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Contaminating viral sequences in high-throughput sequencing viromics: a linkage study of 700 sequencing libraries.
Asplund, M; Kjartansdóttir, K R; Mollerup, S; Vinner, L; Fridholm, H; Herrera, J A R; Friis-Nielsen, J; Hansen, T A; Jensen, R H; Nielsen, I B; Richter, S R; Rey-Iglesia, A; Matey-Hernandez, M L; Alquezar-Planas, D E; Olsen, P V S; Sicheritz-Pontén, T; Willerslev, E; Lund, O; Brunak, S; Mourier, T; Nielsen, L P; Izarzugaza, J M G; Hansen, A J.
Afiliación
  • Asplund M; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. Electronic address: amasplund@snm.ku.dk.
  • Kjartansdóttir KR; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
  • Mollerup S; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
  • Vinner L; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
  • Fridholm H; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark; Department of Autoimmunology and Biomarkers, Statens Serum Institut, Copenhagen, Denmark.
  • Herrera JAR; Disease Systems Biology Programme, Panum Instituttet, Copenhagen, Denmark; Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark.
  • Friis-Nielsen J; Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark.
  • Hansen TA; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
  • Jensen RH; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
  • Nielsen IB; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
  • Richter SR; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
  • Rey-Iglesia A; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
  • Matey-Hernandez ML; Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark.
  • Alquezar-Planas DE; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
  • Olsen PVS; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
  • Sicheritz-Pontén T; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark; Centre of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Kedah, Malaysia.
  • Willerslev E; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
  • Lund O; Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark.
  • Brunak S; Disease Systems Biology Programme, Panum Instituttet, Copenhagen, Denmark; Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark.
  • Mourier T; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
  • Nielsen LP; Department of Autoimmunology and Biomarkers, Statens Serum Institut, Copenhagen, Denmark.
  • Izarzugaza JMG; Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark.
  • Hansen AJ; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. Electronic address: ajhansen@snm.ku.dk.
Clin Microbiol Infect ; 25(10): 1277-1285, 2019 Oct.
Article en En | MEDLINE | ID: mdl-31059795
OBJECTIVES: Sample preparation for high-throughput sequencing (HTS) includes treatment with various laboratory components, potentially carrying viral nucleic acids, the extent of which has not been thoroughly investigated. Our aim was to systematically examine a diverse repertoire of laboratory components used to prepare samples for HTS in order to identify contaminating viral sequences. METHODS: A total of 322 samples of mainly human origin were analysed using eight protocols, applying a wide variety of laboratory components. Several samples (60% of human specimens) were processed using different protocols. In total, 712 sequencing libraries were investigated for viral sequence contamination. RESULTS: Among sequences showing similarity to viruses, 493 were significantly associated with the use of laboratory components. Each of these viral sequences had sporadic appearance, only being identified in a subset of the samples treated with the linked laboratory component, and some were not identified in the non-template control samples. Remarkably, more than 65% of all viral sequences identified were within viral clusters linked to the use of laboratory components. CONCLUSIONS: We show that high prevalence of contaminating viral sequences can be expected in HTS-based virome data and provide an extensive list of novel contaminating viral sequences that can be used for evaluation of viral findings in future virome and metagenome studies. Moreover, we show that detection can be problematic due to stochastic appearance and limited non-template controls. Although the exact origin of these viral sequences requires further research, our results support laboratory-component-linked viral sequence contamination of both biological and synthetic origin.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Manejo de Especímenes / Virus / Metagenómica / Secuenciación de Nucleótidos de Alto Rendimiento Tipo de estudio: Guideline / Prognostic_studies / Risk_factors_studies Límite: Humans Idioma: En Revista: Clin Microbiol Infect Asunto de la revista: DOENCAS TRANSMISSIVEIS / MICROBIOLOGIA Año: 2019 Tipo del documento: Article Pais de publicación: Reino Unido
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Manejo de Especímenes / Virus / Metagenómica / Secuenciación de Nucleótidos de Alto Rendimiento Tipo de estudio: Guideline / Prognostic_studies / Risk_factors_studies Límite: Humans Idioma: En Revista: Clin Microbiol Infect Asunto de la revista: DOENCAS TRANSMISSIVEIS / MICROBIOLOGIA Año: 2019 Tipo del documento: Article Pais de publicación: Reino Unido