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

Research output: Contribution to journalArticle

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 languageEnglish (US)
Pages (from-to)e90
JournalEmerging microbes & infections
Volume5
Issue number8
DOIs
StatePublished - Aug 17 2016

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Picornaviridae
High-Throughput Nucleotide Sequencing
Zoonoses
Cardiovirus
Arthropod Vectors
Theilovirus
Viruses
Encephalomyelitis
Microbiota
Livestock
Virus Diseases
Disease Outbreaks
Genome
RNA
Polymerase Chain Reaction
DNA

ASJC Scopus subject areas

  • Epidemiology
  • Parasitology
  • Microbiology
  • Immunology
  • Drug Discovery
  • Infectious Diseases
  • Virology

Cite this

Hansen, T. A., Mollerup, S., Nguyen, N. P., White, N. E., Coghlan, M., Alquezar-Planas, D. E., ... Hansen, A. J. (2016). High diversity of picornaviruses in rats from different continents revealed by deep sequencing. Emerging microbes & infections, 5(8), e90. https://doi.org/10.1038/emi.2016.90

High diversity of picornaviruses in rats from different continents revealed by deep sequencing. / Hansen, Thomas Arn; Mollerup, Sarah; Nguyen, Nam Phuong; White, Nicole E.; Coghlan, Megan; Alquezar-Planas, David E.; Joshi, Tejal; Jensen, Randi Holm; Fridholm, Helena; Kjartansdóttir, Kristín Rós; Mourier, Tobias; Warnow, Tandy; Belsham, Graham J.; Bunce, Michael; Willerslev, Eske; Nielsen, Lars Peter; Vinner, Lasse; Hansen, Anders Johannes.

In: Emerging microbes & infections, Vol. 5, No. 8, 17.08.2016, p. e90.

Research output: Contribution to journalArticle

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 & infections, vol. 5, no. 8, pp. e90. https://doi.org/10.1038/emi.2016.90
Hansen TA, Mollerup S, Nguyen NP, White NE, Coghlan M, Alquezar-Planas DE et al. High diversity of picornaviruses in rats from different continents revealed by deep sequencing. Emerging microbes & infections. 2016 Aug 17;5(8):e90. https://doi.org/10.1038/emi.2016.90
Hansen, Thomas Arn ; Mollerup, Sarah ; Nguyen, Nam Phuong ; White, Nicole E. ; Coghlan, Megan ; Alquezar-Planas, David E. ; Joshi, Tejal ; Jensen, Randi Holm ; Fridholm, Helena ; Kjartansdóttir, Kristín Rós ; Mourier, Tobias ; Warnow, Tandy ; Belsham, Graham J. ; Bunce, Michael ; Willerslev, Eske ; Nielsen, Lars Peter ; Vinner, Lasse ; Hansen, Anders Johannes. / High diversity of picornaviruses in rats from different continents revealed by deep sequencing. In: Emerging microbes & infections. 2016 ; Vol. 5, No. 8. pp. e90.
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