Since the era of waterborne jaundice and poliovirus, diseases spread by viruses were present prior to our understanding of these unique biological entities. Pathogenic viruses remain of great concern because they are more environmentally stable as compared to bacteria, display resistance to various conventional methods used for controlling bacterial pathogens and cause high probability of infection at low doses. The actual burden of waterborne infections caused by pathogenic viruses is likely underestimated because they are not routinely monitored in clinical and environmental samples. There is currently no established method to fully describe the broad diversity of human viral pathogens in environmental samples despite the increasing importance of environmental viral infections in global public health. The advent of molecular tools and high throughput sequencing technologies coupled with metagenomics offers an opportunity to identify human viral pathogens in various environmental samples without a priori knowledge of what viruses may be present. Moreover, environmental surveillance for the presence of pathogenic viruses is important for development of rational disease control strategies. The advances in high throughput next-generation sequencing (NGS) have greatly enhanced our understanding of the water microbiome. Using these techniques emerging human viruses including human picobirnavirus, novel astrovirus MLB strains, cosavirus, cardiovirus, bocavirus, Aichi virus, parechovirus and salivirus, were detected in sewage. Full-scale evaluation of wastewater treatment designs to handle wet weather-sewage flows were evaluated to examine removal of enteric viruses (cultivatable and by qPCR) and male specific phage. Recommendations for controlling viruses by wastewater treatment and improved monitoring will be discussed.

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