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Setting a baseline for global urban virome surveillance in sewage
research-article
Author(s):
David F. Nieuwenhuijse
1 ,
Bas B. Oude Munnink
1 ,
My V. T. Phan
1 ,
the Global Sewage Surveillance project consortium,
Patrick Munk
2 ,
Shweta Venkatakrishnan
1 ,
Frank M. Aarestrup
2 ,
Matthew Cotten
1 ,
Marion P. G. Koopmans
1
,
Publication date (Electronic):
13 August 2020
Journal:
Scientific Reports
Publisher:
Nature Publishing Group UK
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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.
Related collections
Most cited references37
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CD-HIT: accelerated for clustering the next-generation sequencing data
Limin Fu, Beifang Niu, Zhengwei Zhu … (2012)
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Redefining the invertebrate RNA virosphere
Mang Shi, Xian-Dan Lin, Jun-Hua Tian … (2017)
Current knowledge of RNA virus biodiversity is both biased and fragmentary, reflecting a focus on culturable or disease-causing agents. Here we profile the transcriptomes of over 220 invertebrate species sampled across nine animal phyla and report the discovery of 1,445 RNA viruses, including some that are sufficiently divergent to comprise new families. The identified viruses fill major gaps in the RNA virus phylogeny and reveal an evolutionary history that is characterized by both host switching and co-divergence. The invertebrate virome also reveals remarkable genomic flexibility that includes frequent recombination, lateral gene transfer among viruses and hosts, gene gain and loss, and complex genomic rearrangements. Together, these data present a view of the RNA virosphere that is more phylogenetically and genomically diverse than that depicted in current classification schemes and provide a more solid foundation for studies in virus ecology and evolution.
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Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets
Robert Schmieder, Robert Edwards (2011)
High-throughput sequencing technologies have strongly impacted microbiology, providing a rapid and cost-effective way of generating draft genomes and exploring microbial diversity. However, sequences obtained from impure nucleic acid preparations may contain DNA from sources other than the sample. Those sequence contaminations are a serious concern to the quality of the data used for downstream analysis, causing misassembly of sequence contigs and erroneous conclusions. Therefore, the removal of sequence contaminants is a necessary and required step for all sequencing projects. We developed DeconSeq, a robust framework for the rapid, automated identification and removal of sequence contamination in longer-read datasets ( 150 bp mean read length). DeconSeq is publicly available as standalone and web-based versions. The results can be exported for subsequent analysis, and the databases used for the web-based version are automatically updated on a regular basis. DeconSeq categorizes possible contamination sequences, eliminates redundant hits with higher similarity to non-contaminant genomes, and provides graphical visualizations of the alignment results and classifications. Using DeconSeq, we conducted an analysis of possible human DNA contamination in 202 previously published microbial and viral metagenomes and found possible contamination in 145 (72%) metagenomes with as high as 64% contaminating sequences. This new framework allows scientists to automatically detect and efficiently remove unwanted sequence contamination from their datasets while eliminating critical limitations of current methods. DeconSeq's web interface is simple and user-friendly. The standalone version allows offline analysis and integration into existing data processing pipelines. DeconSeq's results reveal whether the sequencing experiment has succeeded, whether the correct sample was sequenced, and whether the sample contains any sequence contamination from DNA preparation or host. In addition, the analysis of 202 metagenomes demonstrated significant contamination of the non-human associated metagenomes, suggesting that this method is appropriate for screening all metagenomes. DeconSeq is available at http://deconseq.sourceforge.net/.
Author and article information
Contributors
Marion P. G. Koopmans: m.koopmans@erasmusmc.nl
Journal
Journal ID (nlm-ta): Sci Rep
Journal ID (iso-abbrev): Sci Rep
Title:
Scientific Reports
Publisher:
Nature Publishing Group UK
(London
)
ISSN
(Electronic):
2045-2322
Publication date
(Electronic):
13
August
2020
Publication date PMC-release: 13
August
2020
Publication date Collection: 2020
Volume: 10
Electronic Location Identifier: 13748
Affiliations
[1
]GRID grid.5645.2, ISNI 000000040459992X, Viroscience Department, , Erasmus Medical Center, ; Rotterdam, The Netherlands
[2
]GRID grid.5170.3, ISNI 0000 0001 2181 8870, National Food Institute, , Technical University of Denmark, ; Lyngby, Denmark
[4
]GRID grid.468069.5, ISNI 0000 0004 0407 4680, Melbourne Water Corporation, ; Docklands, Australia
[8
]GRID grid.414107.7, ISNI 0000 0001 2224 6253, Austrian Agency for Health and Food Safety (AGES), ; Vienna, Austria
[9
]GRID grid.448573.9, ISNI 0000 0004 1785 2090, Botswana International University of Science and Technology, ; Palapye, Botswana
[11
]GRID grid.419273.a, ISNI 0000 0004 0469 0184, National Center of Infectious and Parasitic Diseases, ; Sofia, Bulgaria
[15
]GRID grid.411964.f, ISNI 0000 0001 2224 0804, Centro de Biotecnología de los Recursos Naturales, , Universidad Católica del Maule, ; Talca, Chile
[16
]GRID grid.198530.6, ISNI 0000 0000 8803 2373, Guangdong Provincial Center for Disease Control and Prevention, ; Guangzhou, China
[17
]GRID grid.411679.c, ISNI 0000 0004 0605 3373, Shantou University Medical College, ; Shantou, China
[18
]GRID grid.466621.1, ISNI 0000 0001 1703 2808, Corporacion Colombiana de Investigacion Agropecuaria (AGROSAVIA), ; Mosquera, Colombia
[19
]GRID grid.418523.9, ISNI 0000 0004 0475 3667, Institut Pasteur de Côte d’Ivoire, ; Abidjan, Côte d’Ivoire
[20
]GRID grid.4808.4, ISNI 0000 0001 0657 4636, Faculty of Science, , University of Zagreb, ; Zagreb, Croatia
[22
]GRID grid.426567.4, ISNI 0000 0001 2285 286X, Veterinary Research Institute, ; Brno, Czech Republic
[26
]GRID grid.492557.8, Instituto Nacional de Investigación en Salud Pública-INSPI (CRNRAM), ; Quito, Galápagos, Ecuador
[27
]GRID grid.463484.9, National Public Health Laboratories, Ministry of Health and Social Welfare, , Kotu Layout, ; Kotu, Gambia
[28
]GRID grid.429654.8, ISNI 0000 0004 5345 9480, National Center for Disease Control and Public Health, ; Tbilisi, Georgia
[30
]GRID grid.442305.4, ISNI 0000 0004 0441 5393, University for Development Studies, ; Tamale, Ghana
[31
]GRID grid.11804.3c, ISNI 0000 0001 0942 9821, Semmelweis University, Institute of Medical Microbiology, ; Budapest, Hungary
[32
]GRID grid.483037.b, ISNI 0000 0001 2226 5083, University of Veterinary Medicine, ; Budapest, Hungary
[33
]GRID grid.14013.37, ISNI 0000 0004 0640 0021, Institute for Experimental Pathology, , University of Iceland, ; Keldur, Reykjavík, Iceland
[34
]GRID grid.411771.5, ISNI 0000 0001 2189 9308, Cochin University of Science and Technology, ; Cochin, India
[35
]GRID grid.411600.2, Pediatric Infections Research Center, Research Institute for Children’s Health, , Shahid Beheshti University of Medical Sciences, ; Tehran, Iran
[36
]GRID grid.6142.1, ISNI 0000 0004 0488 0789, National University of Ireland Galway, ; Galway, Ireland
[37
]GRID grid.7489.2, ISNI 0000 0004 1937 0511, School of Public Health, , Ben Gurion University of the Negev and Ministry of Health, ; Beer-Sheva, Israel
[41
]GRID grid.33058.3d, ISNI 0000 0001 0155 5938, Kenya Medical Research Institute, ; Nairobi, Kenya
[42
]GRID grid.449627.a, ISNI 0000 0000 9804 9646, University of Prishtina “Hasan Prishtina” & National Institute of Public Health of
Kosovo, ; Pristina, Kosovo
[43
]GRID grid.493428.0, ISNI 0000 0004 0452 6958, Institute of Food Safety, , Animal Health and Environment “BIOR”, ; Riga, Latvia
[46
]GRID grid.444449.d, ISNI 0000 0004 0627 9137, Centre of Excellence for Omics-Driven Computational Biodiscovery, Faculty of Applied
Sciences, , AIMST University, ; Kedah, Malaysia
[49
]GRID grid.31147.30, ISNI 0000 0001 2208 0118, National Institute for Public, Health and the Environment (RIVM), ; Bilthoven, Netherlands
[53
]GRID grid.418193.6, ISNI 0000 0001 1541 4204, Norwegian Institute of Public Health, ; Oslo, Norway
[58
]GRID grid.493421.9, Institute of Public Health of the Republic of Macedonia, ; Skopje, Republic of Macedonia
[59
]GRID grid.28224.3e, ISNI 0000 0004 0401 2738, State Medical and Pharmaceutical University, ; Chişinău, Republic of Moldova
[62
]GRID grid.59025.3b, ISNI 0000 0001 2224 0361, Nanyang Technological University Food Technology Centre (NAFTEC), Nanyang Technological
University (NTU), ; Singapore, Singapore
[63
]GRID grid.59025.3b, ISNI 0000 0001 2224 0361, Nanyang Technological University, Singapore Centre for Environmental Life Sciences
Engineering (SCELSE), ; Singapore, Singapore
[64
]GRID grid.437898.9, ISNI 0000 0004 0441 0146, Public Health Authority of the Slovak Republic, ; Bratislava, Slovakia
[66
]GRID grid.11951.3d, ISNI 0000 0004 1937 1135, University of the Witwatersrand, ; Johannesburg, South Africa
[68
]GRID grid.8581.4, ISNI 0000 0001 1943 6646, IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), ; Bellaterra, Spain
[70
]GRID grid.8761.8, ISNI 0000 0000 9919 9582, The Sahlgrenska Academy at the University of Gothenburg, ; Gothenburg, Sweden
[71
]GRID grid.6341.0, ISNI 0000 0000 8578 2742, Swedish University of Agricultural Sciences, ; Uppsala, Sweden
[73
]GRID grid.412898.e, ISNI 0000 0004 0648 0439, Kilimanjaro Clinical Research Institute, ; Moshi, Tanzania
Article
Publisher ID: 69869DOI: 10.1038/s41598-020-69869-0
PMC ID: 7426863
PubMed ID: 32792677
SO-VID: 4a081f2a-e342-47fa-9d4c-e679d7efc0b1
Copyright © © The Author(s) 2020
License:
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
History
Date
received
: 28
January
2020
Date
accepted
: 29
June
2020
Funding
Funded by: FundRef http://dx.doi.org/10.13039/100010661, Horizon 2020 Framework Programme;
Award ID: 643476
Award ID: 643476
Award ID: 643476
Award ID: 643476
Award ID: 643476
Award ID: 643476
Award ID: 643476
Award ID: 643476
Award ID: 643476
Award Recipient
:
David F. Nieuwenhuijse
Bas B. Oude Munnink
My V. T. Phan
Patrick Munk
Shweta Venkatakrishnan
Frank M. Aarestrup
Matthew Cotten
Marion P. G. Koopmans
Funded by: FundRef http://dx.doi.org/10.13039/501100009708, Novo Nordisk Fonden;
Award ID: NNF16OC0021856: Global Surveillance of Antimicrobial Resistance
Award ID: NNF16OC0021856: Global Surveillance of Antimicrobial Resistance
Award ID: NNF16OC0021856: Global Surveillance of Antimicrobial Resistance
Award Recipient
:
Shweta Venkatakrishnan
Matthew Cotten
Marion P. G. Koopmans
Funded by: FundRef http://dx.doi.org/10.13039/100004423, World Health Organization;
Categories
Subject:
Article
Custom metadata
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ScienceOpen disciplines: Uncategorized