteritis (AGE) in Kuwait. METHODS We have investigated 84 stool samples from infants and children aged one month to ten years old with signs and symptoms of gastroenteritis who attended Mubarak Al-Kabeer and Al-Amiri hospitals in Kuwait from January to December 2017. A metagenomics approach using NGS to characterise viruses in clinical samples was used. Also, the commercial Real-Time PCR assay was used to detect viruses causing gastroenteritis. RESULTS Metagenomics analysis revealed an average of 280,768 reads in which 5% of the reads were derived from viruses. The analysis of viral sequences verified that single infection of human adenovirus was the leading cause of gastroenteritis among infants and children, which was detected in 23.2% of the patients, followed by a mixed infection of human adenovirus and other viruses, which was detected in 20.9% of patients. Also, the newly discovered viruses known to cause gastroenteritis were detected, such as astrovirus MLB2, primate bocaparvovirus-1, Aichivirus A, cardiovirus, parechovirus A, astrovirus VA4, cosavirus-F, and bufavirus-3. Our results showed 71% agreement (k = 0.445, P = 0.000) between multiplex Real-Time PCR, which is used as a routine diagnostic test and metagenomics approach in the detection of viruses causing gastroenteritis in clinical samples. CONCLUSION Despite the difficulties in sample preparation and analysis process, we showed that metagenomics approach is a powerful and promising tool for the detection and characterisation of different viruses in clinical samples.

中文翻译：

---

使用Metagenomics方法分析科威特婴幼儿急性胃肠炎的粪便样本中的病毒多样性。

背景技术当前的分子靶标依赖性方法仅用于检测已知病毒。但是，基于下一代测序（NGS）技术的宏基因组学是一种独立于靶标的测定法，能够同时检测和检测样品中存在的所有微生物的基因组特征。在这项研究中，我们旨在使用NGS开发一种宏基因组学方法，以鉴定和表征科威特患有急性胃肠炎（AGE）的婴儿和儿童粪便样本中的病毒。方法我们调查了2017年1月至2017年12月在科威特的Mubarak Al-Kabeer和Al-Amiri医院就诊的1个月至10岁的婴儿和肠胃炎的体征和症状的粪便样本。采用NGS进行宏基因组学分析使用临床样品中的病毒。也，商业实时荧光定量PCR技术用于检测引起肠胃炎的病毒。结果Metagenomics分析显示平均有280,768个读段，其中5％的读段来自病毒。病毒序列分析证实，人腺病毒的单次感染是婴幼儿胃肠炎的主要原因，在23.2％的患者中被发现，其次是人腺病毒和其他病毒的混合感染，在20.9％的患者被发现％的患者。此外，还检测到了新发现的已知会引起肠胃炎的病毒，例如星状病毒MLB2，灵长类bocaparvovirus-1，爱知病毒A，心脏病毒，副病毒A，星状病毒VA4，cosavirus-F和bufavirus-3。我们的结果显示，多重实时PCR之间的一致性为71％（k = 0.445，P = 0.000），用作常规诊断测试和宏基因组学方法，用于检测临床样品中引起胃肠炎的病毒。结论尽管样品制备和分析过程中存在困难，但我们证明，宏基因组学方法是检测和表征临床样品中不同病毒的有力且有前途的工具。