Viromic analysis of wastewater input to a river catchment reveals a diverse assemblage of RNA viruses
Viromic analysis of wastewater input to a river catchment reveals a diverse assemblage of RNA viruses
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对流域废水的病毒学分析揭示了 RNA 病毒的多样化组合
DOI：
10.1101/248203
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发表时间：
2018
期刊：
影响因子：
--
通讯作者：
Adriaenssens E
中科院分区：
文献类型：
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作者：
Adriaenssens E
环境中病毒的检测在很大程度上依赖于基于PCR的方法，这些方法需要参考序列进行引物设计。虽然这种策略可以准确地检测已知的病毒，但它不会发现新的基因型或新出现的入侵病毒物种。在这项研究中，我们调查了病毒组学的使用，即，对生物圈的病毒组分进行高通量测序，以检测联合王国威尔士康威河集水区的人类/动物病原性RNA病毒。使用过滤和核酸酶处理的组合，我们从废水和河口河水和沉积物中提取病毒组分，然后在Illumina HiSeq平台上进行高通量RNA测序（RNA-Seq）分析，以发现RNA病毒基因组。我们发现了更高的丰富度的RNA病毒在废水样品比河水和沉积物中，我们组装了一个完整的诺如病毒基因型GI.2基因组从废水流出物，这是不能同时检测到的常规逆转录-定量PCR（qRT-PCR）。废水中同时存在多种轮状病毒特征表明该地区存在人畜共患感染的可能性，并表明养猪场的径流可能是这些病毒的来源。我们的研究结果表明，病毒组学可以是一个重要的工具，在发现环境中的致病性病毒，并可用于通知和优化基于参考的检测方法提供适当和严格的控制included.IMPORTANCEEnteric病毒引起胃肠道疾病，通常是通过粪-口途径传播。当废水排入河流系统时，这些病毒会污染环境。我们的研究结果表明，我们可以使用病毒组学来发现环境中存在的潜在致病病毒的范围，并确定流行的基因型。最终目标是追踪这些致病病毒从起源到对人类健康构成威胁的命运，为基于参考的检测方法和水质管理提供信息。
Detection of viruses in the environment is heavily dependent on PCR-based approaches that require reference sequences for primer design. While this strategy can accurately detect known viruses, it will not find novel genotypes or emerging and invasive viral species. In this study, we investigated the use of viromics, i.e., high-throughput sequencing of the biosphere’s viral fraction, to detect human-/animal-pathogenic RNA viruses in the Conwy river catchment area in Wales, United Kingdom. Using a combination of filtering and nuclease treatment, we extracted the viral fraction from wastewater and estuarine river water and sediment, followed by high-throughput RNA sequencing (RNA-Seq) analysis on the Illumina HiSeq platform, for the discovery of RNA virus genomes. We found a higher richness of RNA viruses in wastewater samples than in river water and sediment, and we assembled a complete norovirus genotype GI.2 genome from wastewater effluent, which was not contemporaneously detected by conventional reverse transcription-quantitative PCR (qRT-PCR). The simultaneous presence of diverse rotavirus signatures in wastewater indicated the potential for zoonotic infections in the area and suggested runoff from pig farms as a possible origin of these viruses. Our results show that viromics can be an important tool in the discovery of pathogenic viruses in the environment and can be used to inform and optimize reference-based detection methods provided appropriate and rigorous controls are included.IMPORTANCEEnteric viruses cause gastrointestinal illness and are commonly transmitted through the fecal-oral route. When wastewater is released into river systems, these viruses can contaminate the environment. Our results show that we can use viromics to find the range of potentially pathogenic viruses that are present in the environment and identify prevalent genotypes. The ultimate goal is to trace the fate of these pathogenic viruses from origin to the point where they are a threat to human health, informing reference-based detection methods and water quality management.