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Birkelund T, Johansen RF, Illum DG, Dyrskog SE, Østergaard JA, Falconer TM, Andersen C, Fridholm H, Overballe-Petersen S, Jensen JS. Fatal 3-Nitropropionic Acid Poisoning after Consuming Coconut Water. Emerg Infect Dis 2021; 27:278-280. [PMID: 33350928 PMCID: PMC7774558 DOI: 10.3201/eid2701.202222] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We describe the fatal course of a patient with initial symptoms of vomiting and nausea who developed symptoms of dystonia, encephalopathy, and coma. The cause of death was poisoning with 3-nitropropionic acid from coconut water spoiled with the fungus Arthrinium saccharicola. We present the clinical findings and forensic analysis.
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2
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Mollerup S, Asplund M, Friis-Nielsen J, Kjartansdóttir KR, Fridholm H, Hansen TA, Herrera JAR, Barnes CJ, Jensen RH, Richter SR, Nielsen IB, Pietroni C, Alquezar-Planas DE, Rey-Iglesia A, Olsen PVS, Rajpert-De Meyts E, Groth-Pedersen L, von Buchwald C, Jensen DH, Gniadecki R, Høgdall E, Langhoff JL, Pete I, Vereczkey I, Baranyai Z, Dybkaer K, Johnsen HE, Steiniche T, Hokland P, Rosenberg J, Baandrup U, Sicheritz-Pontén T, Willerslev E, Brunak S, Lund O, Mourier T, Vinner L, Izarzugaza JMG, Nielsen LP, Hansen AJ. High-Throughput Sequencing-Based Investigation of Viruses in Human Cancers by Multienrichment Approach. J Infect Dis 2020; 220:1312-1324. [PMID: 31253993 PMCID: PMC6743825 DOI: 10.1093/infdis/jiz318] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 06/27/2019] [Indexed: 01/10/2023] Open
Abstract
Background Viruses and other infectious agents cause more than 15% of human cancer cases. High-throughput sequencing-based studies of virus-cancer associations have mainly focused on cancer transcriptome data. Methods In this study, we applied a diverse selection of presequencing enrichment methods targeting all major viral groups, to characterize the viruses present in 197 samples from 18 sample types of cancerous origin. Using high-throughput sequencing, we generated 710 datasets constituting 57 billion sequencing reads. Results Detailed in silico investigation of the viral content, including exclusion of viral artefacts, from de novo assembled contigs and individual sequencing reads yielded a map of the viruses detected. Our data reveal a virome dominated by papillomaviruses, anelloviruses, herpesviruses, and parvoviruses. More than half of the included samples contained 1 or more viruses; however, no link between specific viruses and cancer types were found. Conclusions Our study sheds light on viral presence in cancers and provides highly relevant virome data for future reference.
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Affiliation(s)
- Sarah Mollerup
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Maria Asplund
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Jens Friis-Nielsen
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | | | - Helena Fridholm
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Thomas Arn Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - José Alejandro Romero Herrera
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | | | - Randi Holm Jensen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Stine Raith Richter
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Ida Broman Nielsen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Carlotta Pietroni
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - David E Alquezar-Planas
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Alba Rey-Iglesia
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Pernille V S Olsen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Ewa Rajpert-De Meyts
- Department of Growth and Reproduction, Copenhagen University Hospital (Rigshospitalet), Denmark
| | - Line Groth-Pedersen
- Department of Pediatrics and Adolescent Medicine, University Hospital Rigshospitalet, Denmark
| | - Christian von Buchwald
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, Rigshospitalet, Copenhagen University Hospital
| | - David H Jensen
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, Rigshospitalet, Copenhagen University Hospital
| | - Robert Gniadecki
- Department of Dermato-Venerology, Faculty of Health Sciences, Copenhagen University Hospital, Bispebjerg Hospital, Denmark
| | - Estrid Høgdall
- Department of Pathology, Herlev and Gentofte Hospital, University of Copenhagen, Denmark
| | - Jill Levin Langhoff
- Department of Pathology, Herlev and Gentofte Hospital, University of Copenhagen, Denmark
| | - Imre Pete
- National Institute of Oncology, Department of Gynecology, Budapest, Hungary
| | - Ildikó Vereczkey
- National Institute of Oncology, Department of Gynecology, Budapest, Hungary
| | - Zsolt Baranyai
- 1st Department of Surgery, Semmelweis University, Budapest, Hungary
| | - Karen Dybkaer
- Department of Clinical Medicine, Aalborg University, Denmark
| | | | | | - Peter Hokland
- Department of Clinical Medicine, Department of Haematology, Aarhus University Hospital, Denmark
| | - Jacob Rosenberg
- Department of Surgery, Herlev and Gentofte Hospital, University of Copenhagen, Denmark
| | - Ulrik Baandrup
- Center for Clinical Research, North Denmark Regional Hospital and Department of Clinical Medicine, Aalborg University, Hjørring, Denmark
| | - Thomas Sicheritz-Pontén
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark.,Centre of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Kedah, Malaysia
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Søren Brunak
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Ole Lund
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - Tobias Mourier
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Lasse Vinner
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Jose M G Izarzugaza
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - Lars Peter Nielsen
- Department of Autoimmunology and Biomarkers, Statens Serum Institut, Copenhagen S, Denmark
| | - Anders Johannes Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
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3
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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. Contaminating viral sequences in high-throughput sequencing viromics: a linkage study of 700 sequencing libraries. Clin Microbiol Infect 2019; 25:1277-1285. [PMID: 31059795 DOI: 10.1016/j.cmi.2019.04.028] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 04/12/2019] [Accepted: 04/18/2019] [Indexed: 12/11/2022]
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.
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Affiliation(s)
- M Asplund
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
| | - K R Kjartansdóttir
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - S Mollerup
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - L Vinner
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - H Fridholm
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark; Department of Autoimmunology and Biomarkers, Statens Serum Institut, Copenhagen, Denmark
| | - J A R Herrera
- Disease Systems Biology Programme, Panum Instituttet, Copenhagen, Denmark; Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - J Friis-Nielsen
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - T A Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - R H Jensen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - I B Nielsen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - S R Richter
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - A Rey-Iglesia
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - M L Matey-Hernandez
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - D E Alquezar-Planas
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - P V S Olsen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - T Sicheritz-Pontén
- 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
| | - E Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - O Lund
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - S Brunak
- Disease Systems Biology Programme, Panum Instituttet, Copenhagen, Denmark; Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - T Mourier
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - L P Nielsen
- Department of Autoimmunology and Biomarkers, Statens Serum Institut, Copenhagen, Denmark
| | - J M G Izarzugaza
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - A J Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
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4
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Olesen ML, Jørgensen LL, Blixenkrone-Møller M, Sandberg E, Frandsen PL, Østergaard E, Bækdahl ER, Fridholm H, Fomsgaard A, Rosenstierne MW. Screening for viral extraneous agents in live-attenuated avian vaccines by using a microbial microarray and sequencing. Biologicals 2018; 51:37-45. [DOI: 10.1016/j.biologicals.2017.10.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 06/30/2017] [Accepted: 10/17/2017] [Indexed: 11/28/2022] Open
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5
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Mollerup S, Fridholm H, Vinner L, Kjartansdóttir KR, Friis-Nielsen J, Asplund M, Herrera JAR, Steiniche T, Mourier T, Brunak S, Willerslev E, Izarzugaza JMG, Hansen AJ, Nielsen LP. Cutavirus in Cutaneous Malignant Melanoma. Emerg Infect Dis 2017; 23:363-365. [PMID: 28098541 PMCID: PMC5324802 DOI: 10.3201/eid2302.161564] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
A novel human protoparvovirus related to human bufavirus and preliminarily named cutavirus has been discovered. We detected cutavirus in a sample of cutaneous malignant melanoma by using viral enrichment and high-throughput sequencing. The role of cutaviruses in cutaneous cancers remains to be investigated.
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6
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Hansen TA, Mollerup S, Nguyen NP, White NE, Coghlan M, Alquezar-Planas DE, Joshi T, Jensen RH, Fridholm H, Kjartansdóttir KR, Mourier T, Warnow T, Belsham GJ, Bunce M, Willerslev E, Nielsen LP, Vinner L, Hansen AJ. High diversity of picornaviruses in rats from different continents revealed by deep sequencing. Emerg Microbes Infect 2016; 5:e90. [PMID: 27530749 PMCID: PMC5034103 DOI: 10.1038/emi.2016.90] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 05/30/2016] [Accepted: 06/13/2016] [Indexed: 12/02/2022]
Abstract
Outbreaks of zoonotic diseases in humans and livestock are not uncommon, and an important component in containment of such emerging viral diseases is rapid and reliable diagnostics. Such methods are often PCR-based and hence require the availability of sequence data from the pathogen. Rattus norvegicus (R. norvegicus) is a known reservoir for important zoonotic pathogens. Transmission may be direct via contact with the animal, for example, through exposure to its faecal matter, or indirectly mediated by arthropod vectors. Here we investigated the viral content in rat faecal matter (n=29) collected from two continents by analyzing 2.2 billion next-generation sequencing reads derived from both DNA and RNA. Among other virus families, we found sequences from members of the Picornaviridae to be abundant in the microbiome of all the samples. Here we describe the diversity of the picornavirus-like contigs including near-full-length genomes closely related to the Boone cardiovirus and Theiler's encephalomyelitis virus. From this study, we conclude that picornaviruses within R. norvegicus are more diverse than previously recognized. The virome of R. norvegicus should be investigated further to assess the full potential for zoonotic virus transmission.
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Affiliation(s)
- Thomas Arn Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark
| | - Sarah Mollerup
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark
| | - Nam-Phuong Nguyen
- Carl R. Woese Institute for Genomic Biology, The University of Illinois at Urbana-Champaign, Urbana, IL 61801-2302, USA
| | - Nicole E White
- Trace and Environmental DNA Lab and Australian Wildlife Forensic Services, Curtin University, Perth, Western Australia 6102, Australia
| | - Megan Coghlan
- Trace and Environmental DNA Lab and Australian Wildlife Forensic Services, Curtin University, Perth, Western Australia 6102, Australia
| | - David E Alquezar-Planas
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark
| | - Tejal Joshi
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, DK-2800 Kongens Lyngby, Denmark
| | - Randi Holm Jensen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark
| | - Helena Fridholm
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.,Virus Research and Development, Statens Serum Institut, DK-2300 Copenhagen, Denmark
| | - Kristín Rós Kjartansdóttir
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark
| | - Tobias Mourier
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark
| | - Tandy Warnow
- Departments of Bioengineering and Computer Science, The University of Illinois at Urbana-Champaign, Urbana, IL 61801-2302, USA
| | - Graham J Belsham
- National Veterinary Institute, Technical University of Denmark, Lindholm, DK-4771 Kalvehave, Denmark
| | - Michael Bunce
- Trace and Environmental DNA Lab and Australian Wildlife Forensic Services, Curtin University, Perth, Western Australia 6102, Australia
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark
| | - Lars Peter Nielsen
- Department of Autoimmunology and Biomarkers, Statens Serum Institut, DK-2300 Copenhagen, Denmark
| | - Lasse Vinner
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark
| | - Anders Johannes Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark
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7
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Friis-Nielsen J, Kjartansdóttir KR, Mollerup S, Asplund M, Mourier T, Jensen RH, Hansen TA, Rey-Iglesia A, Richter SR, Nielsen IB, Alquezar-Planas DE, Olsen PVS, Vinner L, Fridholm H, Nielsen LP, Willerslev E, Sicheritz-Pontén T, Lund O, Hansen AJ, Izarzugaza JMG, Brunak S. Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers. Viruses 2016; 8:E53. [PMID: 26907326 PMCID: PMC4776208 DOI: 10.3390/v8020053] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 01/29/2016] [Accepted: 02/05/2016] [Indexed: 12/17/2022] Open
Abstract
Virus discovery from high throughput sequencing data often follows a bottom-up approach where taxonomic annotation takes place prior to association to disease. Albeit effective in some cases, the approach fails to detect novel pathogens and remote variants not present in reference databases. We have developed a species independent pipeline that utilises sequence clustering for the identification of nucleotide sequences that co-occur across multiple sequencing data instances. We applied the workflow to 686 sequencing libraries from 252 cancer samples of different cancer and tissue types, 32 non-template controls, and 24 test samples. Recurrent sequences were statistically associated to biological, methodological or technical features with the aim to identify novel pathogens or plausible contaminants that may associate to a particular kit or method. We provide examples of identified inhabitants of the healthy tissue flora as well as experimental contaminants. Unmapped sequences that co-occur with high statistical significance potentially represent the unknown sequence space where novel pathogens can be identified.
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Affiliation(s)
- Jens Friis-Nielsen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
| | - Kristín Rós Kjartansdóttir
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Sarah Mollerup
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Maria Asplund
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Tobias Mourier
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Randi Holm Jensen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Thomas Arn Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Alba Rey-Iglesia
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Stine Raith Richter
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Ida Broman Nielsen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - David E Alquezar-Planas
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Pernille V S Olsen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Lasse Vinner
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Helena Fridholm
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Lars Peter Nielsen
- Department of Autoimmunology and Biomarkers, Statens Serum Institut, DK-2300 Copenhagen S, Denmark.
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Thomas Sicheritz-Pontén
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
| | - Ole Lund
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
| | - Anders Johannes Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Jose M G Izarzugaza
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
| | - Søren Brunak
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
- NNF Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark.
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8
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Jensen RH, Mollerup S, Mourier T, Hansen TA, Fridholm H, Nielsen LP, Willerslev E, Hansen AJ, Vinner L. Target-dependent enrichment of virions determines the reduction of high-throughput sequencing in virus discovery. PLoS One 2015; 10:e0122636. [PMID: 25853649 PMCID: PMC4390369 DOI: 10.1371/journal.pone.0122636] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 02/23/2015] [Indexed: 11/20/2022] Open
Abstract
Viral infections cause many different diseases stemming both from well-characterized viral pathogens but also from emerging viruses, and the search for novel viruses continues to be of great importance. High-throughput sequencing is an important technology for this purpose. However, viral nucleic acids often constitute a minute proportion of the total genetic material in a sample from infected tissue. Techniques to enrich viral targets in high-throughput sequencing have been reported, but the sensitivity of such methods is not well established. This study compares different library preparation techniques targeting both DNA and RNA with and without virion enrichment. By optimizing the selection of intact virus particles, both by physical and enzymatic approaches, we assessed the effectiveness of the specific enrichment of viral sequences as compared to non-enriched sample preparations by selectively looking for and counting read sequences obtained from shotgun sequencing. Using shotgun sequencing of total DNA or RNA, viral targets were detected at concentrations corresponding to the predicted level, providing a foundation for estimating the effectiveness of virion enrichment. Virion enrichment typically produced a 1000-fold increase in the proportion of DNA virus sequences. For RNA virions the gain was less pronounced with a maximum 13-fold increase. This enrichment varied between the different sample concentrations, with no clear trend. Despite that less sequencing was required to identify target sequences, it was not evident from our data that a lower detection level was achieved by virion enrichment compared to shotgun sequencing.
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Affiliation(s)
- Randi Holm Jensen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
| | - Sarah Mollerup
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Tobias Mourier
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Arn Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Helena Fridholm
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Lars Peter Nielsen
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Anders Johannes Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Lasse Vinner
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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9
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Abstract
Telomeres, the chromatin structures at the ends of eukaryotic chromosomes, are essential for chromosome stability. The telomere terminates with a TG-rich 3' overhang, which is bound by sequence-specific proteins that both protect the end and regulate the telomerase elongation process. Here, we demonstrate the presence of 3' overhangs as long as 200 nt in asynchronously growing cells of the budding yeast Saccharomyces castellii. The 3' overhangs show a wide distribution of 14-200 nt in length, thus resembling the distribution found in human cells. A substantially large fraction of the 3' overhangs resides in the 70-200 nt range. Remarkably, we found an accumulation of a distinct class of 70-nt-long 3' overhangs in the S phase of the cell cycle. Cells without a functional telomerase showed the same wide distribution of 3' overhangs, but significantly, lacked the specific fraction of 70-nt 3' overhangs. Hence, our data show that the highly defined 70-nt 3' overhangs are generated by a telomerase-dependent mechanism, which is uncoupled to the mechanisms producing the bulk of the 3' overhangs. These data provide new insights that will be helpful for deciphering the complex interplay between the specialized telomere replication machinery and the conventional DNA replication.
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Affiliation(s)
- Helena Fridholm
- Department of Biology, Genetics Group, Lund University, Lund, Sweden
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10
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Fridholm H, Everitt E. Virion glycosylation governs integrity and infectivity of infectious pancreatic necrosis virus. J Fish Dis 2011; 34:663-75. [PMID: 21838710 PMCID: PMC7197461 DOI: 10.1111/j.1365-2761.2011.01280.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Revised: 02/09/2011] [Accepted: 03/24/2011] [Indexed: 05/05/2023]
Abstract
The possible importance of the O-linked glycosylation in virion stability and infectivity of infectious pancreatic necrosis virus (IPNV) was analysed. Enzymatic treatment with O-glycosidase of radiolabelled virions under different ionic conditions, to allow for possible alternative exposure of glycosidic enzyme cleavage sites, did not alter the specific infectivity of virions re-isolated after rate-zonal centrifugation in glycerol gradients. As an alternative method to assess the significance of carbohydrates in IPNV integrity, periodate oxidation in the presence of an aldehyde quencher was chosen. Following re-isolation of viruses, a 3-5 (10)log-unit reduction in specific infectivity was revealed and, at higher concentrations, a total disruption or virion aggregation was observed. The loss of infectivity of intact virions was not because of a lack of attachment to cells. Additionally, re-evaluation of reading values from UV-spectra of purified IPNV yielded a specific infectivity of 3 × 10(11) TCID(50)-units mg(-1) of protein and a ratio of 40 virions per TCID(50)-unit in the CHSE-214 cell system.
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Affiliation(s)
- H Fridholm
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PEI, Canada.
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Fridholm H, Eliasson L, Everitt E. Immunogenicity Properties of Authentic and Heterologously Synthesized Structural Protein VP2 of Infectious Pancreatic Necrosis Virus. Viral Immunol 2007; 20:635-48. [DOI: 10.1089/vim.2007.0043] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Helena Fridholm
- Department of Cell and Organism Biology, Lund University, Biology Building, Lund, Sweden
| | - Linda Eliasson
- Department of Cell and Organism Biology, Lund University, Biology Building, Lund, Sweden
| | - Einar Everitt
- Department of Cell and Organism Biology, Lund University, Biology Building, Lund, Sweden
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Fridholm H, Everitt E. Rapid and reproducible infectivity end-point titration of virulent phage in a microplate system. J Virol Methods 2005; 128:67-71. [PMID: 15893387 DOI: 10.1016/j.jviromet.2005.04.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2005] [Revised: 04/06/2005] [Accepted: 04/07/2005] [Indexed: 11/24/2022]
Abstract
The standard method for measuring the number of infectious phages in solution has traditionally been the plaque forming assay. An alternative method is described where the number of lytic, infectious phages is determined in an endpoint titration assay adapted for a microplate system. In this model system, susceptible Escherichia coli B6 at a density of 4 x 10(7) cells/ml, were mixed with an equal volume (100 microl) of PhiX174 diluted serially in a microtest plate. After 3h of incubation on a microplate shaker the endpoint was determined spectrophotometrically and calculated according to the method of Reed and Muench. A well was considered positive for infection if the OD630-value was < or = 10% compared to the OD630-value of the negative control of uninfected cells. ID50-titers were 2.5x higher than the PFU-titers (CV 15%) and the intra assay reproducibility revealed a CV of 9%. The method has several advantages as compared with the conventional PFU-titration. It is less time and material consuming with the possibility to assess several samples at the same time.
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Affiliation(s)
- Helena Fridholm
- Department of Cell and Organism Biology, Lund University, Biology Bldg, Sölvegatan 35, SE-223 62 Lund, Sweden
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