Setting a baseline for global urban virome surveillance in sewage

• Published in: Scientific reports Vol. 10; no. 1; p. 13748
• 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.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 13.08.2020; Nature Publishing Group
• Subjects: 631/326/596/2142; 692/700/478; Biological Sciences; Biologiska vetenskaper; Cross-Sectional Studies; Disease Outbreaks; Environmental Monitoring - methods; Folkhälsovetenskap, global hälsa, socialmedicin och epidemiologi; Food Contamination; Humanities and Social Sciences; Humans; Industrial Biotechnology; Industriell bioteknik; Medical Biotechnology; Medicinsk bioteknologi; Megacities; Metagenome - genetics; Metagenomics; Metagenomics - methods; multidisciplinary; Pathogens; Pilot Projects; Public Health, Global Health, Social Medicine and Epidemiology; Science; Science (multidisciplinary); Sewage; Sewage - virology; Urban areas; Vegetables - virology; Virome - genetics; Viruses - classification; Viruses - genetics; Viruses - isolation & purification
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-020-69869-0

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.