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

被引：95

作者：

Asplund, M. ^{[1
]}

Kjartansdottir, K. R. ^{[1
]}

Mollerup, S. ^{[1
]}

Vinner, L. ^{[1
]}

Fridholm, H. ^{[1
,2
]}

Herrera, J. A. R. ^{[3
,4
]}

Friis-Nielsen, J. ^{[4
]}

Hansen, T. A. ^{[1
]}

Jensen, R. H. ^{[1
]}

Nielsen, I. B. ^{[1
]}

Richter, S. R. ^{[1
]}

Rey-Iglesia, A. ^{[1
]}

Matey-Hernandez, M. L. ^{[4
]}

Alquezar-Planas, D. E. ^{[1
]}

Olsen, P. V. S. ^{[1
]}

Sicheritz-Ponten, T. ^{[1
,5
]}

Willerslev, E. ^{[1
]}

Lund, O. ^{[4
]}

Brunak, S. ^{[3
,4
]}

Mourier, T. ^{[1
]}

Nielsen, L. P. ^{[2
]}

Izarzugaza, J. M. G. ^{[4
]}

Hansen, A. J. ^{[1
]}

机构：

[1] Univ Copenhagen, Nat Hist Museum Denmark, Ctr GeoGenet, Copenhagen, Denmark

[2] Statens Serum Inst, Dept Autoimmunol & Biomarkers, Copenhagen, Denmark

[3] Panum Inst, Dis Syst Biol Programme, Copenhagen, Denmark

[4] Tech Univ Denmark, Dept Bio & Hlth Informat, Lyngby, Denmark

[5] AIMST Univ, Ctr Excellence Omics Driven Computat Biodiscovery, Kedah, Malaysia

来源：

CLINICAL MICROBIOLOGY AND INFECTION | 2019年 / 25卷 / 10期

基金：

新加坡国家研究基金会;

关键词：

Cluster; Contamination; High-throughput sequencing; Laboratory component; Metagenomic; Next-generation sequencing; Nucleic acid; Virome; Virus; CHLOROVIRUS ATCV-1; DNA VIRUS; GENERATION; DISCOVERY; METAGENOMICS; RETROVIRUS; ORIGIN; TOOLS; BLOOD; XMRV;

D O I：

10.1016/j.cmi.2019.04.028

中图分类号：

R51 [传染病];

学科分类号：

100401 ;

摘要：

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. (c) 2019 The Author(s). Published by Elsevier Ltd on behalf of European Society of Clinical Microbiology and Infectious Diseases. This is an open access article under the CC BY-NC-ND license

引用

页码：1277 / 1285

页数：9

共 41 条

[1] Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J].

Altschul, SF ;

Madden, TL ;

Schaffer, AA ;

Zhang, JH ;

Zhang, Z ;

Miller, W ;

Lipman, DJ .

NUCLEIC ACIDS RESEARCH, 1997, 25 (17) :3389-3402

[2]

Atkins Gregory J., 2008, Expert Reviews in Molecular Medicine, V10, P1, DOI 10.1017/S1462399408000859

[3] Genetic Detection and Characterization of Lujo Virus, a New Hemorrhagic Fever-Associated Arenavirus from Southern Africa [J].

Briese, Thomas ;

Paweska, Janusz T. ;

McMullan, Laura K. ;

Hutchison, Stephen K. ;

Street, Craig ;

Palacios, Gustavo ;

Khristova, Marina L. ;

Weyer, Jacqueline ;

Swanepoel, Robert ;

Egholm, Michael ;

Nichol, Stuart T. ;

Lipkin, W. Ian .

PLOS PATHOGENS, 2009, 5 (05)

[4]

Bukowska-Osko I., 2016, Adv Exp Med Biol

[5] Viral pathogen discovery [J].

Chius, Charles Y. .

CURRENT OPINION IN MICROBIOLOGY, 2013, 16 (04) :468-478

[6] Discovery of Novel Viruses in Mosquitoes from the Zambezi Valley of Mozambique [J].

Cholleti, Harindranath ;

Hayer, Juliette ;

Abilio, Ana Paula ;

Mulandane, Fernando Chanisso ;

Verner-Carlsson, Jenny ;

Falk, Kerstin I. ;

Fafetine, Jose M. ;

Berg, Mikael ;

Blomstrom, Anne-Lie .

PLOS ONE, 2016, 11 (09)

[7] Rapid, high level protein production using DNA-based semliki forest virus vectors [J].

DiCiommo, DP ;

Bremner, R .

JOURNAL OF BIOLOGICAL CHEMISTRY, 1998, 273 (29) :18060-18066

[8] DNA Extraction Columns Contaminated with Murine Sequences [J].

Erlwein, Otto ;

Robinson, Mark J. ;

Dustan, Simon ;

Weber, Jonathan ;

Kaye, Steve ;

McClure, Myra O. .

PLOS ONE, 2011, 6 (08)

[9]

Feng HC, 2008, SCIENCE, V319, P1096, DOI 10.1126/science.1152586

[10] Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers [J].

Friis-Nielsen, Jens ;

Kjartansdottir, Kristin Ros ;

Mollerup, Sarah ;

Asplund, Maria ;

Mourier, Tobias ;

Jensen, Randi Holm ;

Hansen, Thomas Arn ;

Rey-Iglesia, Alba ;

Richter, Stine Raith ;

Nielsen, Ida Broman ;

Alquezar-Planas, David E. ;

Olsen, Pernille V. S. ;

Vinner, Lasse ;

Fridholm, Helena ;

Nielsen, Lars Peter ;

Willerslev, Eske ;

Sicheritz-Ponten, Thomas ;

Lund, Ole ;

Hansen, Anders Johannes ;

Izarzugaza, Jose M. G. ;

Brunak, Soren .

VIRUSES-BASEL, 2016, 8 (02)

← 1 2 3 4 5 →