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.; 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.; Koopmans M.P.G. · Scientific Reports (2020) · DOI: 10.1038/s41598-020-69869-0

Resumen

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.