Setting a baseline for global urban virome surveillance in sewage
David F. Nieuwenhuijse, Bas B. Oude Munnink, My V. T. Phan, René S. Hendriksen, Artan Bego, Catherine A. Rees, Elizabeth Heather Jakobsen Neilson, 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 Hrenović, Matijana Jergović, Renáta Karpíšková, Bodil Elsborg, Mengistu Legesse, Tadesse Eguale, Annamari Heikinheimo, José E. Villacís, Bakary Sanneh, Lile Malania, Andreas Nitsche, Annika Brinkmann, Courage Kosi Setsoafia Saba, Béla Kocsis, Norbert Solymosi, Thorunn R. Thorsteinsdottir, A. A. Mohamed Hatha, Masoud Alebouyeh, Dearbháile Morris, Louise O’Connor, Martin Cormican, Jacob Moran‐Gilad, Antonio Battisti, Patricia Alba, Zeinegul Shakenova, Ciira Kiiyukia, Eric Ng’eno, Lul Raka, Aivars Bērziņš, Jeļena Avsejenko, Vadims Bartkevičs, Christian Penny, Heraa Rajandas, Sivachandran Parimannan, Malcolm Vella Haber, Pushkar Pal, Heike Schmitt, Mark van Passel, Milou G.M. van de Schans, T. Zuidema, Gert‐Jan Jeunen, Neil J. Gemmell, Kayode Fashae, Astrid Louise Wester, Rune Holmstad, Rumina Hasan, Sadia Shakoor, Maria Luz Zamudio Rojas, Dariusz Wasyl, Golubinka Boševska, Mihail Kochubovski, Radu Cojocaru, Amy Gassama, Vladimir Radosavljević, Moon Y. F. Tay, Rogelio Zuniga-Montanez, Stefan Wuertz, Dagmar Gavačová, Marija Trkov, Karen H. Keddy, Kerneels Esterhuyse, Marta Cerdà‐Cuéllar, Sujatha Pathirage, D. G. Joakim Larsson, Leif Norrgren, Stefan Örn, Tanja Van der Heijden, Happiness Kumburu, Ana Maria de Roda-Husman, Berthe‐Marie Njanpop‐Lafourcade, Pawou Bidjada, Somtinda Christelle Nikiema-Pessinaba, Belkıs Levent, John Scott Meschke, Nicola K. Beck, Chinh Van Dang
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.