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Viral metagenomic analysis of feces of wild small carnivores

Rogier Bodewes1*, Aritz Ruiz-Gonzalez234, Claudia ME Schapendonk1, Judith MA van den Brand1, Albert DME Osterhaus15 and Saskia L Smits15

Author Affiliations

1 Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands

2 Department of Zoology and Animal Cell Biology, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain

3 Systematics, Biogeography and Population Dynamics Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain

4 Conservation Genetics Laboratory, National Institute for Environmental Protection and Research (ISPRA), Bologna, Ozzano dell’Emilia (BO), Italy

5 ViroClinics BioSciences BV, Rotterdam, The Netherlands

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Virology Journal 2014, 11:89  doi:10.1186/1743-422X-11-89

Published: 15 May 2014

Abstract

Background

Recent studies have clearly demonstrated the enormous virus diversity that exists among wild animals. This exemplifies the required expansion of our knowledge of the virus diversity present in wildlife, as well as the potential transmission of these viruses to domestic animals or humans.

Methods

In the present study we evaluated the viral diversity of fecal samples (n = 42) collected from 10 different species of wild small carnivores inhabiting the northern part of Spain using random PCR in combination with next-generation sequencing. Samples were collected from American mink (Neovison vison), European mink (Mustela lutreola), European polecat (Mustela putorius), European pine marten (Martes martes), stone marten (Martes foina), Eurasian otter (Lutra lutra) and Eurasian badger (Meles meles) of the family of Mustelidae; common genet (Genetta genetta) of the family of Viverridae; red fox (Vulpes vulpes) of the family of Canidae and European wild cat (Felis silvestris) of the family of Felidae.

Results

A number of sequences of possible novel viruses or virus variants were detected, including a theilovirus, phleboviruses, an amdovirus, a kobuvirus and picobirnaviruses.

Conclusions

Using random PCR in combination with next generation sequencing, sequences of various novel viruses or virus variants were detected in fecal samples collected from Spanish carnivores. Detected novel viruses highlight the viral diversity that is present in fecal material of wild carnivores.

Keywords:
Theilovirus; Viral metagenomics; Picobirnavirus; Amdovirus; Phlebovirus; Carnivore; Wild carnivore; Wildlife; Red fox; Fox; Otter; Common gennet; Bunyavirus