Metagenomics and the development of viral water quality tools

Abstract

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.

Persistence of emerging viral fecal indicators in large-scale freshwater mesocosms

“…Viruses are predicted to be the greatest source of infectious risk due to exposure from sewage-contaminated waters ( Boehm et al., 2015 ; Crank et al., 2019 ). Viral indicators have been proposed to better represent viruses in sewage contaminated water than FIB ( Bibby et al., 2019 ; Hjelmsø et al., 2017 ). Indicator organisms do not necessarily have to be nonpathogenic; they can be any microorganism (pathogenic or nonpathogenic) that is present in sewage.…”

SARS-CoV-2 in environmental perspective: Occurrence, persistence, surveillance, inactivation and challenges

“…WBE ability to detect low levels of viruses especially at early stages of an outbreak or when infection levels are decreasing following intervention is also critical [38] . Virome analysis of wastewater will enable to detect novel viruses before their clinical recognition in a community, allowing for early preventative measures and allocation of resources to potentially affected areas [52] , [233] , [234] , [235] . The major limitations to WBE in establishing quantitative predictions from viral RNA results in over or underestimation of infected cases due to the complexity of wastewater, the dilute nature of biomarker in wastewater and inability to pinpoint specific locations [124] , [150] , [236] .…”

COVID-19 Crisis Creates Opportunity towards Global Monitoring & Surveillance

“…SARS-CoV-2 carriers with the presymptomatic condition or paucisymptomatic manifestation usually remain undetected in health surveillance systems and hence are the silent reservoir via which the disease is spread [172,[212][213][214][215]. Therefore, comprehensive and cost-effective long term surveillance using wastewater-based epidemiology for SARS-CoV-2 will flourish in the near future [216], and prediction models based on estimated viral RNA copy numbers observed in the wastewater will be used to assess the forthcoming disease burden and disease prevalence using simulation studies [140,166,217,218]. The cost involved in a single round of clinical mass screening, depending on the population size of the country, may range from millions to billions of US$, and wastewater-based epidemiology (WBE) is a hugely cost-effective alternative [145,161].…”