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.
Highlights
The rapid development of megacities, and their growing connectedness across the world is becoming a distinct driver for emerging disease outbreaks
Detection or ruling out of high impact infections as causes of disease is a hallmark of preparedness, but research in response to recent outbreaks of Ebola, Zika and yellow fever has shown that these pathogens circulated for extended periods of time before being recognized, leading to costly delays in public health r esponse[2,3,4,5]
The changing dynamics of infectious diseases related to global change, require rethinking of this model for public health preparedness, as incidence-based surveillance provides a fragmented and limited scope of which pathogens are circulating in the general population, in low resource settings where access to healthcare and laboratory diagnostics is r estricted[6,7]
Summary
The rapid development of megacities, and their growing connectedness across the world is becoming a distinct driver for emerging disease outbreaks. Small-scale studies have already shown the potential for using metagenomic sequencing of sewage extracts for the detection of a range of virus families[18,19,20] (Table 1 in Appendix) While these studies have largely focused on viruses with a replication phase in the gastro-intestinal tract, the fecal and/or urinary shedding of, for instance, measles virus, yellow fever virus, Zika virus, West Nile virus, Ebola virus, SARS coronavirus, and MERS coronavirus suggests the potential utility of sewage testing to capture circulation of these pathogens as w ell[21,22,23,24,25]. We provide a critical appraisal of technical and analytical biases and discuss the potential utility for human and animal disease monitoring and surveillance, as well as the additional steps needed to go towards routine implementation
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