Setting a baseline for global urban virome surveillance in sewage

Sci Rep. 2020 Aug 13;10(1):13748. doi: 10.1038/s41598-020-69869-0.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cross-Sectional Studies
  • Disease Outbreaks
  • Environmental Monitoring / methods*
  • Food Contamination
  • Humans
  • Metagenome / genetics
  • Metagenomics / methods
  • Pilot Projects
  • Sewage / virology*
  • Vegetables / virology
  • Virome / genetics*
  • Viruses / classification*
  • Viruses / genetics
  • Viruses / isolation & purification*

Substances

  • Sewage