Setting a baseline for global urban virome surveillance in sewage

Nieuwenhuijse, D. F. et al. (2020) Setting a baseline for global urban virome surveillance in sewage. Scientific Reports, 10, 13748. (doi: 10.1038/s41598-020-69869-0) (PMID:32792677) (PMCID:PMC7426863)

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.

• Item Type: Articles
• Additional 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). My V. T. Phan was supported by a Marie Sklodowska-Curie Individual Fellowship, funded by the EU H2020 research and innovation programme (Grant Agreement No. 799417). We would like to thank Miranda de Graaf for the technical assistance at Erasmus MC.
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Cotten, Professor Matthew
• Authors: 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., 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., Battisti, A., Alba, P., Shakenova, Z., Kiiyukia, C., Ng’eno, E., Raka, L., Bērziņš, A., Avsejenko, J., Bartkevics, V., Penny, C., Rajandas, H., Parimannan, S., Haber, M. V., Pal, P., Schmitt, H., van Passel, M., van de Schans, M. G.M., Zuidema, T., Jeunen, G.-J., Gemmell, N., Fashae, K., Wester, A. L., Holmstad, R., Hasan, R., Shakoor, S., Rojas, M. L. Z., Wasyl, D., Bosevska, G., Kochubovski, M., Radu, C., Gassama†, A., Radosavljevic, V., Tay, M. Y.F., Zuniga-Montanez, R., Wuertz, S., Gavačová, D., Trkov, M., Keddy, K., Esterhuyse, K., Cerdà-Cuéllar, M., Pathirage, S., Larsson, D.G.J., Norrgren, L., Örn, S., Van der Heijden, T., Kumburu, H. H., de RodaHusman, A. M., Njanpop-Lafourcade, B.-M., Bidjada, P., Nikiema-Pessinaba, S. C., Levent, B., Meschke, J. S., Beck, N. K., Van Dang, C., Tran, D. M. N., Do Phuc, N., Kwenda, G., Munk, P., Venkatakrishnan, S., Aarestrup, F. M., Cotten, M., and Koopmans, M. P. G.
• College/School: College of Medical Veterinary and Life Sciences > School of Infection & Immunity; College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research
• Journal Name: Scientific Reports
• Publisher: Nature Research
• ISSN: 2045-2322
• ISSN (Online): 2045-2322
• Copyright Holders: Copyright © 2020 The Authors
• First Published: First published in Scientific Reports 10: 13748
• Publisher Policy: Reproduced under a Creative Commons License

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