Setting a baseline for global urban virome surveillance in sewage

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  • David F. Nieuwenhuijse
  • Bas B. Oude Munnink
  • My V.T. Phan
  • Rene S. Hendriksen
  • Artan Bego
  • Catherine Rees
  • Neilson, Elizabeth Heather Jakobsen
  • Kris Coventry
  • Peter Collignon
  • Franz Allerberger
  • Teddie O. Rahube
  • Guilherme Oliveira
  • Ivan Ivanov
  • Thet Sopheak
  • Yith Vuthy
  • Christopher K. Yost
  • Djim adjim Tabo
  • Sara Cuadros-Orellana
  • Changwen Ke
  • Huanying Zheng
  • Li Baisheng
  • Xiaoyang Jiao
  • Pilar Donado-Godoy
  • Kalpy Julien Coulibaly
  • Jasna Hrenovic
  • Matijana Jergović
  • Renáta Karpíšková
  • Bodil Elsborg
  • Mengistu Legesse
  • Tadesse Eguale
  • Annamari Heikinheimo
  • Jose Eduardo Villacis
  • Bakary Sanneh
  • Lile Malania
  • Andreas Nitsche
  • Annika Brinkmann
  • Courage Kosi Setsoafia Saba
  • Bela Kocsis
  • Norbert Solymosi
  • Thorunn R. Thorsteinsdottir
  • Abdulla Mohamed Hatha
  • Masoud Alebouyeh
  • Dearbhaile Morris
  • Louise O’Connor
  • Martin Cormican
  • Jacob Moran-Gilad
  • Antonio Battisti
  • Patricia Alba
  • Zeinegul Shakenova
  • Ciira Kiiyukia
  • the Global Sewage Surveillance project consortium

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.

TidsskriftScientific Reports
StatusUdgivet - 2020

Bibliografisk note

Funding Information:
This study has received funding from the European Union’s Horizon 2020 research and innovation program under Grant agreement no. 643476 (COMPARE), the World Health Organization, and The Novo Nordisk Foundation (NNF16OC0021856: Global Surveillance of Antimicrobial Resistance). We would like to thank Miranda de Graaf for the technical assistance at Erasmus MC.

Publisher Copyright:
© 2020, The Author(s).

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