Human exposure to pathogenic viruses in environmental waters results in a significant global disease burden. Current microbial water quality monitoring approaches, mainly based on fecal indicator bacteria, insufficiently capture human health impacts posed by pathogenic viruses in water. The emergence of the ‘microbiome era’ and high-throughput metagenome sequencing has led to the discovery of novel human-associated viruses, including both pathogenic and commensal viruses in the human microbiome. The discovery of novel human-associated viruses is often followed by their detection in wastewater, highlighting the great diversity of human-associated viruses potentially present in the water environment. Novel human-associated viruses provide a rich reservoir to develop viral water quality management tools with diverse applications, such as regulating wastewater reuse and monitoring agricultural and recreational waters. Here, we review the pathway from viral discovery to water quality monitoring tool, and highlight select human-associated viruses identified by metagenomics and subsequently detected in the water environment (namely Bocavirus, Cosavirus, CrAssphage, Klassevirus, and Pepper Mild Mottle Virus). We also discuss research needs to enable the application of recently discovered human-associated viruses in water quality monitoring, including investigating the geographic distribution, environmental fate, and viability of potential indicator viruses. Examples suggest that recently discovered human pathogens are likely to be less abundant in sewage, while other human-associated viruses (e.g., bacteriophages or viruses from food) are more abundant but less human-specific. The improved resolution of human-associated viral diversity enabled by metagenomic tools provides a significant opportunity for improved viral water quality management tools.

人类暴露于环境水域中的致病病毒会导致严重的全球疾病负担。当前主要基于粪便指示剂细菌的微生物水质监测方法无法充分捕获水中病原性病毒对人类健康的影响。“微生物组时代”和高通量元基因组测序的出现导致发现了新型的人类相关病毒，包括人类微生物组中的致病病毒和普通病毒。在发现新型人类相关病毒后，通常会在废水中对其进行检测，从而突显出水环境中潜在存在的人类相关病毒的多样性。新型人类相关病毒为开发具有多种应用程序的病毒水质管理工具提供了丰富的资源，例如规范废水回用和监测农业和娱乐用水。在这里，我们回顾了从病毒发现到水质监测工具的途径，并重点介绍了通过宏基因组学鉴定并随后在水环境中检测到的精选人类相关病毒（即Bocavirus，Cosavirus，CrAssphage，Klassevirus和Pepper Mild Mottle Virus）。我们还讨论了将新发现的人类相关病毒应用于水质监测的研究需求，包括调查潜在指示病毒的地理分布，环境命运和生存能力。实例表明，最近发现的人类病原体在污水中的含量可能较低，而其他与人类相关的病毒（例如，噬菌体或食物中的病毒）则含量较高，但对人类的特异性较低。