Setting a baseline for global urban virome surveillance in sewage
Authors: Nieuwenhuijse David F. , Oude Munnink Bas B. , Phan My V. T. ,   the Global Sewage Surveillance project consortium, Hendriksen Rene S. , Bego Artan , Rees Catherine , Neilson Elizabeth Heather , Coventry Kris , Collignon Peter , Allerberger Franz , Rahube Teddie O. , Oliveira Guilherme , Ivanov Ivan , Sopheak Thet , Vuthy Yith , Yost Christopher K. , Tabo Djim-adjim , Cuadros-Orellana Sara , Ke Changwen , Zheng Huanying , Baisheng Li , Jiao Xiaoyang , Donado-Godoy Pilar , Coulibaly Kalpy Julien , Hrenovic Jasna , Jergović Matijana , Karpíšková Renáta , Elsborg Bodil , Legesse Mengistu , Eguale Tadesse , Heikinheimo Annamari , Villacis Jose Eduardo , Sanneh Bakary , Malania Lile , Nitsche Andreas , Brinkmann Annika , Saba Courage Kosi Setsoafia , Kocsis Bela , Solymosi Norbert , Thorsteinsdottir Thorunn R. , Hatha Abdulla Mohamed , Alebouyeh Masoud , Morris Dearbhaile , O’Connor Louise , Cormican Martin , Moran-Gilad Jacob , Battisti Antonio , Alba Patricia , Shakenova Zeinegul , Kiiyukia Ciira , Ng’eno Eric , Raka Lul , Bērziņš Aivars , Avsejenko Jeļena , Bartkevics Vadims , Penny Christian , Rajandas Heraa , Parimannan Sivachandran , Haber Malcolm Vella , Pal Pushkar , Schmitt Heike , van Passel Mark , van de Schans Milou G.M. , Zuidema Tina , Jeunen Gert-Jan , Gemmell Neil , Fashae Kayode , Wester Astrid Louise , Holmstad Rune , Hasan Rumina , Shakoor Sadia , Rojas Maria Luz Zamudio , Wasyl Dariusz , Bosevska Golubinka , Kochubovski Mihail , Radu Cojocaru , Gassama† Amy , Radosavljevic Vladimir , Tay Moon Y.F. , Zuniga-Montanez Rogelio , Wuertz Stefan , Gavačová Dagmar , Trkov Marija , Keddy Karen , Esterhuyse Kerneels , Cerdà-Cuéllar Marta , Pathirage Sujatha , Larsson D.G.Joakim , Norrgren Leif , Örn Stefan , Van der Heijden Tanja , Kumburu Happiness Houka , de RodaHusman Ana Maria , Njanpop-Lafourcade Berthe-Marie , Bidjada Pawou , Nikiema-Pessinaba Somtinda Christelle , Levent Belkis , Meschke John Scott , Beck Nicola Koren , Van Dang Chinh , Tran Doan Minh Nguyen , Do Phuc Nguyen , Kwenda Geoffrey , Munk Patrick , Venkatakrishnan Shweta , Aarestrup Frank M. , Cotten Matthew , Koopmans Marion P. G. 
Published: August 2020

AbstractThe 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.