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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DOI：
10.1128/msystems.00025-18
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发表时间：
2018-05
期刊：
影响因子：
6.4
通讯作者：
McCarthy AJ
中科院分区：
文献类型：
--
作者：
Adriaenssens EM;Farkas K;Harrison C;Jones DL;Allison HE;McCarthy AJ
肠道病毒会引起胃肠道疾病，通常通过粪便-口腔途径传播。当废水排放到河流系统中时，这些病毒会污染环境。我们的结果表明，我们可以使用病毒剂来发现环境中存在的潜在致病病毒的范围，并确定流行的基因类型。最终目标是追踪这些致病病毒的命运，从起源到它们对人类健康构成威胁的程度，为基于参考的检测方法和水质管理提供信息。环境中病毒的检测在很大程度上依赖于基于聚合酶链式反应的方法，这种方法需要参考序列来设计引物。虽然这一策略可以准确地检测已知的病毒，但它不会发现新的基因类型或新出现的和入侵的病毒物种。在这项研究中，我们调查了病毒物的使用，即生物圈病毒部分的高通量测序，以检测英国威尔士康威河集水区的人/动物致病RNA病毒。采用过滤和核酸酶处理相结合的方法，从废水、河口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。我们在废水中发现了比河水和沉积物中更丰富的RNA病毒，并从废水中构建了一个完整的诺如病毒GI.2基因基因组，这是常规的逆转录-定量聚合酶链式反应(qRT-PCR)不能同时检测到的。废水中同时存在不同的轮状病毒特征，表明该地区可能存在人畜共患感染，并表明养猪场的径流可能是这些病毒的来源。我们的结果表明，病毒物可以成为发现环境中致病病毒的重要工具，并可用于通知和优化基于参考的检测方法，只要包括适当和严格的控制。重要：肠道病毒会引起胃肠道疾病，通常通过粪便-口腔途径传播。当废水排放到河流系统中时，这些病毒会污染环境。我们的结果表明，我们可以使用病毒剂来发现环境中存在的潜在致病病毒的范围，并确定流行的基因类型。最终目标是追踪这些致病病毒的命运，从起源到它们对人类健康构成威胁的程度，为基于参考的检测方法和水质管理提供信息。
Enteric 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. 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. IMPORTANCE Enteric 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.