M Asplund1, K R Kjartansdóttir2, S Mollerup2, L Vinner2, H Fridholm3, J A R Herrera4, J Friis-Nielsen5, T A Hansen2, R H Jensen2, I B Nielsen2, S R Richter2, A Rey-Iglesia2, M L Matey-Hernandez5, D E Alquezar-Planas2, P V S Olsen2, T Sicheritz-Pontén6, E Willerslev2, O Lund5, S Brunak4, T Mourier2, L P Nielsen7, J M G Izarzugaza5, A J Hansen8. 1. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. Electronic address: amasplund@snm.ku.dk. 2. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. 3. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark; Department of Autoimmunology and Biomarkers, Statens Serum Institut, Copenhagen, Denmark. 4. Disease Systems Biology Programme, Panum Instituttet, Copenhagen, Denmark; Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark. 5. Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark. 6. 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. 7. Department of Autoimmunology and Biomarkers, Statens Serum Institut, Copenhagen, Denmark. 8. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark. Electronic address: ajhansen@snm.ku.dk.
Abstract
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.
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.
Authors: Thomas Junier; Michael Huber; Stefan Schmutz; Verena Kufner; Osvaldo Zagordi; Stefan Neuenschwander; Alban Ramette; Jakub Kubacki; Claudia Bachofen; Weihong Qi; Florian Laubscher; Samuel Cordey; Laurent Kaiser; Christian Beuret; Valérie Barbié; Jacques Fellay; Aitana Lebrand Journal: Genes (Basel) Date: 2019-08-28 Impact factor: 4.096
Authors: Manuel Schibler; Francisco Brito; Marie-Céline Zanella; Evgeny M Zdobnov; Florian Laubscher; Arnaud G L'Huillier; Juan Ambrosioni; Noémie Wagner; Klara M Posfay-Barbe; Mylène Docquier; Eduardo Schiffer; Georges L Savoldelli; Roxane Fournier; Lauriane Lenggenhager; Samuel Cordey; Laurent Kaiser Journal: Genes (Basel) Date: 2019-08-19 Impact factor: 4.096