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.

Results

Data quality evaluation

Urban sewage samples and associated metadata (Supp. File 1) were obtained from 62 countries across all continents between January and April 2016 from the influent of wastewater treatment plants prior to treatment or from open sewage systems in low- and middle-income countries. All samples were previously processed for the detection of bacterial antimicrobial resistance genes using DNA metagenomics26. Here we focus solely on viral DNA and RNA metagenomics (methods) and the analysis of the viral data. Sewage samples are highly variable in terms of composition and DNA abundance and therefore potential biases that might impact the final read abundance and diversity of the sewage virome were evaluated.