Contaminating viral sequences in high-throughput sequencing viromics: a linkage study of 700 sequencing libraries

Maria Asplund; Kristín Rós Kjartansdóttir; Sarah Mollerup; Lasse Vinner; Helena Fridholm; José A R Herrera; Jens Friis-Nielsen; Thomas Arn Hansen; Randi Holm Jensen; Ida Broman Nielsen; Stine Raith Richter; Alba Rey-Iglesia; Maria Luisa Matey-Hernandez; David E Alquezar-Planas; Pernille V S Olsen; Thomas Sicheritz-Pontén; Eske Willerslev; Ole Lund; Søren Brunak; Tobias Mourier; Lars Peter Nielsen; Jose M G Izarzugaza; Anders Johannes Hansen

doi:10.1016/j.cmi.2019.04.028

Contaminating viral sequences in high-throughput sequencing viromics: a linkage study of 700 sequencing libraries

Maria Asplund, Kristín Rós Kjartansdóttir, Sarah Mollerup, Lasse Vinner, Helena Fridholm, José A R Herrera, Jens Friis-Nielsen, Thomas Arn Hansen, Randi Holm Jensen, Ida Broman Nielsen, Stine Raith Richter, Alba Rey-Iglesia, Maria Luisa Matey-Hernandez, David E Alquezar-Planas, Pernille V S Olsen, Thomas Sicheritz-Pontén, Eske Willerslev, Ole Lund, Søren Brunak, Tobias MourierLars Peter Nielsen, Jose M G Izarzugaza, Anders Johannes Hansen

Disease Systems Biology Program

38 Citations (Scopus)

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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.

Original language	English
Journal	Clinical Microbiology and Infection
Volume	25
Issue number	10
Pages (from-to)	1277-1285
ISSN	1198-743X
DOIs	https://doi.org/10.1016/j.cmi.2019.04.028
Publication status	Published - Oct 2019

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10.1016/j.cmi.2019.04.028Licence: CC BY-NC-ND

Contaminating viral sequences in high-throughput sequencing viromics: a linkage study of 700 sequencing librariesFinal published version, 2.02 MBLicence: CC BY-NC-ND

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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., ... Hansen, A. J. (2019). Contaminating viral sequences in high-throughput sequencing viromics: a linkage study of 700 sequencing libraries. Clinical Microbiology and Infection, 25(10), 1277-1285. https://doi.org/10.1016/j.cmi.2019.04.028

Asplund, M, Kjartansdóttir, KR, Mollerup, S, Vinner, L, Fridholm, H, Herrera, JAR, Friis-Nielsen, J, Hansen, TA, Jensen, RH, Nielsen, IB, Richter, SR, Rey-Iglesia, A, Matey-Hernandez, ML, Alquezar-Planas, DE, Olsen, PVS , Sicheritz-Pontén, T , Willerslev, E, Lund, O, Brunak, S, Mourier, T, Nielsen, LP, Izarzugaza, JMG & Hansen, AJ 2019, 'Contaminating viral sequences in high-throughput sequencing viromics: a linkage study of 700 sequencing libraries', Clinical Microbiology and Infection, vol. 25, no. 10, pp. 1277-1285. https://doi.org/10.1016/j.cmi.2019.04.028

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title = "Contaminating viral sequences in high-throughput sequencing viromics: a linkage study of 700 sequencing libraries",

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.",

author = "Maria Asplund and Kjartansd{\'o}ttir, {Krist{\'i}n R{\'o}s} and Sarah Mollerup and Lasse Vinner and Helena Fridholm and Herrera, {Jos{\'e} A R} and Jens Friis-Nielsen and Hansen, {Thomas Arn} and Jensen, {Randi Holm} and Nielsen, {Ida Broman} and Richter, {Stine Raith} and Alba Rey-Iglesia and Matey-Hernandez, {Maria Luisa} and Alquezar-Planas, {David E} and Olsen, {Pernille V S} and Thomas Sicheritz-Pont{\'e}n and Eske Willerslev and Ole Lund and S{\o}ren Brunak and Tobias Mourier and Nielsen, {Lars Peter} and Izarzugaza, {Jose M G} and Hansen, {Anders Johannes}",

year = "2019",

month = oct,

doi = "10.1016/j.cmi.2019.04.028",

language = "English",

volume = "25",

pages = "1277--1285",

journal = "Clinical Microbiology and Infection",

issn = "1198-743X",

publisher = "Elsevier",

number = "10",

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TY - JOUR

T1 - Contaminating viral sequences in high-throughput sequencing viromics

T2 - a linkage study of 700 sequencing libraries

AU - Asplund, Maria

AU - Kjartansdóttir, Kristín Rós

AU - Mollerup, Sarah

AU - Vinner, Lasse

AU - Fridholm, Helena

AU - Herrera, José A R

AU - Friis-Nielsen, Jens

AU - Hansen, Thomas Arn

AU - Jensen, Randi Holm

AU - Nielsen, Ida Broman

AU - Richter, Stine Raith

AU - Rey-Iglesia, Alba

AU - Matey-Hernandez, Maria Luisa

AU - Alquezar-Planas, David E

AU - Olsen, Pernille V S

AU - Sicheritz-Pontén, Thomas

AU - Willerslev, Eske

AU - Lund, Ole

AU - Brunak, Søren

AU - Mourier, Tobias

AU - Nielsen, Lars Peter

AU - Izarzugaza, Jose M G

AU - Hansen, Anders Johannes

PY - 2019/10

Y1 - 2019/10

N2 - 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.

AB - 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.

U2 - 10.1016/j.cmi.2019.04.028

DO - 10.1016/j.cmi.2019.04.028

M3 - Journal article

C2 - 31059795

SN - 1198-743X

VL - 25

SP - 1277

EP - 1285

JO - Clinical Microbiology and Infection

JF - Clinical Microbiology and Infection

IS - 10

ER -

Contaminating viral sequences in high-throughput sequencing viromics: a linkage study of 700 sequencing libraries

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