Setting a baseline for global urban virome surveillance in sewage

David F. Nieuwenhuijse, Bas B. Oude Munnink, My V.T. Phan, Rene S. Hendriksen, Artan Bego, Catherine Rees, Elizabeth Heather 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 ZhengLi 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, Mark van Passel, Milou G.M. van de Schans, Tina Zuidema, Marion P.G. Koopmans*

*Corresponding author for this work

    Research output: Contribution to journalArticleAcademicpeer-review

    15 Citations (Scopus)

    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.

    Original languageEnglish
    Article number13748
    JournalScientific Reports
    Volume10
    Issue number1
    DOIs
    Publication statusPublished - 13 Aug 2020

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    • Correction to: Setting a baseline for global urban virome surveillance in sewage

      Nieuwenhuijse, D. F., Oude Munnink, B. B., Phan, M. V. T., Hendriksen, R. S., Bego, A., Rees, C., Neilson, E. H., Coventry, K., Collignon, P., Allerberger, F., Rahube, T. O., Oliveira, G., Ivanov, I., Sopheak, T., Vuthy, Y., Yost, C. K., Tabo, D. A., Cuadros-Orellana, S., Ke, C., Zheng, H. & 30 others, Baisheng, L., Jiao, X., Donado-Godoy, P., Coulibaly, K. J., Hrenovic, J., Jergović, M., Karpíšková, R., Elsborg, B., Legesse, M., Eguale, T., Heikinheimo, A., Villacis, J. E., Sanneh, B., Malania, L., Nitsche, A., Brinkmann, A., Saba, C. K. S., Kocsis, B., Solymosi, N., Thorsteinsdottir, T. R., Hatha, A. M., Alebouyeh, M., Morris, D., O’Connor, L., Cormican, M., Moran-Gilad, J., van Passel, M., van de Schans, M. G. M., Zuidema, T. & Koopmans, M. P. G., 25 Aug 2021, In: Scientific Reports. 11, 1, 17446.

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