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 Zheng; Li 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; Antonio Battisti; Patricia Alba; Zeinegul Shakenova; Ciira Kiiyukia; Eric Ng’eno; Lul Raka; Aivars Bērziņš; Jeļena Avsejenko; Vadims Bartkevics; Christian Penny; Heraa Rajandas; Sivachandran Parimannan; Malcolm Vella Haber; Pushkar Pal; Heike Schmitt; Mark van Passel; Milou G.M. van de Schans; Tina Zuidema; Gert Jan Jeunen; Neil Gemmell; Kayode Fashae; Astrid Louise Wester; Rune Holmstad; Rumina Hasan; Sadia Shakoor; Maria Luz Zamudio Rojas; Dariusz Wasyl; Golubinka Bosevska; Mihail Kochubovski; Cojocaru Radu; Amy Gassama†; Vladimir Radosavljevic; Moon Y.F. Tay; Rogelio Zuniga-Montanez; Stefan Wuertz; Dagmar Gavačová; Marija Trkov; Karen Keddy; Kerneels Esterhuyse; Marta Cerdà-Cuéllar; Sujatha Pathirage; D. G.Joakim Larsson; Leif Norrgren; Stefan Örn; Tanja Van der Heijden; Happiness Houka Kumburu; Ana Maria de RodaHusman; Berthe Marie Njanpop-Lafourcade; Pawou Bidjada; Somtinda Christelle Nikiema-Pessinaba; Belkis Levent; John Scott Meschke; Nicola Koren Beck; Chinh Van Dang; Doan Minh Nguyen Tran; Nguyen Do Phuc; Geoffrey Kwenda; Patrick Munk; Shweta Venkatakrishnan; Frank M. Aarestrup; Matthew Cotten; Marion P.G. Koopmans

doi:10.1038/s41598-020-69869-0

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, Antonio Battisti, Patricia Alba, Zeinegul Shakenova, Ciira Kiiyukia, Eric Ng’eno, Lul Raka, Aivars Bērziņš, Jeļena Avsejenko, Vadims Bartkevics, Christian Penny, Heraa Rajandas, Sivachandran Parimannan, Malcolm Vella Haber, Pushkar Pal, Heike Schmitt, Mark van Passel, Milou G.M. van de Schans, Tina Zuidema, Gert Jan Jeunen, Neil Gemmell, Kayode Fashae, Astrid Louise Wester, Rune Holmstad, Rumina Hasan, Sadia Shakoor, Maria Luz Zamudio Rojas, Dariusz Wasyl, Golubinka Bosevska, Mihail Kochubovski, Cojocaru Radu, Amy Gassama†, Vladimir Radosavljevic, Moon Y.F. Tay, Rogelio Zuniga-Montanez, Stefan Wuertz, Dagmar Gavačová, Marija Trkov, Karen Keddy, Kerneels Esterhuyse, Marta Cerdà-Cuéllar, Sujatha Pathirage, D. G.Joakim Larsson, Leif Norrgren, Stefan Örn, Tanja Van der Heijden, Happiness Houka Kumburu, Ana Maria de RodaHusman, Berthe Marie Njanpop-Lafourcade, Pawou Bidjada, Somtinda Christelle Nikiema-Pessinaba, Belkis Levent, John Scott Meschke, Nicola Koren Beck, Chinh Van Dang, Doan Minh Nguyen Tran, Nguyen Do Phuc, Geoffrey Kwenda, Patrick Munk, Shweta Venkatakrishnan, Frank M. Aarestrup, Matthew Cotten, Marion P.G. Koopmans

IRAS OH Epidemiology Microbial Agents

Research output: Contribution to journal › Article › Academic › peer-review

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 language	English
Article number	13748
Pages (from-to)	1-13
Journal	Scientific Reports
Volume	10
Issue number	1
DOIs	https://doi.org/10.1038/s41598-020-69869-0
Publication status	Published - Aug 2020

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1038/s41598-020-69869-0

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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., ... Koopmans, M. P. G. (2020). Setting a baseline for global urban virome surveillance in sewage. Scientific Reports, 10(1), 1-13. Article 13748. https://doi.org/10.1038/s41598-020-69869-0

@article{6ec3a84a16694891b2bfb7748ff778b4,

title = "Setting a baseline for global urban virome surveillance in sewage",

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.",

author = "Nieuwenhuijse, {David F.} and {Oude Munnink}, {Bas B.} and Phan, {My V.T.} and Hendriksen, {Rene S.} and Artan Bego and Catherine Rees and Neilson, {Elizabeth Heather} and Kris Coventry and Peter Collignon and Franz Allerberger and Rahube, {Teddie O.} and Guilherme Oliveira and Ivan Ivanov and Thet Sopheak and Yith Vuthy and Yost, {Christopher K.} and Tabo, {Djim adjim} and Sara Cuadros-Orellana and Changwen Ke and Huanying Zheng and Li Baisheng and Xiaoyang Jiao and Pilar Donado-Godoy and Coulibaly, {Kalpy Julien} and Jasna Hrenovic and Matijana Jergovi{\'c} and Ren{\'a}ta Karp{\'i}{\v s}kov{\'a} and Bodil Elsborg and Mengistu Legesse and Tadesse Eguale and Annamari Heikinheimo and Villacis, {Jose Eduardo} and Bakary Sanneh and Lile Malania and Andreas Nitsche and Annika Brinkmann and Saba, {Courage Kosi Setsoafia} and Bela Kocsis and Norbert Solymosi and Thorsteinsdottir, {Thorunn R.} and Hatha, {Abdulla Mohamed} and Masoud Alebouyeh and Dearbhaile Morris and Louise O{\textquoteright}Connor and Martin Cormican and Jacob Moran-Gilad and Antonio Battisti and Patricia Alba and Zeinegul Shakenova and Ciira Kiiyukia and Eric Ng{\textquoteright}eno and Lul Raka and Aivars Bērziņ{\v s} and Jeļena Avsejenko and Vadims Bartkevics and Christian Penny and Heraa Rajandas and Sivachandran Parimannan and Haber, {Malcolm Vella} and Pushkar Pal and Heike Schmitt and {van Passel}, Mark and {van de Schans}, {Milou G.M.} and Tina Zuidema and Jeunen, {Gert Jan} and Neil Gemmell and Kayode Fashae and Wester, {Astrid Louise} and Rune Holmstad and Rumina Hasan and Sadia Shakoor and Rojas, {Maria Luz Zamudio} and Dariusz Wasyl and Golubinka Bosevska and Mihail Kochubovski and Cojocaru Radu and Amy Gassama† and Vladimir Radosavljevic and Tay, {Moon Y.F.} and Rogelio Zuniga-Montanez and Stefan Wuertz and Dagmar Gava{\v c}ov{\'a} and Marija Trkov and Karen Keddy and Kerneels Esterhuyse and Marta Cerd{\`a}-Cu{\'e}llar and Sujatha Pathirage and Larsson, {D. G.Joakim} and Leif Norrgren and Stefan {\"O}rn and {Van der Heijden}, Tanja and Kumburu, {Happiness Houka} and {de RodaHusman}, {Ana Maria} and Njanpop-Lafourcade, {Berthe Marie} and Pawou Bidjada and Nikiema-Pessinaba, {Somtinda Christelle} and Belkis Levent and Meschke, {John Scott} and Beck, {Nicola Koren} and {Van Dang}, Chinh and Tran, {Doan Minh Nguyen} and {Do Phuc}, Nguyen and Geoffrey Kwenda and Patrick Munk and Shweta Venkatakrishnan and Aarestrup, {Frank M.} and Matthew Cotten and Koopmans, {Marion P.G.}",

year = "2020",

month = aug,

doi = "10.1038/s41598-020-69869-0",

language = "English",

volume = "10",

pages = "1--13",

journal = "Scientific Reports",

issn = "2045-2322",

publisher = "Nature Publishing Group",

number = "1",

}

Nieuwenhuijse, DF, Oude Munnink, BB, Phan, MVT, Hendriksen, RS, Bego, A, Rees, C, Neilson, EH, Coventry, K, Collignon, P, Allerberger, F, Rahube, TO, Oliveira, G, Ivanov, I, Sopheak, T, Vuthy, Y, Yost, CK, Tabo, DA, Cuadros-Orellana, S, Ke, C, Zheng, H, Baisheng, L, Jiao, X, Donado-Godoy, P, Coulibaly, KJ, Hrenovic, J, Jergović, M, Karpíšková, R, Elsborg, B, Legesse, M, Eguale, T, Heikinheimo, A, Villacis, JE, Sanneh, B, Malania, L, Nitsche, A, Brinkmann, A, Saba, CKS, Kocsis, B, Solymosi, N, Thorsteinsdottir, TR, Hatha, AM, 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, MV, Pal, P, Schmitt, H, van Passel, M, van de Schans, MGM, Zuidema, T, Jeunen, GJ, Gemmell, N, Fashae, K, Wester, AL, Holmstad, R, Hasan, R, Shakoor, S, Rojas, MLZ, Wasyl, D, Bosevska, G, Kochubovski, M, Radu, C, Gassama†, A, Radosavljevic, V, Tay, MYF, Zuniga-Montanez, R, Wuertz, S, Gavačová, D, Trkov, M, Keddy, K, Esterhuyse, K, Cerdà-Cuéllar, M, Pathirage, S, Larsson, DGJ, Norrgren, L, Örn, S, Van der Heijden, T, Kumburu, HH, de RodaHusman, AM, Njanpop-Lafourcade, BM, Bidjada, P, Nikiema-Pessinaba, SC, Levent, B, Meschke, JS, Beck, NK, Van Dang, C, Tran, DMN, Do Phuc, N, Kwenda, G, Munk, P, Venkatakrishnan, S, Aarestrup, FM, Cotten, M & Koopmans, MPG 2020, 'Setting a baseline for global urban virome surveillance in sewage', Scientific Reports, vol. 10, no. 1, 13748, pp. 1-13. https://doi.org/10.1038/s41598-020-69869-0

TY - JOUR

T1 - Setting a baseline for global urban virome surveillance in sewage

AU - Nieuwenhuijse, David F.

AU - Oude Munnink, Bas B.

AU - Phan, My V.T.

AU - Hendriksen, Rene S.

AU - Bego, Artan

AU - Rees, Catherine

AU - Neilson, Elizabeth Heather

AU - Coventry, Kris

AU - Collignon, Peter

AU - Allerberger, Franz

AU - Rahube, Teddie O.

AU - Oliveira, Guilherme

AU - Ivanov, Ivan

AU - Sopheak, Thet

AU - Vuthy, Yith

AU - Yost, Christopher K.

AU - Tabo, Djim adjim

AU - Cuadros-Orellana, Sara

AU - Ke, Changwen

AU - Zheng, Huanying

AU - Baisheng, Li

AU - Jiao, Xiaoyang

AU - Donado-Godoy, Pilar

AU - Coulibaly, Kalpy Julien

AU - Hrenovic, Jasna

AU - Jergović, Matijana

AU - Karpíšková, Renáta

AU - Elsborg, Bodil

AU - Legesse, Mengistu

AU - Eguale, Tadesse

AU - Heikinheimo, Annamari

AU - Villacis, Jose Eduardo

AU - Sanneh, Bakary

AU - Malania, Lile

AU - Nitsche, Andreas

AU - Brinkmann, Annika

AU - Saba, Courage Kosi Setsoafia

AU - Kocsis, Bela

AU - Solymosi, Norbert

AU - Thorsteinsdottir, Thorunn R.

AU - Hatha, Abdulla Mohamed

AU - Alebouyeh, Masoud

AU - Morris, Dearbhaile

AU - O’Connor, Louise

AU - Cormican, Martin

AU - Moran-Gilad, Jacob

AU - Battisti, Antonio

AU - Alba, Patricia

AU - Shakenova, Zeinegul

AU - Kiiyukia, Ciira

AU - Ng’eno, Eric

AU - Raka, Lul

AU - Bērziņš, Aivars

AU - Avsejenko, Jeļena

AU - Bartkevics, Vadims

AU - Penny, Christian

AU - Rajandas, Heraa

AU - Parimannan, Sivachandran

AU - Haber, Malcolm Vella

AU - Pal, Pushkar

AU - Schmitt, Heike

AU - van Passel, Mark

AU - van de Schans, Milou G.M.

AU - Zuidema, Tina

AU - Jeunen, Gert Jan

AU - Gemmell, Neil

AU - Fashae, Kayode

AU - Wester, Astrid Louise

AU - Holmstad, Rune

AU - Hasan, Rumina

AU - Shakoor, Sadia

AU - Rojas, Maria Luz Zamudio

AU - Wasyl, Dariusz

AU - Bosevska, Golubinka

AU - Kochubovski, Mihail

AU - Radu, Cojocaru

AU - Gassama†, Amy

AU - Radosavljevic, Vladimir

AU - Tay, Moon Y.F.

AU - Zuniga-Montanez, Rogelio

AU - Wuertz, Stefan

AU - Gavačová, Dagmar

AU - Trkov, Marija

AU - Keddy, Karen

AU - Esterhuyse, Kerneels

AU - Cerdà-Cuéllar, Marta

AU - Pathirage, Sujatha

AU - Larsson, D. G.Joakim

AU - Norrgren, Leif

AU - Örn, Stefan

AU - Van der Heijden, Tanja

AU - Kumburu, Happiness Houka

AU - de RodaHusman, Ana Maria

AU - Njanpop-Lafourcade, Berthe Marie

AU - Bidjada, Pawou

AU - Nikiema-Pessinaba, Somtinda Christelle

AU - Levent, Belkis

AU - Meschke, John Scott

AU - Beck, Nicola Koren

AU - Van Dang, Chinh

AU - Tran, Doan Minh Nguyen

AU - Do Phuc, Nguyen

AU - Kwenda, Geoffrey

AU - Munk, Patrick

AU - Venkatakrishnan, Shweta

AU - Aarestrup, Frank M.

AU - Cotten, Matthew

AU - Koopmans, Marion P.G.

PY - 2020/8

Y1 - 2020/8

N2 - 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.

AB - 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.

UR - https://www.mendeley.com/catalogue/5fcdc7c6-eee4-3703-a15a-13ae7f234898/

U2 - 10.1038/s41598-020-69869-0

DO - 10.1038/s41598-020-69869-0

M3 - Article

C2 - 32792677

SN - 2045-2322

VL - 10

SP - 1

EP - 13

JO - Scientific Reports

JF - Scientific Reports

IS - 1

M1 - 13748

ER -

Setting a baseline for global urban virome surveillance in sewage

Abstract

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