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 anima...
Published in: | PLoS ONE |
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Online Access: | https://pure.eur.nl/en/publications/61c36271-59f4-415b-85e9-1997638a735c https://doi.org/10.1371/journal.pone.0105227 https://pure.eur.nl/ws/files/47591247/Repub_90419_O-A.PDF http://hdl.handle.net/1765/90419 |
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fturottercrispub:oai:pure.eur.nl:publications/61c36271-59f4-415b-85e9-1997638a735c 2023-05-15T14:25:55+02:00 Metagenomic Survey for Viruses in Western Arctic Caribou, Alaska, through Iterative Assembly of Taxonomic Units Schürch, Anita van Eck - Schipper, Debby Bijl, MA (Maarten) Dau, J Beckmen, KB Schapendonk, Claudia Victor, Stalinraj Osterhaus, Ab Haagmans, Bart Tryland, M Smits, Saskia 2014 application/pdf https://pure.eur.nl/en/publications/61c36271-59f4-415b-85e9-1997638a735c https://doi.org/10.1371/journal.pone.0105227 https://pure.eur.nl/ws/files/47591247/Repub_90419_O-A.PDF http://hdl.handle.net/1765/90419 und unknown info:eu-repo/semantics/openAccess Schürch , A , van Eck - Schipper , D , Bijl , MA , Dau , J , Beckmen , KB , Schapendonk , C , Victor , S , Osterhaus , A , Haagmans , B , Tryland , M & Smits , S 2014 , ' Metagenomic Survey for Viruses in Western Arctic Caribou, Alaska, through Iterative Assembly of Taxonomic Units ' , PLoS One (print) , vol. 9 , no. 8 . https://doi.org/10.1371/journal.pone.0105227 /dk/atira/pure/sustainabledevelopmentgoals/good_health_and_well_being SDG 3 - Good Health and Well-being article 2014 fturottercrispub https://doi.org/10.1371/journal.pone.0105227 2022-06-01T10:32:08Z 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. Article in Journal/Newspaper Arctic Arctic caribou Rangifer tarandus Alaska Erasmus University Rotterdam & Erasmus MC Research Portal Arctic PLoS ONE 9 8 e105227 |
institution |
Open Polar |
collection |
Erasmus University Rotterdam & Erasmus MC Research Portal |
op_collection_id |
fturottercrispub |
language |
unknown |
topic |
/dk/atira/pure/sustainabledevelopmentgoals/good_health_and_well_being SDG 3 - Good Health and Well-being |
spellingShingle |
/dk/atira/pure/sustainabledevelopmentgoals/good_health_and_well_being SDG 3 - Good Health and Well-being Schürch, Anita van Eck - Schipper, Debby Bijl, MA (Maarten) Dau, J Beckmen, KB Schapendonk, Claudia Victor, Stalinraj Osterhaus, Ab Haagmans, Bart Tryland, M Smits, Saskia Metagenomic Survey for Viruses in Western Arctic Caribou, Alaska, through Iterative Assembly of Taxonomic Units |
topic_facet |
/dk/atira/pure/sustainabledevelopmentgoals/good_health_and_well_being SDG 3 - Good Health and Well-being |
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 in Journal/Newspaper |
author |
Schürch, Anita van Eck - Schipper, Debby Bijl, MA (Maarten) Dau, J Beckmen, KB Schapendonk, Claudia Victor, Stalinraj Osterhaus, Ab Haagmans, Bart Tryland, M Smits, Saskia |
author_facet |
Schürch, Anita van Eck - Schipper, Debby Bijl, MA (Maarten) Dau, J Beckmen, KB Schapendonk, Claudia Victor, Stalinraj Osterhaus, Ab Haagmans, Bart Tryland, M Smits, Saskia |
author_sort |
Schürch, Anita |
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 |
publishDate |
2014 |
url |
https://pure.eur.nl/en/publications/61c36271-59f4-415b-85e9-1997638a735c https://doi.org/10.1371/journal.pone.0105227 https://pure.eur.nl/ws/files/47591247/Repub_90419_O-A.PDF http://hdl.handle.net/1765/90419 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic Arctic caribou Rangifer tarandus Alaska |
genre_facet |
Arctic Arctic caribou Rangifer tarandus Alaska |
op_source |
Schürch , A , van Eck - Schipper , D , Bijl , MA , Dau , J , Beckmen , KB , Schapendonk , C , Victor , S , Osterhaus , A , Haagmans , B , Tryland , M & Smits , S 2014 , ' Metagenomic Survey for Viruses in Western Arctic Caribou, Alaska, through Iterative Assembly of Taxonomic Units ' , PLoS One (print) , vol. 9 , no. 8 . https://doi.org/10.1371/journal.pone.0105227 |
op_rights |
info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.1371/journal.pone.0105227 |
container_title |
PLoS ONE |
container_volume |
9 |
container_issue |
8 |
container_start_page |
e105227 |
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1766298412514279424 |