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Kandathil AJ, Blair PW, Lu J, Anantharam R, Kobba K, Robinson ML, Alharthi S, Ndawula EC, Dumler JS, Kakooza F, Lamorde M, Thomas DL, Salzberg SL, Manabe YC. Metagenomic next generation sequencing of plasma RNA for diagnosis of unexplained, acute febrile illness in Uganda. PLoS Negl Trop Dis 2024; 18:e0012451. [PMID: 39298515 PMCID: PMC11460704 DOI: 10.1371/journal.pntd.0012451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 10/08/2024] [Accepted: 08/11/2024] [Indexed: 09/21/2024] Open
Abstract
Metagenomic next generation metagenomic sequencing (mNGS) has proven to be a useful tool in the diagnosis and identification of novel human pathogens and pathogens not identified on routine clinical microbiologic tests. In this study, we applied mNGS to characterize plasma RNA isolated from 42 study participants with unexplained acute febrile illness (AFI) admitted to tertiary referral hospitals in Mubende and Arua, Uganda. Study participants were selected based on clinical criteria suggestive of viral infection (i.e., thrombocytopenia, leukopenia). The study population had a median age of 28 years (IQR:24 to 38.5) and median platelet count of 114 x103 cells/mm3 (IQR:66,500 to 189,800). An average of 25 million 100 bp reads were generated per sample. We identified strong signals from diverse virus, bacteria, fungi, or parasites in 10 (23.8%) of the study participants. These included well recognized pathogens like Helicobacter pylori, human herpes virus-8, Plasmodium falciparum, Neisseria gonorrhoeae, and Rickettsia conorii. We further confirmed Rickettsia conorii infection, the cause of Mediterranean Spotted Fever (MSF), using PCR assays and Sanger sequencing. mNGS was a useful addition for detection of otherwise undetected pathogens and well-recognized non-pathogens. This is the first report to describe the molecular confirmation of a hospitalized case of MSF in sub-Saharan Africa (SSA). Further studies are needed to determine the utility of mNGS for disease surveillance in similar settings.
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Affiliation(s)
- Abraham J. Kandathil
- Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Paul W. Blair
- Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
- Department of Pathology, Uniformed Services University, Bethesda, Maryland, United States of America
| | - Jennifer Lu
- Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Raghavendran Anantharam
- Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Kenneth Kobba
- Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - Matthew L. Robinson
- Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Sultanah Alharthi
- Department of Pathology, Uniformed Services University, Bethesda, Maryland, United States of America
| | - Edgar C. Ndawula
- Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - J. Stephen Dumler
- Department of Pathology, Uniformed Services University, Bethesda, Maryland, United States of America
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Francis Kakooza
- Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - Mohammed Lamorde
- Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - David L. Thomas
- Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Steven L. Salzberg
- Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- Departments of Computer Science and Biostatistics, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Yukari C. Manabe
- Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
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Kandathil AJ, Thomas DL. The Blood Virome: A new frontier in biomedical science. Biomed Pharmacother 2024; 175:116608. [PMID: 38703502 PMCID: PMC11184943 DOI: 10.1016/j.biopha.2024.116608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/12/2024] [Accepted: 04/17/2024] [Indexed: 05/06/2024] Open
Abstract
Recent advances in metagenomic testing opened a new window into the mammalian blood virome. Comprised of well-known viruses like human immunodeficiency virus, hepatitis C virus, and hepatitis B virus, the virome also includes many other eukaryotic viruses and phages whose medical significance, lifecycle, epidemiology, and impact on human health are less well known and thus regarded as commensals. This review synthesizes available information for the so-called commensal virome members that circulate in the blood of humans considering their restriction to and interaction with the human host, their natural history, and their impact on human health and physiology.
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Affiliation(s)
- Abraham J Kandathil
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David L Thomas
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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3
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Richard JC, Blevins E, Dunn CD, Leis EM, Goldberg TL. Viruses of Freshwater Mussels during Mass Mortality Events in Oregon and Washington, USA. Viruses 2023; 15:1719. [PMID: 37632061 PMCID: PMC10458741 DOI: 10.3390/v15081719] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/04/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Freshwater mussels (Unionida) are globally imperiled, in part due to largely unexplained mass mortality events (MMEs). While recent studies have begun to investigate the possibility that mussel MMEs in the Eastern USA may be caused by infectious diseases, mussels in the Western USA have received relatively little attention in this regard. We conducted a two-year epidemiologic investigation of the role of viruses in ongoing MMEs of the Western pearlshell (Margaritifera falcata) and the Western ridged mussel (Gonidea angulata) in the Chehalis River and Columbia River watersheds in the Western USA. We characterized viromes of mussel hemolymph from 5 locations in 2018 and 2020 using metagenomic methods and identified 557 viruses based on assembled contiguous sequences, most of which are novel. We also characterized the distribution and diversity of a previously identified mussel Gammarhabdovirus related to pathogenic finfish viruses. Overall, we found few consistent associations between viruses and mussel health status. Variation in mussel viromes was most strongly driven by location, with little influence from date, species, or health status, though these variables together only explained ~1/3 of variation in virome composition. Our results demonstrate that Western freshwater mussels host remarkably diverse viromes, but no single virus or combination of viruses appears to be associated with morbidity or mortality during MMEs. Our findings have implications for the conservation of imperiled freshwater mussels, including efforts to enhance natural populations through captive propagation.
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Affiliation(s)
- Jordan C. Richard
- Department of Pathobiological Sciences and Freshwater & Marine Sciences Program, University of Wisconsin-Madison, Madison, WI 53706, USA;
- Southwestern Virginia Field Office, U.S. Fish and Wildlife Service, Abingdon, VA 24210, USA
| | - Emilie Blevins
- Xerces Society for Invertebrate Conservation, Portland, OR 97232, USA;
| | - Christopher D. Dunn
- Department of Pathobiological Sciences and Freshwater & Marine Sciences Program, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Eric M. Leis
- La Crosse Fish Health Center, Midwest Fisheries Center, U.S. Fish and Wildlife Service, Onalaska, WI 54650, USA;
| | - Tony L. Goldberg
- Department of Pathobiological Sciences and Freshwater & Marine Sciences Program, University of Wisconsin-Madison, Madison, WI 53706, USA;
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4
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Jurasz H, Pawłowski T, Perlejewski K. Contamination Issue in Viral Metagenomics: Problems, Solutions, and Clinical Perspectives. Front Microbiol 2021; 12:745076. [PMID: 34745046 PMCID: PMC8564396 DOI: 10.3389/fmicb.2021.745076] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/17/2021] [Indexed: 12/16/2022] Open
Abstract
We describe the most common internal and external sources and types of contamination encountered in viral metagenomic studies and discuss their negative impact on sequencing results, particularly for low-biomass samples and clinical applications. We also propose some basic recommendations for reducing the background noise in viral shotgun metagenomic (SM) studies, which would limit the bias introduced by various classes of contaminants. Regardless of the specific viral SM protocol, contamination cannot be totally avoided; in particular, the issue of reagent contamination should always be addressed with high priority. There is an urgent need for the development and validation of standards for viral metagenomic studies especially if viral SM protocols will be more widely applied in diagnostics.
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Affiliation(s)
- Henryk Jurasz
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Tomasz Pawłowski
- Division of Psychotherapy and Psychosomatic Medicine, Department of Psychiatry, Wrocław Medical University, Wrocław, Poland
| | - Karol Perlejewski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
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5
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van Boheemen S, van Rijn AL, Pappas N, Carbo EC, Vorderman RHP, Sidorov I, van T Hof PJ, Mei H, Claas ECJ, Kroes ACM, de Vries JJC. Retrospective Validation of a Metagenomic Sequencing Protocol for Combined Detection of RNA and DNA Viruses Using Respiratory Samples from Pediatric Patients. J Mol Diagn 2020; 22:196-207. [PMID: 31837435 PMCID: PMC7106021 DOI: 10.1016/j.jmoldx.2019.10.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 09/16/2019] [Accepted: 10/07/2019] [Indexed: 02/07/2023] Open
Abstract
Viruses are the main cause of respiratory tract infections. Metagenomic next-generation sequencing (mNGS) enables unbiased detection of all potential pathogens. To apply mNGS in viral diagnostics, sensitive and simultaneous detection of RNA and DNA viruses is needed. Herein, were studied the performance of an in-house mNGS protocol for routine diagnostics of viral respiratory infections with potential for automated pan-pathogen detection. The sequencing protocol and bioinformatics analysis were designed and optimized, including exogenous internal controls. Subsequently, the protocol was retrospectively validated using 25 clinical respiratory samples. The developed protocol using Illumina NextSeq 500 sequencing showed high repeatability. Use of the National Center for Biotechnology Information's RefSeq database as opposed to the National Center for Biotechnology Information's nucleotide database led to enhanced specificity of classification of viral pathogens. A correlation was established between read counts and PCR cycle threshold value. Sensitivity of mNGS, compared with PCR, varied up to 83%, with specificity of 94%, dependent on the cutoff for defining positive mNGS results. Viral pathogens only detected by mNGS, not present in the routine diagnostic workflow, were influenza C, KI polyomavirus, cytomegalovirus, and enterovirus. Sensitivity and analytical specificity of this mNGS protocol were comparable to PCR and higher when considering off-PCR target viral pathogens. One single test detected all potential viral pathogens and simultaneously obtained detailed information on detected viruses.
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Affiliation(s)
- Sander van Boheemen
- Department of Medical Microbiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Anneloes L van Rijn
- Department of Medical Microbiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands.
| | - Nikos Pappas
- Sequencing Analysis Support Core, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Ellen C Carbo
- Department of Medical Microbiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Ruben H P Vorderman
- Sequencing Analysis Support Core, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Igor Sidorov
- Department of Medical Microbiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Peter J van T Hof
- Sequencing Analysis Support Core, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Eric C J Claas
- Department of Medical Microbiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Aloys C M Kroes
- Department of Medical Microbiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Jutte J C de Vries
- Department of Medical Microbiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
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Ji P, Aw TG, Van Bonn W, Rose JB. Evaluation of a portable nanopore-based sequencer for detection of viruses in water. J Virol Methods 2019; 278:113805. [PMID: 31891731 DOI: 10.1016/j.jviromet.2019.113805] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 12/18/2019] [Accepted: 12/19/2019] [Indexed: 12/20/2022]
Abstract
The newly emerged nanopore sequencing technology such as MinION™ allows for real-time detection of long DNA/RNA fragments on a portable device, yet few have examined its performance for environmental viromes. Here we seeded one RNA virus bacteriophage MS2 and one DNA virus bacteriophage PhiX174 into 10 L well water at three levels ranging from 1 to 21,100 plaque-forming units (PFU)/mL. Two workflows were established to maximize the number of sequencing reads of RNA and DNA viruses using MinION™. With dead-end ultrafiltration, PEG precipitation, and random amplification, MinION™ was capable of detecting MS2 at 155 PFU/mL and PhiX174 at 1-2 PFU/mL. While the DNA workflow only detected PhiX174, the RNA workflow detected both MS2 and PhiX174. The virus concentration, or relative abundance of viral nucleic acids in total nucleic acids, is critical to the proportion of viral reads in sequencing results. Our findings also highlight the importance of including control samples in sequencing runs for environmental water samples with low virus abundance.
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Affiliation(s)
- Pan Ji
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824, USA
| | - Tiong Gim Aw
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - William Van Bonn
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824, USA; A. Watson Armour III Center for Animal Health and Welfare, John G. Shedd Aquarium, Chicago, IL 60605, USA
| | - Joan B Rose
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824, USA.
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Collinet A, Garcia G, Wellehan J, Childress A, Carrera-Justiz S. Investigation of astrovirus and bornavirus in the cerebrospinal fluid of dogs clinically diagnosed with meningoencephalitis of unknown etiology. J Vet Intern Med 2019; 34:232-236. [PMID: 31785029 PMCID: PMC6979266 DOI: 10.1111/jvim.15677] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 11/20/2019] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Non-suppurative encephalitides in a variety of species, including humans and dogs, have been linked to infection by astroviruses and bornaviruses. HYPOTHESIS/OBJECTIVES To determine whether or not ribonucleic acid of astroviruses or bornaviruses was present in the cerebrospinal fluid (CSF) of dogs with clinically diagnosed meningoencephalomyelitis of unknown etiology (MUE). ANIMALS Twenty-five client-owned dogs evaluated by CSF analysis at a single university referral hospital. METHODS Prospective case-control study. Cerebrospinal fluid was collected from clinically diagnosed MUE and control cases and evaluated by reverse-transcriptase polymerase chain reaction for the presence of astrovirus and bornavirus. RESULTS Neither astrovirus nor bornavirus nucleic acids were identified in CSF collected from 20 clinically diagnosed MUE and 5 control cases. CONCLUSIONS AND CLINICAL IMPORTANCE The negative results of this investigation suggest that astrovirus and bornavirus are not commonly detectable in CSF of dogs with MUE.
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Affiliation(s)
- Audrey Collinet
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida
| | - Gabriel Garcia
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida
| | - Jim Wellehan
- Department of Comparative Diagnostic and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, Florida
| | - April Childress
- Department of Comparative Diagnostic and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, Florida
| | - Sheila Carrera-Justiz
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida
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8
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Alawi M, Burkhardt L, Indenbirken D, Reumann K, Christopeit M, Kröger N, Lütgehetmann M, Aepfelbacher M, Fischer N, Grundhoff A. DAMIAN: an open source bioinformatics tool for fast, systematic and cohort based analysis of microorganisms in diagnostic samples. Sci Rep 2019; 9:16841. [PMID: 31727957 PMCID: PMC6856179 DOI: 10.1038/s41598-019-52881-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 10/24/2019] [Indexed: 12/12/2022] Open
Abstract
We describe DAMIAN, an open source bioinformatics tool designed for the identification of pathogenic microorganisms in diagnostic samples. By using authentic clinical samples and comparing our results to those from established analysis pipelines as well as conventional diagnostics, we demonstrate that DAMIAN rapidly identifies pathogens in different diagnostic entities, and accurately classifies viral agents down to the strain level. We furthermore show that DAMIAN is able to assemble full-length viral genomes even in samples co-infected with multiple virus strains, an ability which is of considerable advantage for the investigation of outbreak scenarios. While DAMIAN, similar to other pipelines, analyzes single samples to perform classification of sequences according to their likely taxonomic origin, it also includes a tool for cohort-based analysis. This tool uses cross-sample comparisons to identify sequence signatures that are frequently present in a sample group of interest (e.g., a disease-associated cohort), but occur less frequently in control cohorts. As this approach does not require homology searches in databases, it principally allows the identification of not only known, but also completely novel pathogens. Using samples from a meningitis outbreak, we demonstrate the feasibility of this approach in identifying enterovirus as the causative agent.
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Affiliation(s)
- Malik Alawi
- Heinrich-Pette-Institute (HPI), Leibniz Institute for Experimental Virology, Research Group Virus Genomics, Hamburg, Germany.,Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lia Burkhardt
- Heinrich-Pette-Institute (HPI), Leibniz Institute for Experimental Virology, Research Group Virus Genomics, Hamburg, Germany
| | - Daniela Indenbirken
- Heinrich-Pette-Institute (HPI), Leibniz Institute for Experimental Virology, Research Group Virus Genomics, Hamburg, Germany
| | - Kerstin Reumann
- Heinrich-Pette-Institute (HPI), Leibniz Institute for Experimental Virology, Research Group Virus Genomics, Hamburg, Germany
| | - Maximilian Christopeit
- Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Nicolaus Kröger
- Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Marc Lütgehetmann
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Martin Aepfelbacher
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Nicole Fischer
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany. .,German Center for Infection Research, DZIF, partner site Hamburg-Borstel-Lübeck-Riems, Germany.
| | - Adam Grundhoff
- Heinrich-Pette-Institute (HPI), Leibniz Institute for Experimental Virology, Research Group Virus Genomics, Hamburg, Germany. .,German Center for Infection Research, DZIF, partner site Hamburg-Borstel-Lübeck-Riems, Germany.
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9
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Park SJ, Onizuka S, Seki M, Suzuki Y, Iwata T, Nakai K. A systematic sequencing-based approach for microbial contaminant detection and functional inference. BMC Biol 2019; 17:72. [PMID: 31519179 PMCID: PMC6743104 DOI: 10.1186/s12915-019-0690-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 08/20/2019] [Indexed: 12/16/2022] Open
Abstract
Background Microbial contamination poses a major difficulty for successful data analysis in biological and biomedical research. Computational approaches utilizing next-generation sequencing (NGS) data offer promising diagnostics to assess the presence of contaminants. However, as host cells are often contaminated by multiple microorganisms, these approaches require careful attention to intra- and interspecies sequence similarities, which have not yet been fully addressed. Results We present a computational approach that rigorously investigates the genomic origins of sequenced reads, including those mapped to multiple species that have been discarded in previous studies. Through the analysis of large-scale synthetic and public NGS samples, we estimate that 1000–100,000 contaminating microbial reads are detected per million host reads sequenced by RNA-seq. The microbe catalog we established included Cutibacterium as a prevalent contaminant, suggesting that contamination mostly originates from the laboratory environment. Importantly, by applying a systematic method to infer the functional impact of contamination, we revealed that host-contaminant interactions cause profound changes in the host molecular landscapes, as exemplified by changes in inflammatory and apoptotic pathways during Mycoplasma infection of lymphoma cells. Conclusions We provide a computational method for profiling microbial contamination on NGS data and suggest that sources of contamination in laboratory reagents and the experimental environment alter the molecular landscape of host cells leading to phenotypic changes. These findings reinforce the concept that precise determination of the origins and functional impacts of contamination is imperative for quality research and illustrate the usefulness of the proposed approach to comprehensively characterize contamination landscapes. Electronic supplementary material The online version of this article (10.1186/s12915-019-0690-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sung-Joon Park
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8693, Japan
| | - Satoru Onizuka
- Institute of Advanced Biomedical Engineering and Science, Tokyo Women's Medical University, Tokyo, 162-8666, Japan.,Division of Periodontology, Department of Oral Function, Kyushu Dental University, Fukuoka, 803-8580, Japan
| | - Masahide Seki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8568, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8568, Japan
| | - Takanori Iwata
- Institute of Advanced Biomedical Engineering and Science, Tokyo Women's Medical University, Tokyo, 162-8666, Japan.,Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, 113-8549, Japan
| | - Kenta Nakai
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8693, Japan. .,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8568, Japan.
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10
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Pratas D, Hosseini M, Grilo G, Pinho AJ, Silva RM, Caetano T, Carneiro J, Pereira F. Metagenomic Composition Analysis of an Ancient Sequenced Polar Bear Jawbone from Svalbard. Genes (Basel) 2018; 9:E445. [PMID: 30200636 PMCID: PMC6162538 DOI: 10.3390/genes9090445] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/03/2018] [Accepted: 09/03/2018] [Indexed: 12/17/2022] Open
Abstract
The sequencing of ancient DNA samples provides a novel way to find, characterize, and distinguish exogenous genomes of endogenous targets. After sequencing, computational composition analysis enables filtering of undesired sources in the focal organism, with the purpose of improving the quality of assemblies and subsequent data analysis. More importantly, such analysis allows extinct and extant species to be identified without requiring a specific or new sequencing run. However, the identification of exogenous organisms is a complex task, given the nature and degradation of the samples, and the evident necessity of using efficient computational tools, which rely on algorithms that are both fast and highly sensitive. In this work, we relied on a fast and highly sensitive tool, FALCON-meta, which measures similarity against whole-genome reference databases, to analyse the metagenomic composition of an ancient polar bear (Ursus maritimus) jawbone fossil. The fossil was collected in Svalbard, Norway, and has an estimated age of 110,000 to 130,000 years. The FASTQ samples contained 349 GB of nonamplified shotgun sequencing data. We identified and localized, relative to the FASTQ samples, the genomes with significant similarities to reference microbial genomes, including those of viruses, bacteria, and archaea, and to fungal, mitochondrial, and plastidial sequences. Among other striking features, we found significant similarities between modern-human, some bacterial and viral sequences (contamination) and the organelle sequences of wild carrot and tomato relative to the whole samples. For each exogenous candidate, we ran a damage pattern analysis, which in addition to revealing shallow levels of damage in the plant candidates, identified the source as contamination.
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Affiliation(s)
- Diogo Pratas
- Institute of Electronics and Informatics Engineering of Aveiro, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Morteza Hosseini
- Institute of Electronics and Informatics Engineering of Aveiro, University of Aveiro, 3810-193 Aveiro, Portugal.
- Department of Electronics, Telecommunications and Informatics, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Gonçalo Grilo
- Institute of Electronics and Informatics Engineering of Aveiro, University of Aveiro, 3810-193 Aveiro, Portugal.
- Department of Electronics, Telecommunications and Informatics, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Armando J Pinho
- Institute of Electronics and Informatics Engineering of Aveiro, University of Aveiro, 3810-193 Aveiro, Portugal.
- Department of Electronics, Telecommunications and Informatics, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Raquel M Silva
- Institute of Electronics and Informatics Engineering of Aveiro, University of Aveiro, 3810-193 Aveiro, Portugal.
- Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal.
- Institute for Biomedicine, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Tânia Caetano
- Department of Biology, University of Aveiro, University of Aveiro, 3810-193 Aveiro, Portugal.
- Centre for Environmental and Marine Studies, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - João Carneiro
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Matosinhos, Portugal.
| | - Filipe Pereira
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Matosinhos, Portugal.
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11
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Tang KW, Larsson E. Tumour virology in the era of high-throughput genomics. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0265. [PMID: 28893932 PMCID: PMC5597732 DOI: 10.1098/rstb.2016.0265] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/09/2017] [Indexed: 12/12/2022] Open
Abstract
With the advent of massively parallel sequencing, oncogenic viruses in tumours can now be detected in an unbiased and comprehensive manner. Additionally, new viruses or strains can be discovered based on sequence similarity with known viruses. Using this approach, the causative agent for Merkel cell carcinoma was identified. Subsequent studies using data from large collections of tumours have confirmed models built during decades of hypothesis-driven and low-throughput research, and a more detailed and comprehensive description of virus-tumour associations have emerged. Notably, large cohorts and high sequencing depth, in combination with newly developed bioinformatical techniques, have made it possible to rule out several suggested virus-tumour associations with a high degree of confidence. In this review we discuss possibilities, limitations and insights gained from using massively parallel sequencing to characterize tumours with viral content, with emphasis on detection of viral sequences and genomic integration events.This article is part of the themed issue 'Human oncogenic viruses'.
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Affiliation(s)
- Ka-Wei Tang
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 9A, 405 30 Gothenburg, Sweden
| | - Erik Larsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 9A, 405 30 Gothenburg, Sweden
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12
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Chang Y, Moore PS, Weiss RA. Human oncogenic viruses: nature and discovery. Philos Trans R Soc Lond B Biol Sci 2017; 372:20160264. [PMID: 28893931 PMCID: PMC5597731 DOI: 10.1098/rstb.2016.0264] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/24/2017] [Indexed: 12/13/2022] Open
Abstract
Seven kinds of virus collectively comprise an important cause of cancer, particularly in less developed countries and for people with damaged immune systems. Discovered over the past 54 years, most of these viruses are common infections of humankind for which malignancy is a rare consequence. Various cofactors affect the complex interaction between virus and host and the likelihood of cancer emerging. Although individual human tumour viruses exert their malignant effects in different ways, there are common features that illuminate mechanisms of oncogenesis more generally, whether or not there is a viral aetiology.This article is part of the themed issue 'Human oncogenic viruses'.
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Affiliation(s)
- Yuan Chang
- University of Pittsburgh Cancer Institute, 5117 Centre Ave, Res Pav 1.8, Pittsburgh, PA 15213, USA
| | - Patrick S Moore
- University of Pittsburgh Cancer Institute, 5117 Centre Ave, Res Pav 1.8, Pittsburgh, PA 15213, USA
| | - Robin A Weiss
- Division of Infection and Immunity, University College London, Cruciform Bldg 1.3, Gower Street, London WC1 6BT, UK
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13
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Magnetic nanowires for rapid and ultrasensitive isolation of DNA from cervical specimens for the detection of multiple human papillomaviruses genotypes. Biosens Bioelectron 2016; 86:864-870. [DOI: 10.1016/j.bios.2016.07.066] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 07/18/2016] [Accepted: 07/19/2016] [Indexed: 11/22/2022]
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14
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Ngoi CN, Siqueira J, Li L, Deng X, Mugo P, Graham SM, Price MA, Sanders EJ, Delwart E. The plasma virome of febrile adult Kenyans shows frequent parvovirus B19 infections and a novel arbovirus (Kadipiro virus). J Gen Virol 2016; 97:3359-3367. [PMID: 27902331 DOI: 10.1099/jgv.0.000644] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Viral nucleic acids present in the plasma of 498 Kenyan adults with unexplained fever were characterized by metagenomics analysis of 51 sample pools. The highest to lowest fraction of plasma pools was positive for parvovirus B19 (75 %), pegivirus C (GBV-C) (67 %), alpha anellovirus (59 %), gamma anellovirus (55 %), beta anellovirus (41 %), dengue virus genotype 2 (DENV-2) (16 %), human immunodeficiency virus type 1 (6 %), human herpesvirus 6 (6 %), HBV (4 %), rotavirus (4 %), hepatitis B virus (4 %), rhinovirus C (2 %), Merkel cell polyomavirus (MCPyV; 2 %) and Kadipiro virus (2 %). Ranking by overall percentage of viral reads yielded similar results. Characterization of viral nucleic acids in the plasma of a febrile East African population showed a high frequency of parvovirus B19 and DENV infections and detected a reovirus (Kadipiro virus) previously reported only in Asian Culex mosquitoes, providing a baseline to compare with future virome studies to detect emerging viruses in this region.
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Affiliation(s)
- Carolyne N Ngoi
- Centre for Geographic Medicine Research - Coast, Kenya Medical Research Institute, Kilifi, Kenya
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Juliana Siqueira
- Blood Systems Research Institute, San Francisco, CA, USA
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Linlin Li
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Peter Mugo
- Centre for Geographic Medicine Research - Coast, Kenya Medical Research Institute, Kilifi, Kenya
| | - Susan M Graham
- Centre for Geographic Medicine Research - Coast, Kenya Medical Research Institute, Kilifi, Kenya
- University of Washington, Seattle, WA, USA
| | - Matt A Price
- International AIDS Vaccine Initiative, New York, NY, USA
- Department of Epidemiology and Biostatistics, University of California at San Francisco, CA, USA
| | - Eduard J Sanders
- Centre for Geographic Medicine Research - Coast, Kenya Medical Research Institute, Kilifi, Kenya
- Nuffield Department of Medicine, University of Oxford, Headington, UK
| | - Eric Delwart
- Department of Laboratory Medicine, University of California at San Francisco, CA, USA
- Blood Systems Research Institute, San Francisco, CA, USA
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15
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Kim J, Maeng JH, Lim JS, Son H, Lee J, Lee JH, Kim S. Vecuum: identification and filtration of false somatic variants caused by recombinant vector contamination. Bioinformatics 2016; 32:3072-3080. [PMID: 27334474 DOI: 10.1093/bioinformatics/btw383] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Accepted: 06/14/2016] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Advances in sequencing technologies have remarkably lowered the detection limit of somatic variants to a low frequency. However, calling mutations at this range is still confounded by many factors including environmental contamination. Vector contamination is a continuously occurring issue and is especially problematic since vector inserts are hardly distinguishable from the sample sequences. Such inserts, which may harbor polymorphisms and engineered functional mutations, can result in calling false variants at corresponding sites. Numerous vector-screening methods have been developed, but none could handle contamination from inserts because they are focusing on vector backbone sequences alone. RESULTS We developed a novel method-Vecuum-that identifies vector-originated reads and resultant false variants. Since vector inserts are generally constructed from intron-less cDNAs, Vecuum identifies vector-originated reads by inspecting the clipping patterns at exon junctions. False variant calls are further detected based on the biased distribution of mutant alleles to vector-originated reads. Tests on simulated and spike-in experimental data validated that Vecuum could detect 93% of vector contaminants and could remove up to 87% of variant-like false calls with 100% precision. Application to public sequence datasets demonstrated the utility of Vecuum in detecting false variants resulting from various types of external contamination. AVAILABILITY AND IMPLEMENTATION Java-based implementation of the method is available at http://vecuum.sourceforge.net/ CONTACT: swkim@yuhs.acSupplementary information: Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Junho Kim
- Severance Biomedical Science Institute, Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Ju Heon Maeng
- Severance Biomedical Science Institute, Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Jae Seok Lim
- Graduate School of Medical Science and Engineering, KAIST, Daejeon 34141, South Korea
| | - Hyeonju Son
- Severance Biomedical Science Institute, Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Junehawk Lee
- Department of Convergence Technology Research, Korea Institute of Science and Technology Information, Daejeon 34141, South Korea
| | - Jeong Ho Lee
- Graduate School of Medical Science and Engineering, KAIST, Daejeon 34141, South Korea
| | - Sangwoo Kim
- Severance Biomedical Science Institute, Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, South Korea
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16
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Wang D. Astroviruses-Emerging Neurotropic Pathogens. J Pediatric Infect Dis Soc 2016; 5:188-9. [PMID: 26407288 DOI: 10.1093/jpids/piv058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 08/01/2015] [Indexed: 11/13/2022]
Affiliation(s)
- David Wang
- Departments of Molecular Microbiology and Pathology & Immunology, Washington University School of Medicine in St. Louis, Missouri
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Mikheikin A, Olsen A, Picco L, Payton O, Mishra B, Gimzewski JK, Reed J. High-Speed Atomic Force Microscopy Revealing Contamination in DNA Purification Systems. Anal Chem 2016; 88:2527-32. [PMID: 26878668 DOI: 10.1021/acs.analchem.5b04023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Andrey Mikheikin
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Anita Olsen
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Loren Picco
- Interface
Analysis Centre, H. H. Wills Physics Laboratory, University of Bristol, Tyndall Avenue, Bristol, BS8 1TL, United Kingdom
| | - Oliver Payton
- Interface
Analysis Centre, H. H. Wills Physics Laboratory, University of Bristol, Tyndall Avenue, Bristol, BS8 1TL, United Kingdom
| | - Bud Mishra
- Departments
of Computer Science and Mathematics, Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, United States
| | - James K. Gimzewski
- Department
of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
- California
NanoSystems Institute (CNSI) at the University of California, Los Angeles, Los
Angeles, California 90095, United States
| | - Jason Reed
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
- VCU Massey Cancer Center, Richmond, Virginia 23298, United States
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18
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Practices of Sequencing Quality Assurance. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch53] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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19
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Pandit KR, Nanayakkara IA, Cao W, Raghavan SR, White IM. Capture and Direct Amplification of DNA on Chitosan Microparticles in a Single PCR-Optimal Solution. Anal Chem 2015; 87:11022-9. [DOI: 10.1021/acs.analchem.5b03006] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | | | - Weidong Cao
- Canon U.S. Life
Sciences, Inc., Rockville, Maryland, United States
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20
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Rose G, Wooldridge DJ, Anscombe C, Mee ET, Misra RV, Gharbia S. Challenges of the Unknown: Clinical Application of Microbial Metagenomics. Int J Genomics 2015; 2015:292950. [PMID: 26451363 PMCID: PMC4584244 DOI: 10.1155/2015/292950] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 08/18/2015] [Indexed: 12/17/2022] Open
Abstract
Availability of fast, high throughput and low cost whole genome sequencing holds great promise within public health microbiology, with applications ranging from outbreak detection and tracking transmission events to understanding the role played by microbial communities in health and disease. Within clinical metagenomics, identifying microorganisms from a complex and host enriched background remains a central computational challenge. As proof of principle, we sequenced two metagenomic samples, a known viral mixture of 25 human pathogens and an unknown complex biological model using benchtop technology. The datasets were then analysed using a bioinformatic pipeline developed around recent fast classification methods. A targeted approach was able to detect 20 of the viruses against a background of host contamination from multiple sources and bacterial contamination. An alternative untargeted identification method was highly correlated with these classifications, and over 1,600 species were identified when applied to the complex biological model, including several species captured at over 50% genome coverage. In summary, this study demonstrates the great potential of applying metagenomics within the clinical laboratory setting and that this can be achieved using infrastructure available to nondedicated sequencing centres.
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Affiliation(s)
- Graham Rose
- Genomic Research Unit, Public Health England, Microbiology Services, 61 Colindale Avenue, London NW9 5HT, UK
| | - David J. Wooldridge
- Genomic Research Unit, Public Health England, Microbiology Services, 61 Colindale Avenue, London NW9 5HT, UK
| | - Catherine Anscombe
- Genomic Research Unit, Public Health England, Microbiology Services, 61 Colindale Avenue, London NW9 5HT, UK
| | - Edward T. Mee
- Division of Virology, National Institute for Biological Standards and Control, Medicines and Healthcare Products Regulatory Agency, South Mimms, Hertfordshire EN6 3QG, UK
| | - Raju V. Misra
- Genomic Research Unit, Public Health England, Microbiology Services, 61 Colindale Avenue, London NW9 5HT, UK
| | - Saheer Gharbia
- Genomic Research Unit, Public Health England, Microbiology Services, 61 Colindale Avenue, London NW9 5HT, UK
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21
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Mee ET, Minor PD, Martin J. High resolution identity testing of inactivated poliovirus vaccines. Vaccine 2015; 33:3533-41. [PMID: 26049003 PMCID: PMC4504004 DOI: 10.1016/j.vaccine.2015.05.052] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 05/19/2015] [Accepted: 05/21/2015] [Indexed: 12/02/2022]
Abstract
Identity testing is a critical step in the quality control process. Serological testing is the current approved method, but has certain limitations. Existing molecular methods (qPCR) provide information about small genomic regions. Random amplification and shotgun sequencing provide full genome coverage. Distinction of highly similar viruses, and manufacturer-specific differences is possible.
Background Definitive identification of poliovirus strains in vaccines is essential for quality control, particularly where multiple wild-type and Sabin strains are produced in the same facility. Sequence-based identification provides the ultimate in identity testing and would offer several advantages over serological methods. Methods We employed random RT-PCR and high throughput sequencing to recover full-length genome sequences from monovalent and trivalent poliovirus vaccine products at various stages of the manufacturing process. Results All expected strains were detected in previously characterised products and the method permitted identification of strains comprising as little as 0.1% of sequence reads. Highly similar Mahoney and Sabin 1 strains were readily discriminated on the basis of specific variant positions. Analysis of a product known to contain incorrect strains demonstrated that the method correctly identified the contaminants. Conclusion Random RT-PCR and shotgun sequencing provided high resolution identification of vaccine components. In addition to the recovery of full-length genome sequences, the method could also be easily adapted to the characterisation of minor variant frequencies and distinction of closely related products on the basis of distinguishing consensus and low frequency polymorphisms.
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Affiliation(s)
- Edward T Mee
- Division of Virology, National Institute for Biological Standards and Control, Medicines and Healthcare products Regulatory Agency, South Mimms EN6 3QG, Hertfordshire, UK.
| | - Philip D Minor
- Division of Virology, National Institute for Biological Standards and Control, Medicines and Healthcare products Regulatory Agency, South Mimms EN6 3QG, Hertfordshire, UK
| | - Javier Martin
- Division of Virology, National Institute for Biological Standards and Control, Medicines and Healthcare products Regulatory Agency, South Mimms EN6 3QG, Hertfordshire, UK
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22
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Wang J, Moore NE, Murray ZL, McInnes K, White DJ, Tompkins DM, Hall RJ. Discovery of novel virus sequences in an isolated and threatened bat species, the New Zealand lesser short-tailed bat (Mystacina tuberculata). J Gen Virol 2015; 96:2442-2452. [PMID: 25900137 PMCID: PMC4681071 DOI: 10.1099/vir.0.000158] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Bats harbour a diverse array of viruses, including significant human pathogens. Extensive metagenomic studies of material from bats, in particular guano, have revealed a large number of novel or divergent viral taxa that were previously unknown. New Zealand has only two extant indigenous terrestrial mammals, which are both bats, Mystacina tuberculata (the lesser short-tailed bat) and Chalinolobus tuberculatus (the long-tailed bat). Until the human introduction of exotic mammals, these species had been isolated from all other terrestrial mammals for over 1 million years (potentially over 16 million years for M. tuberculata). Four bat guano samples were collected from M. tuberculata roosts on the isolated offshore island of Whenua hou (Codfish Island) in New Zealand. Metagenomic analysis revealed that this species still hosts a plethora of divergent viruses. Whilst the majority of viruses detected were likely to be of dietary origin, some putative vertebrate virus sequences were identified. Papillomavirus, polyomavirus, calicivirus and hepevirus were found in the metagenomic data and subsequently confirmed using independent PCR assays and sequencing. The new hepevirus and calicivirus sequences may represent new genera within these viral families. Our findings may provide an insight into the origins of viral families, given their detection in an isolated host species.
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Affiliation(s)
- Jing Wang
- Institute of Environmental Science & Research (ESR), at the National Centre for Biosecurity & Infectious Disease, PO Box 40158, Upper Hutt 5140, New Zealand
| | - Nicole E Moore
- Institute of Environmental Science & Research (ESR), at the National Centre for Biosecurity & Infectious Disease, PO Box 40158, Upper Hutt 5140, New Zealand
| | - Zak L Murray
- Institute of Environmental Science & Research (ESR), at the National Centre for Biosecurity & Infectious Disease, PO Box 40158, Upper Hutt 5140, New Zealand
| | - Kate McInnes
- Department of Conservation, , 18-32 Manners Street, PO Box 6011, Wellington, New Zealand
| | - Daniel J White
- Landcare Research, Private Bag 1930, Dunedin, New Zealand
| | | | - Richard J Hall
- Institute of Environmental Science & Research (ESR), at the National Centre for Biosecurity & Infectious Disease, PO Box 40158, Upper Hutt 5140, New Zealand
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23
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Hall RJ, Draper JL, Nielsen FGG, Dutilh BE. Beyond research: a primer for considerations on using viral metagenomics in the field and clinic. Front Microbiol 2015; 6:224. [PMID: 25859244 PMCID: PMC4373370 DOI: 10.3389/fmicb.2015.00224] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 03/06/2015] [Indexed: 11/23/2022] Open
Abstract
Powered by recent advances in next-generation sequencing technologies, metagenomics has already unveiled vast microbial biodiversity in a range of environments, and is increasingly being applied in clinics for difficult-to-diagnose cases. It can be tempting to suggest that metagenomics could be used as a “universal test” for all pathogens without the need to conduct lengthy serial testing using specific assays. While this is an exciting prospect, there are issues that need to be addressed before metagenomic methods can be applied with rigor as a diagnostic tool, including the potential for incidental findings, unforeseen consequences for trade and regulatory authorities, privacy and cultural issues, data sharing, and appropriate reporting of results to end-users. These issues will require consideration and discussion across a range of disciplines, with inclusion of scientists, ethicists, clinicians, diagnosticians, health practitioners, and ultimately the public. Here, we provide a primer for consideration on some of these issues.
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Affiliation(s)
- Richard J Hall
- Institute of Environmental Science and Research, National Centre for Biosecurity and Infectious Disease, Upper Hutt New Zealand
| | - Jenny L Draper
- Ministry for Primary Industries Animal Health Laboratory, National Centre for Biosecurity and Infectious Disease, Upper Hutt New Zealand
| | | | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht Netherlands ; Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen Netherlands ; Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro Brazil
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24
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Houldcroft CJ, Breuer J. Tales from the crypt and coral reef: the successes and challenges of identifying new herpesviruses using metagenomics. Front Microbiol 2015; 6:188. [PMID: 25821447 PMCID: PMC4358218 DOI: 10.3389/fmicb.2015.00188] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 02/20/2015] [Indexed: 12/14/2022] Open
Abstract
Herpesviruses are ubiquitous double-stranded DNA viruses infecting many animals, with the capacity to cause disease in both immunocompetent and immunocompromised hosts. Different herpesviruses have different cell tropisms, and have been detected in a diverse range of tissues and sample types. Metagenomics—encompassing viromics—analyses the nucleic acid of a tissue or other sample in an unbiased manner, making few or no prior assumptions about which viruses may be present in a sample. This approach has successfully discovered a number of novel herpesviruses. Furthermore, metagenomic analysis can identify herpesviruses with high degrees of sequence divergence from known herpesviruses and does not rely upon culturing large quantities of viral material. Metagenomics has had success in two areas of herpesvirus sequencing: firstly, the discovery of novel exogenous and endogenous herpesviruses in primates, bats and cnidarians; and secondly, in characterizing large areas of the genomes of herpesviruses previously only known from small fragments, revealing unexpected diversity. This review will discuss the successes and challenges of using metagenomics to identify novel herpesviruses, and future directions within the field.
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Affiliation(s)
- Charlotte J Houldcroft
- Infection, Inflammation and Rheumatology, Institute of Child Health, University College London , London, UK
| | - Judith Breuer
- Infection, Inflammation and Rheumatology, Institute of Child Health, University College London , London, UK ; Division of Infection and Immunity, University College London , London, UK
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Sajantila A. Editors' Pick: Contamination has always been the issue! INVESTIGATIVE GENETICS 2014; 5:106. [PMID: 25551017 PMCID: PMC4279886 DOI: 10.1186/s13323-014-0017-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 12/03/2014] [Indexed: 11/10/2022]
Affiliation(s)
- Antti Sajantila
- University of Helsinki, Department of Forensic Medicine, P.O.Box 40, 00014 Helsinki, Finland
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26
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Li L, Deng X, Mee ET, Collot-Teixeira S, Anderson R, Schepelmann S, Minor PD, Delwart E. Comparing viral metagenomics methods using a highly multiplexed human viral pathogens reagent. J Virol Methods 2014; 213:139-46. [PMID: 25497414 PMCID: PMC4344864 DOI: 10.1016/j.jviromet.2014.12.002] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 11/26/2014] [Accepted: 12/03/2014] [Indexed: 10/29/2022]
Abstract
Unbiased metagenomic sequencing holds significant potential as a diagnostic tool for the simultaneous detection of any previously genetically described viral nucleic acids in clinical samples. Viral genome sequences can also inform on likely phenotypes including drug susceptibility or neutralization serotypes. In this study, different variables of the laboratory methods often used to generate viral metagenomics libraries were compared for their abilities to detect multiple viruses and generate full genome coverage. A biological reagent consisting of 25 different human RNA and DNA viral pathogens was used to estimate the effect of filtration and nuclease digestion, DNA/RNA extraction methods, pre-amplification and the use of different library preparation kits on the detection of viral nucleic acids. Filtration and nuclease treatment led to slight decreases in the percentage of viral sequence reads and number of viruses detected. For nucleic acid extractions silica spin columns improved viral sequence recovery relative to magnetic beads and Trizol extraction. Pre-amplification using random RT-PCR while generating more viral sequence reads resulted in detection of fewer viruses, more overlapping sequences, and lower genome coverage. The ScriptSeq library preparation method retrieved more viruses and a greater fraction of their genomes than the TruSeq and Nextera methods. Viral metagenomics sequencing was able to simultaneously detect up to 22 different viruses in the biological reagent analyzed including all those detected by qPCR. Further optimization will be required for the detection of viruses in biologically more complex samples such as tissues, blood, or feces.
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Affiliation(s)
- Linlin Li
- Blood Systems Research Institute, San Francisco, CA, USA; Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, CA, USA; Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Edward T Mee
- Division of Virology, National Institute for Biological Reagents and Control, Medicines and Healthcare Products Regulatory Agency, Hertfordshire, UK
| | - Sophie Collot-Teixeira
- Division of Virology, National Institute for Biological Reagents and Control, Medicines and Healthcare Products Regulatory Agency, Hertfordshire, UK
| | - Rob Anderson
- Division of Virology, National Institute for Biological Reagents and Control, Medicines and Healthcare Products Regulatory Agency, Hertfordshire, UK
| | - Silke Schepelmann
- Division of Virology, National Institute for Biological Reagents and Control, Medicines and Healthcare Products Regulatory Agency, Hertfordshire, UK
| | - Philip D Minor
- Division of Virology, National Institute for Biological Reagents and Control, Medicines and Healthcare Products Regulatory Agency, Hertfordshire, UK
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA, USA; Department of Laboratory Medicine, University of California, San Francisco, CA, USA.
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Strong MJ, Xu G, Morici L, Splinter Bon-Durant S, Baddoo M, Lin Z, Fewell C, Taylor CM, Flemington EK. Microbial contamination in next generation sequencing: implications for sequence-based analysis of clinical samples. PLoS Pathog 2014; 10:e1004437. [PMID: 25412476 PMCID: PMC4239086 DOI: 10.1371/journal.ppat.1004437] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The high level of accuracy and sensitivity of next generation sequencing for quantifying genetic material across organismal boundaries gives it tremendous potential for pathogen discovery and diagnosis in human disease. Despite this promise, substantial bacterial contamination is routinely found in existing human-derived RNA-seq datasets that likely arises from environmental sources. This raises the need for stringent sequencing and analysis protocols for studies investigating sequence-based microbial signatures in clinical samples.
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Affiliation(s)
- Michael J. Strong
- Department of Pathology, Tulane University, New Orleans, Louisiana, United States of America
- Tulane Cancer Center, Tulane University, New Orleans, Louisiana, United States of America
| | - Guorong Xu
- Department of Genomic Medicine, University of California, San Diego, California, United States of America
| | - Lisa Morici
- Department of Microbiology and Immunology, Tulane University, New Orleans, Louisiana, United States of America
| | - Sandra Splinter Bon-Durant
- University of Wisconsin Biotechnology Center, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Melody Baddoo
- Department of Pathology, Tulane University, New Orleans, Louisiana, United States of America
- Tulane Cancer Center, Tulane University, New Orleans, Louisiana, United States of America
| | - Zhen Lin
- Department of Pathology, Tulane University, New Orleans, Louisiana, United States of America
- Tulane Cancer Center, Tulane University, New Orleans, Louisiana, United States of America
| | - Claire Fewell
- Department of Pathology, Tulane University, New Orleans, Louisiana, United States of America
- Tulane Cancer Center, Tulane University, New Orleans, Louisiana, United States of America
| | - Christopher M. Taylor
- Department of Microbiology, Immunology & Parasitology, Louisiana State University School of Medicine, New Orleans, Louisiana, United States of America
- Research Institute for Children, Children's Hospital of New Orleans, New Orleans, Louisiana, United States of America
| | - Erik K. Flemington
- Department of Pathology, Tulane University, New Orleans, Louisiana, United States of America
- Tulane Cancer Center, Tulane University, New Orleans, Louisiana, United States of America
- * E-mail:
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28
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Expanding the conversation on high-throughput virome sequencing standards to include consideration of microbial contamination sources. mBio 2014; 5:e01989. [PMID: 25352620 PMCID: PMC4217176 DOI: 10.1128/mbio.01989-14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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Rosseel T, Pardon B, De Clercq K, Ozhelvaci O, Van Borm S. False-positive results in metagenomic virus discovery: a strong case for follow-up diagnosis. Transbound Emerg Dis 2014; 61:293-9. [PMID: 24912559 DOI: 10.1111/tbed.12251] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Indexed: 11/30/2022]
Abstract
A viral metagenomic approach using virion enrichment, random amplification and next-generation sequencing was used to investigate an undiagnosed cluster of dairy cattle presenting with high persistent fever, unresponsive to anti-microbial and anti-inflammatory treatment, diarrhoea and redness of nose and teat. Serum and whole blood samples were taken in the predicted hyperviraemic state of an animal that a few days later presented with these clinical signs. Bioinformatics analysis of the resulting data from the DNA virus identification workflow (a total of 32 757 sequences with average read length 335 bases) initially demonstrated the presence of parvovirus-like sequences in the tested blood sample. Thorough follow-up using specific real-time RT-PCR assays targeting the detected sequence fragments confirmed the presence of these sequences in the original sample as well as in a sample of an additional animal, but a contamination with an identical genetic signature in negative extraction controls was demonstrated. Further investigation using an alternative extraction method identified a contamination of the originally used Qiagen extraction columns with parvovirus-like nucleic acids or virus particles. Although we did not find any relevant virus that could be associated with the disease, these observations clearly illustrate the importance of using a proper control strategy and follow-up diagnostic tests in any viral metagenomic study.
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Affiliation(s)
- T Rosseel
- Veterinary and Agrochemical Research Centre, Department of Virology, Molecular Platform Unit, Ukkel, Belgium
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Reply to Naccache et al: Viral sequences of NIH-CQV virus, a contamination of DNA extraction method. Proc Natl Acad Sci U S A 2014; 111:E977. [PMID: 24829942 DOI: 10.1073/pnas.1318965111] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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Correction for Xu et al., Hybrid DNA virus in Chinese patients with seronegative hepatitis discovered by deep sequencing. Proc Natl Acad Sci U S A 2014. [DOI: 10.1073/pnas.1402288111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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