Metagenomic survey for viruses in Western Arctic caribou, Alaska, through iterative assembly of taxonomic units.
Pathogen surveillance in animals does not provide a sufficient level of vigilance because it is generally confined to surveillance of pathogens with known economic impact in domestic animals and practically nonexistent in wildlife species. As most (re-)emerging viral infections originate from animal...
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2014
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oai:doaj.org-article:3f74ff3f943545a7b1dd10b83f1d1b532021-11-25T06:04:01ZMetagenomic survey for viruses in Western Arctic caribou, Alaska, through iterative assembly of taxonomic units.1932-620310.1371/journal.pone.0105227https://doaj.org/article/3f74ff3f943545a7b1dd10b83f1d1b532014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/25140520/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Pathogen surveillance in animals does not provide a sufficient level of vigilance because it is generally confined to surveillance of pathogens with known economic impact in domestic animals and practically nonexistent in wildlife species. As most (re-)emerging viral infections originate from animal sources, it is important to obtain insight into viral pathogens present in the wildlife reservoir from a public health perspective. When monitoring living, free-ranging wildlife for viruses, sample collection can be challenging and availability of nucleic acids isolated from samples is often limited. The development of viral metagenomics platforms allows a more comprehensive inventory of viruses present in wildlife. We report a metagenomic viral survey of the Western Arctic herd of barren ground caribou (Rangifer tarandus granti) in Alaska, USA. The presence of mammalian viruses in eye and nose swabs of 39 free-ranging caribou was investigated by random amplification combined with a metagenomic analysis approach that applied exhaustive iterative assembly of sequencing results to define taxonomic units of each metagenome. Through homology search methods we identified the presence of several mammalian viruses, including different papillomaviruses, a novel parvovirus, polyomavirus, and a virus that potentially represents a member of a novel genus in the family Coronaviridae.Anita C SchürchDebby SchipperMaarten A BijlJim DauKimberlee B BeckmenClaudia M E SchapendonkV Stalin RajAlbert D M E OsterhausBart L HaagmansMorten TrylandSaskia L SmitsPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 8, p e105227 (2014) |
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Medicine R Science Q |
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Medicine R Science Q Anita C Schürch Debby Schipper Maarten A Bijl Jim Dau Kimberlee B Beckmen Claudia M E Schapendonk V Stalin Raj Albert D M E Osterhaus Bart L Haagmans Morten Tryland Saskia L Smits Metagenomic survey for viruses in Western Arctic caribou, Alaska, through iterative assembly of taxonomic units. |
| description |
Pathogen surveillance in animals does not provide a sufficient level of vigilance because it is generally confined to surveillance of pathogens with known economic impact in domestic animals and practically nonexistent in wildlife species. As most (re-)emerging viral infections originate from animal sources, it is important to obtain insight into viral pathogens present in the wildlife reservoir from a public health perspective. When monitoring living, free-ranging wildlife for viruses, sample collection can be challenging and availability of nucleic acids isolated from samples is often limited. The development of viral metagenomics platforms allows a more comprehensive inventory of viruses present in wildlife. We report a metagenomic viral survey of the Western Arctic herd of barren ground caribou (Rangifer tarandus granti) in Alaska, USA. The presence of mammalian viruses in eye and nose swabs of 39 free-ranging caribou was investigated by random amplification combined with a metagenomic analysis approach that applied exhaustive iterative assembly of sequencing results to define taxonomic units of each metagenome. Through homology search methods we identified the presence of several mammalian viruses, including different papillomaviruses, a novel parvovirus, polyomavirus, and a virus that potentially represents a member of a novel genus in the family Coronaviridae. |
| format |
article |
| author |
Anita C Schürch Debby Schipper Maarten A Bijl Jim Dau Kimberlee B Beckmen Claudia M E Schapendonk V Stalin Raj Albert D M E Osterhaus Bart L Haagmans Morten Tryland Saskia L Smits |
| author_facet |
Anita C Schürch Debby Schipper Maarten A Bijl Jim Dau Kimberlee B Beckmen Claudia M E Schapendonk V Stalin Raj Albert D M E Osterhaus Bart L Haagmans Morten Tryland Saskia L Smits |
| author_sort |
Anita C Schürch |
| title |
Metagenomic survey for viruses in Western Arctic caribou, Alaska, through iterative assembly of taxonomic units. |
| title_short |
Metagenomic survey for viruses in Western Arctic caribou, Alaska, through iterative assembly of taxonomic units. |
| title_full |
Metagenomic survey for viruses in Western Arctic caribou, Alaska, through iterative assembly of taxonomic units. |
| title_fullStr |
Metagenomic survey for viruses in Western Arctic caribou, Alaska, through iterative assembly of taxonomic units. |
| title_full_unstemmed |
Metagenomic survey for viruses in Western Arctic caribou, Alaska, through iterative assembly of taxonomic units. |
| title_sort |
metagenomic survey for viruses in western arctic caribou, alaska, through iterative assembly of taxonomic units. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2014 |
| url |
https://doaj.org/article/3f74ff3f943545a7b1dd10b83f1d1b53 |
| work_keys_str_mv |
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