Virology Unit, Department of Microbiology, Faculty of Medicine, Kuwait University, P.O.Box 24923, 13110, Safat, Kuwait.
Virol J. 2020 Jan 30;17(1):10. doi: 10.1186/s12985-020-1287-5.
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.
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.
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.
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.
目前基于下一代测序（NGS）技术的宏基因组学方法是一种非靶向方法，可同时检测和分析样本中存在的所有微生物，并对其进行基因组特征分析。本研究旨在开发一种基于 NGS 的宏基因组学方法，以鉴定和分析科威特急性肠胃炎（AGE）患儿粪便样本中的病毒。
我们研究了 2017 年 1 月至 12 月期间，科威特 Mubarak Al-Kabeer 和 Al-Amiri 医院因肠胃炎就诊的 1 个月至 10 岁婴儿和儿童的 84 份粪便样本。采用 NGS 对临床样本中的病毒进行宏基因组学分析，同时采用商用实时 PCR 检测法检测引起肠胃炎的病毒。
宏基因组学分析显示平均有 280768 条reads，其中 5%的 reads 来自病毒。病毒序列分析证实，单纯性人类腺病毒感染是导致婴幼儿肠胃炎的主要原因，在 23.2%的患者中检测到，其次是人类腺病毒与其他病毒的混合感染，在 20.9%的患者中检测到。此外，还检测到了一些新发现的已知引起肠胃炎的病毒，如星状病毒 MLB2、灵长类细小病毒 1、Aichivirus A、小RNA 病毒、肠道病毒、细小病毒 A、星状病毒 VA4、柯萨奇病毒-F 和布法罗病毒-3。我们的研究结果表明，多重实时 PCR 检测法（作为常规诊断检测方法）与宏基因组学方法在检测临床样本中引起肠胃炎的病毒方面具有 71%的一致性（k=0.445，P=0.000）。
尽管样本制备和分析过程存在困难，但我们表明宏基因组学方法是一种强大且有前途的工具，可用于检测和分析临床样本中的不同病毒。
