Setting a baseline for global urban virome surveillance in sewage


D.F. Nieuwenhuijse, B.B. Oude Munnink, M.V.T. Phan, R.S. Hendriksen, A. Bego, C. Rees, E.H. Neilson, K. Coventry, P. Collignon, F. Allerberger, T.O. Rahube, G. Oliveira, I. Ivanov, T. Sopheak, Y. Vuthy, C.K. Yost, D.-A. Tabo, S. Cuadros-Orellana, C. Ke, H. Zheng, L. Baisheng, X. Jiao, P. Donado-Godoy, K.J. Coulibaly, J. Hrenovic, M. Jergović, R. Karpíšková, B. Elsborg, M. Legesse, T. Eguale, A. Heikinheimo, J.E. Villacis, B. Sanneh, L. Malania, A. Nitsche, A. Brinkmann, C.K.S. Saba,  B. Kocsis, N. Solymosi, T.R. Thorsteinsdottir, A.M. Hatha, M. Alebouyeh, D. Morris, L. O’Connor, M. Cormican, J. Moran-Gilad, A. Battisti, P. Alba, Z. Shakenova, C. Kiiyukia, E. Ng’eno, L. Raka, A. Bērziņš, J. Avsejenko, V. Bartkevics, C. Penny, H. Rajandas, S. Parimannan, M.V. Haber, P. Pal, H. Schmitt, M. van Passel, M.G.M. van de Schans, T. Zuidema, G.-J. Jeunen, N. Gemmell, K. Fashae, A.L. Wester, R. Holmstad, R. Hasan, S. Shakoor, M.L.Z. Rojas, D. Wasyl, G. Bosevska, M. Kochubovski, C. Radu, A. Gassama, V. Radosavljevic, M.Y.F. Tay, R. Zuniga-Montanez, S. Wuertz, D. Gavačová, M. Trkov, K. Keddy, K. Esterhuyse, M. Cerdà-Cuéllar, S. Pathirage, D.G.J. Larsson, L. Norrgren, S. Örn, T. Van der Heijden, H.H. Kumburu, A.M. de RodaHusman, B.-M. Njanpop-Lafourcade, P. Bidjada, S.C. Nikiema-Pessinaba, B. Levent, J.S. Meschke, N.K. Beck, C. Van Dang, D.M.N. Tran, N. Do Phuc, G. Kwenda, P. Munk, S. Venkatakrishnan, F.M. Aarestrup, M. Cotten, and M.P.G. Koopmans


Scientific Reports, vol. 10, no. 1, art. no. 13748, 2020


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.



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