High diversity of picornaviruses in rats from different continents revealed by deep sequencing

Thomas Arn Hansen; Sarah Mollerup; Nam phuong Nguyen; Nicole E. White; Megan Coghlan; David E. Alquezar-Planas; Tejal Joshi; Randi Holm Jensen; Helena Fridholm; Kristín Rós Kjartansdóttir; Tobias Mourier; Tandy Warnow; Graham J. Belsham; Michael Bunce; Eske Willerslev; Lars Peter Nielsen; Lasse Vinner; Anders Johannes Hansen

doi:10.1038/emi.2016.90

High diversity of picornaviruses in rats from different continents revealed by deep sequencing

Thomas Arn Hansen, Sarah Mollerup, Nam phuong Nguyen, Nicole E. White, Megan Coghlan, David E. Alquezar-Planas, Tejal Joshi, Randi Holm Jensen, Helena Fridholm, Kristín Rós Kjartansdóttir, Tobias Mourier, Tandy Warnow, Graham J. Belsham, Michael Bunce, Eske Willerslev, Lars Peter Nielsen, Lasse Vinner^*, Anders Johannes Hansen

^*Corresponding author for this work

Biological, Environmental Sciences and Engineering

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

14 Scopus citations

Abstract

Outbreaks of zoonotic diseases in humans and livestock are not uncommon, and an important component in containment of such emerging viral diseases is rapid and reliable diagnostics. Such methods are often PCR-based and hence require the availability of sequence data from the pathogen. Rattus norvegicus (R. norvegicus) is a known reservoir for important zoonotic pathogens. Transmission may be direct via contact with the animal, for example, through exposure to its faecal matter, or indirectly mediated by arthropod vectors. Here we investigated the viral content in rat faecal matter (n=29) collected from two continents by analyzing 2.2 billion next-generation sequencing reads derived from both DNA and RNA. Among other virus families, we found sequences from members of the Picornaviridae to be abundant in the microbiome of all the samples. Here we describe the diversity of the picornavirus-like contigs including near-full-length genomes closely related to the Boone cardiovirus and Theiler’s encephalomyelitis virus. From this study, we conclude that picornaviruses within R. norvegicus are more diverse than previously recognized. The virome of R. norvegicus should be investigated further to assess the full potential for zoonotic virus transmission.

Original language	English (US)
Pages (from-to)	1-8
Number of pages	8
Journal	Emerging Microbes and Infections
Volume	5
Issue number	1
DOIs	https://doi.org/10.1038/emi.2016.90
State	Published - 2016

Bibliographical note

Funding Information:
Villum Fonden and Innovation Fund Denmark (The Genome Denmark platform, grant NO 019-2011-2) funded this study. This study was funded in part by the US National Science Foundation III:AF:1513629 to Tandy Warnow (Departments of Bioengineering and Computer Science, The University of Illinois at Urbana—Champaign, Urbana, Illinois, 61801-2302, USA). We acknowledge Salvatore Cosentino (Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, DK-2800, Kgs. Lyngby, Denmark) and Anne Ahlmann Nielsen (Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark) for valuable input on data analysis and experimental setup, respectively. We acknowledge Claus Schultz, Andy Brigham from Rentokil and Claus Christensen from Hovedstadsområdets Forsyningsselskab (HOFOR) for arranging and assisting with sample collection and the Copenhagen University Hospital (Rigshospitalet) and Section of Heart and Circulatory Research, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark for contributing samples. Also we thank The National High-throughput DNA Sequencing Centre for excellent execution of sequencing.

Publisher Copyright:
© 2016 The Author(s).

Keywords

Rattus norvegicus
cardiovirus
metagenomics
picornavirus
sequencing
viral discovery

ASJC Scopus subject areas

Drug Discovery
Infectious Diseases
Epidemiology
Virology
Parasitology
Microbiology
Immunology

UN SDGs

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

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10.1038/emi.2016.90

Cite this

Hansen, T. A., Mollerup, S., Nguyen, N. P., White, N. E., Coghlan, M., Alquezar-Planas, D. E., Joshi, T., Jensen, R. H., Fridholm, H., Kjartansdóttir, K. R., Mourier, T., Warnow, T., Belsham, G. J., Bunce, M., Willerslev, E., Nielsen, L. P., Vinner, L., & Hansen, A. J. (2016). High diversity of picornaviruses in rats from different continents revealed by deep sequencing. Emerging Microbes and Infections, 5(1), 1-8. https://doi.org/10.1038/emi.2016.90

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title = "High diversity of picornaviruses in rats from different continents revealed by deep sequencing",

abstract = "Outbreaks of zoonotic diseases in humans and livestock are not uncommon, and an important component in containment of such emerging viral diseases is rapid and reliable diagnostics. Such methods are often PCR-based and hence require the availability of sequence data from the pathogen. Rattus norvegicus (R. norvegicus) is a known reservoir for important zoonotic pathogens. Transmission may be direct via contact with the animal, for example, through exposure to its faecal matter, or indirectly mediated by arthropod vectors. Here we investigated the viral content in rat faecal matter (n=29) collected from two continents by analyzing 2.2 billion next-generation sequencing reads derived from both DNA and RNA. Among other virus families, we found sequences from members of the Picornaviridae to be abundant in the microbiome of all the samples. Here we describe the diversity of the picornavirus-like contigs including near-full-length genomes closely related to the Boone cardiovirus and Theiler{\textquoteright}s encephalomyelitis virus. From this study, we conclude that picornaviruses within R. norvegicus are more diverse than previously recognized. The virome of R. norvegicus should be investigated further to assess the full potential for zoonotic virus transmission.",

keywords = "Rattus norvegicus, cardiovirus, metagenomics, picornavirus, sequencing, viral discovery",

author = "Hansen, {Thomas Arn} and Sarah Mollerup and Nguyen, {Nam phuong} and White, {Nicole E.} and Megan Coghlan and Alquezar-Planas, {David E.} and Tejal Joshi and Jensen, {Randi Holm} and Helena Fridholm and Kjartansd{\'o}ttir, {Krist{\'i}n R{\'o}s} and Tobias Mourier and Tandy Warnow and Belsham, {Graham J.} and Michael Bunce and Eske Willerslev and Nielsen, {Lars Peter} and Lasse Vinner and Hansen, {Anders Johannes}",

note = "Funding Information: Villum Fonden and Innovation Fund Denmark (The Genome Denmark platform, grant NO 019-2011-2) funded this study. This study was funded in part by the US National Science Foundation III:AF:1513629 to Tandy Warnow (Departments of Bioengineering and Computer Science, The University of Illinois at Urbana—Champaign, Urbana, Illinois, 61801-2302, USA). We acknowledge Salvatore Cosentino (Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, DK-2800, Kgs. Lyngby, Denmark) and Anne Ahlmann Nielsen (Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark) for valuable input on data analysis and experimental setup, respectively. We acknowledge Claus Schultz, Andy Brigham from Rentokil and Claus Christensen from Hovedstadsomr{\aa}dets Forsyningsselskab (HOFOR) for arranging and assisting with sample collection and the Copenhagen University Hospital (Rigshospitalet) and Section of Heart and Circulatory Research, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark for contributing samples. Also we thank The National High-throughput DNA Sequencing Centre for excellent execution of sequencing. Publisher Copyright: {\textcopyright} 2016 The Author(s).",

year = "2016",

doi = "10.1038/emi.2016.90",

language = "English (US)",

volume = "5",

pages = "1--8",

journal = "Emerging Microbes and Infections",

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Hansen, TA, Mollerup, S, Nguyen, NP, White, NE, Coghlan, M, Alquezar-Planas, DE, Joshi, T, Jensen, RH, Fridholm, H, Kjartansdóttir, KR, Mourier, T, Warnow, T, Belsham, GJ, Bunce, M, Willerslev, E, Nielsen, LP, Vinner, L & Hansen, AJ 2016, 'High diversity of picornaviruses in rats from different continents revealed by deep sequencing', Emerging Microbes and Infections, vol. 5, no. 1, pp. 1-8. https://doi.org/10.1038/emi.2016.90

TY - JOUR

T1 - High diversity of picornaviruses in rats from different continents revealed by deep sequencing

AU - Hansen, Thomas Arn

AU - Mollerup, Sarah

AU - Nguyen, Nam phuong

AU - White, Nicole E.

AU - Coghlan, Megan

AU - Alquezar-Planas, David E.

AU - Joshi, Tejal

AU - Jensen, Randi Holm

AU - Fridholm, Helena

AU - Kjartansdóttir, Kristín Rós

AU - Mourier, Tobias

AU - Warnow, Tandy

AU - Belsham, Graham J.

AU - Bunce, Michael

AU - Willerslev, Eske

AU - Nielsen, Lars Peter

AU - Vinner, Lasse

AU - Hansen, Anders Johannes

N1 - Funding Information: Villum Fonden and Innovation Fund Denmark (The Genome Denmark platform, grant NO 019-2011-2) funded this study. This study was funded in part by the US National Science Foundation III:AF:1513629 to Tandy Warnow (Departments of Bioengineering and Computer Science, The University of Illinois at Urbana—Champaign, Urbana, Illinois, 61801-2302, USA). We acknowledge Salvatore Cosentino (Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, DK-2800, Kgs. Lyngby, Denmark) and Anne Ahlmann Nielsen (Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark) for valuable input on data analysis and experimental setup, respectively. We acknowledge Claus Schultz, Andy Brigham from Rentokil and Claus Christensen from Hovedstadsområdets Forsyningsselskab (HOFOR) for arranging and assisting with sample collection and the Copenhagen University Hospital (Rigshospitalet) and Section of Heart and Circulatory Research, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark for contributing samples. Also we thank The National High-throughput DNA Sequencing Centre for excellent execution of sequencing. Publisher Copyright: © 2016 The Author(s).

PY - 2016

Y1 - 2016

N2 - Outbreaks of zoonotic diseases in humans and livestock are not uncommon, and an important component in containment of such emerging viral diseases is rapid and reliable diagnostics. Such methods are often PCR-based and hence require the availability of sequence data from the pathogen. Rattus norvegicus (R. norvegicus) is a known reservoir for important zoonotic pathogens. Transmission may be direct via contact with the animal, for example, through exposure to its faecal matter, or indirectly mediated by arthropod vectors. Here we investigated the viral content in rat faecal matter (n=29) collected from two continents by analyzing 2.2 billion next-generation sequencing reads derived from both DNA and RNA. Among other virus families, we found sequences from members of the Picornaviridae to be abundant in the microbiome of all the samples. Here we describe the diversity of the picornavirus-like contigs including near-full-length genomes closely related to the Boone cardiovirus and Theiler’s encephalomyelitis virus. From this study, we conclude that picornaviruses within R. norvegicus are more diverse than previously recognized. The virome of R. norvegicus should be investigated further to assess the full potential for zoonotic virus transmission.

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KW - metagenomics

KW - picornavirus

KW - sequencing

KW - viral discovery

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JO - Emerging Microbes and Infections

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ER -

High diversity of picornaviruses in rats from different continents revealed by deep sequencing

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

UN SDGs

Access to Document

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