Setting a baseline for global urban virome surveillance in sewage

• Main Authors: Nieuwenhuijse, David F., Oude Munnink, Bas B., Phan, My V. T., Munk, Patrick, Venkatakrishnan, Shweta, Aarestrup, Frank M., Cotten, Matthew, Koopmans, Marion P. G., Tay, Moon Yue Feng, Zuniga-Montanez, Rogelio, Wuertz, Stefan
• Other Authors: Singapore Centre for Environmental Life Sciences and Engineering
• Format: Article
• Language: English
• Published: 2021
• Subjects: Engineering::Environmental engineering; Metagenomics; Public Health
• Online Access: https://hdl.handle.net/10356/149399
• Institution: Nanyang Technological University

The rapid development of megacities, and their growing connectedness across the world is becoming a distinct driver for emerging disease outbreaks. Early detection of unusual disease emergence and spread should therefore include such cities as part of risk-based surveillance. A catch-all metagenomic sequencing approach of urban sewage could potentially provide an unbiased insight into the dynamics of viral pathogens circulating in a community irrespective of access to care, a potential which already has been proven for the surveillance of poliovirus. Here, we present a detailed characterization of sewage viromes from a snapshot of 81 high density urban areas across the globe, including in-depth assessment of potential biases, as a proof of concept for catch-all viral pathogen surveillance. We show the ability to detect a wide range of viruses and geographical and seasonal differences for specific viral groups. Our findings offer a cross-sectional baseline for further research in viral surveillance from urban sewage samples and place previous studies in a global perspective.