101
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Kennedy PGE, Quan PL, Lipkin WI. Viral Encephalitis of Unknown Cause: Current Perspective and Recent Advances. Viruses 2017; 9:E138. [PMID: 28587310 PMCID: PMC5490815 DOI: 10.3390/v9060138] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 05/30/2017] [Accepted: 05/31/2017] [Indexed: 12/26/2022] Open
Abstract
Viral encephalitis causes acute inflammation of the brain parenchyma and is a significant cause of human morbidity and mortality. Although Herpes Simplex encephalitis is the most frequent known cause of fatal sporadic encephalitis in humans, an increasingly wide range of viruses and other microbial pathogens are implicated. Up to 60% of cases of presumed viral encephalitis remain unexplained due to the failure of conventional laboratory techniques to detect an infectious agent. High-throughput DNA sequencing technologies have the potential to detect any microbial nucleic acid present in a biological specimen without any prior knowledge of the target sequence. While there remain challenges intrinsic to these technologies, they have great promise in virus discovery in unexplained encephalitis.
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Affiliation(s)
- Peter G E Kennedy
- Department of Neurology, Institute of Neurological Sciences, Glasgow University, Southern General Hospital, Glasgow G51 4TF, UK.
| | - Phenix-Lan Quan
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 W 168th Street, New York, NY 10032, USA.
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 W 168th Street, New York, NY 10032, USA.
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102
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Molecular Diagnosis of Orthopedic-Device-Related Infection Directly from Sonication Fluid by Metagenomic Sequencing. J Clin Microbiol 2017; 55:2334-2347. [PMID: 28490492 PMCID: PMC5527411 DOI: 10.1128/jcm.00462-17] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 05/08/2017] [Indexed: 01/08/2023] Open
Abstract
Culture of multiple periprosthetic tissue samples is the current gold standard for microbiological diagnosis of prosthetic joint infections (PJI). Additional diagnostic information may be obtained through culture of sonication fluid from explants. However, current techniques can have relatively low sensitivity, with prior antimicrobial therapy and infection by fastidious organisms influencing results. We assessed if metagenomic sequencing of total DNA extracts obtained direct from sonication fluid can provide an alternative rapid and sensitive tool for diagnosis of PJI. We compared metagenomic sequencing with standard aerobic and anaerobic culture in 97 sonication fluid samples from prosthetic joint and other orthopedic device infections. Reads from Illumina MiSeq sequencing were taxonomically classified using Kraken. Using 50 derivation samples, we determined optimal thresholds for the number and proportion of bacterial reads required to identify an infection and confirmed our findings in 47 independent validation samples. Compared to results from sonication fluid culture, the species-level sensitivity of metagenomic sequencing was 61/69 (88%; 95% confidence interval [CI], 77 to 94%; for derivation samples 35/38 [92%; 95% CI, 79 to 98%]; for validation samples, 26/31 [84%; 95% CI, 66 to 95%]), and genus-level sensitivity was 64/69 (93%; 95% CI, 84 to 98%). Species-level specificity, adjusting for plausible fastidious causes of infection, species found in concurrently obtained tissue samples, and prior antibiotics, was 85/97 (88%; 95% CI, 79 to 93%; for derivation samples, 43/50 [86%; 95% CI, 73 to 94%]; for validation samples, 42/47 [89%; 95% CI, 77 to 96%]). High levels of human DNA contamination were seen despite the use of laboratory methods to remove it. Rigorous laboratory good practice was required to minimize bacterial DNA contamination. We demonstrate that metagenomic sequencing can provide accurate diagnostic information in PJI. Our findings, combined with the increasing availability of portable, random-access sequencing technology, offer the potential to translate metagenomic sequencing into a rapid diagnostic tool in PJI.
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103
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Doggett NA, Mukundan H, Lefkowitz EJ, Slezak TR, Chain PS, Morse S, Anderson K, Hodge DR, Pillai S. Culture-Independent Diagnostics for Health Security. Health Secur 2017; 14:122-42. [PMID: 27314653 DOI: 10.1089/hs.2015.0074] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The past decade has seen considerable development in the diagnostic application of nonculture methods, including nucleic acid amplification-based methods and mass spectrometry, for the diagnosis of infectious diseases. The implications of these new culture-independent diagnostic tests (CIDTs) include bypassing the need to culture organisms, thus potentially affecting public health surveillance systems, which continue to use isolates as the basis of their surveillance programs and to assess phenotypic resistance to antimicrobial agents. CIDTs may also affect the way public health practitioners detect and respond to a bioterrorism event. In response to a request from the Department of Homeland Security, Los Alamos National Laboratory and the Centers for Disease Control and Prevention cosponsored a workshop to review the impact of CIDTs on the rapid detection and identification of biothreat agents. Four panel discussions were held that covered nucleic acid amplification-based diagnostics, mass spectrometry, antibody-based diagnostics, and next-generation sequencing. Exploiting the extensive expertise available at this workshop, we identified the key features, benefits, and limitations of the various CIDT methods for providing rapid pathogen identification that are critical to the response and mitigation of a bioterrorism event. After the workshop we conducted a thorough review of the literature, investigating the current state of these 4 culture-independent diagnostic methods. This article combines information from the literature review and the insights obtained at the workshop.
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104
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Moustafa A, Xie C, Kirkness E, Biggs W, Wong E, Turpaz Y, Bloom K, Delwart E, Nelson KE, Venter JC, Telenti A. The blood DNA virome in 8,000 humans. PLoS Pathog 2017; 13:e1006292. [PMID: 28328962 PMCID: PMC5378407 DOI: 10.1371/journal.ppat.1006292] [Citation(s) in RCA: 199] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 04/03/2017] [Accepted: 03/14/2017] [Indexed: 02/06/2023] Open
Abstract
The characterization of the blood virome is important for the safety of blood-derived transfusion products, and for the identification of emerging pathogens. We explored non-human sequence data from whole-genome sequencing of blood from 8,240 individuals, none of whom were ascertained for any infectious disease. Viral sequences were extracted from the pool of sequence reads that did not map to the human reference genome. Analyses sifted through close to 1 Petabyte of sequence data and performed 0.5 trillion similarity searches. With a lower bound for identification of 2 viral genomes/100,000 cells, we mapped sequences to 94 different viruses, including sequences from 19 human DNA viruses, proviruses and RNA viruses (herpesviruses, anelloviruses, papillomaviruses, three polyomaviruses, adenovirus, HIV, HTLV, hepatitis B, hepatitis C, parvovirus B19, and influenza virus) in 42% of the study participants. Of possible relevance to transfusion medicine, we identified Merkel cell polyomavirus in 49 individuals, papillomavirus in blood of 13 individuals, parvovirus B19 in 6 individuals, and the presence of herpesvirus 8 in 3 individuals. The presence of DNA sequences from two RNA viruses was unexpected: Hepatitis C virus is revealing of an integration event, while the influenza virus sequence resulted from immunization with a DNA vaccine. Age, sex and ancestry contributed significantly to the prevalence of infection. The remaining 75 viruses mostly reflect extensive contamination of commercial reagents and from the environment. These technical problems represent a major challenge for the identification of novel human pathogens. Increasing availability of human whole-genome sequences will contribute substantial amounts of data on the composition of the normal and pathogenic human blood virome. Distinguishing contaminants from real human viruses is challenging. Novel sequencing technologies offer insight into the virome in human samples. Here, we identify the viral DNA sequences in blood of over 8,000 individuals undergoing whole genome sequencing. This approach serves to identify 94 viruses; however, many are shown to reflect widespread DNA contamination of commercial reagents or of environmental origin. While this represents a significant limitation to reliably identify novel viruses infecting humans, we could confidently detect sequences and quantify abundance of 19 human viruses in 42% of individuals. Ancestry, sex, and age were important determinants of viral prevalence. This large study calls attention on the challenge of interpreting next generation sequencing data for the identification of novel viruses. However, it serves to categorize the abundance of human DNA viruses using an unbiased technique.
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Affiliation(s)
- Ahmed Moustafa
- Human Longevity Inc., San Diego, California, United States of America
| | - Chao Xie
- Human Longevity Singapore Pte. Ltd., Singapore
| | - Ewen Kirkness
- Human Longevity Inc., San Diego, California, United States of America
| | - William Biggs
- Human Longevity Inc., San Diego, California, United States of America
| | - Emily Wong
- Human Longevity Inc., San Diego, California, United States of America
| | | | - Kenneth Bloom
- Human Longevity Inc., San Diego, California, United States of America
| | - Eric Delwart
- Blood Systems Research Institute, Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Karen E. Nelson
- J. Craig Venter Institute, La Jolla, California, United States of America
| | - J. Craig Venter
- Human Longevity Inc., San Diego, California, United States of America
- J. Craig Venter Institute, La Jolla, California, United States of America
- * E-mail: (JCV); (AT)
| | - Amalio Telenti
- Human Longevity Inc., San Diego, California, United States of America
- J. Craig Venter Institute, La Jolla, California, United States of America
- * E-mail: (JCV); (AT)
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105
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Abstract
Whole-genome sequencing (WGS) of pathogens is becoming increasingly important not only for basic research but also for clinical science and practice. In virology, WGS is important for the development of novel treatments and vaccines, and for increasing the power of molecular epidemiology and evolutionary genomics. In this Opinion article, we suggest that WGS of viruses in a clinical setting will become increasingly important for patient care. We give an overview of different WGS methods that are used in virology and summarize their advantages and disadvantages. Although there are only partially addressed technical, financial and ethical issues in regard to the clinical application of viral WGS, this technique provides important insights into virus transmission, evolution and pathogenesis.
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Affiliation(s)
- Charlotte J. Houldcroft
- Department of Infection, UK; and the Division of Biological Anthropology, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, University of Cambridge, Cambridge CB2 3QG, UK.,
- and the Division of Biological Anthropology, University of Cambridge, Cambridge CB2 3QG, UK.,
| | - Mathew A. Beale
- Division of Infection and Immunity, University College London, London, WC1E 6BT UK
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA Cambridge UK
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK; and at Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK.,
- and at Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK.,
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106
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van Aerle R, Santos EM. Advances in the application of high-throughput sequencing in invertebrate virology. J Invertebr Pathol 2017; 147:145-156. [PMID: 28249815 DOI: 10.1016/j.jip.2017.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 02/22/2017] [Accepted: 02/24/2017] [Indexed: 10/20/2022]
Abstract
Over the last decade, advances in high-throughput sequencing technologies have revolutionised biological research, making it possible for DNA/RNA sequencing of any organism of interest to be undertaken. Sequencing approaches are now routinely used in the detection and characterisation of (novel) viruses, investigation of host-pathogen interactions, and effective development of disease treatment strategies. For the sequencing and identification of viruses of interest, metagenomics approaches using infected host tissue are frequently used, as it is not always possible to culture and isolate these pathogens. High-throughput sequencing can also be used to investigate host-pathogen interactions by investigating (temporal) transcriptomic responses of both the host and virus, potentially leading to the discovery of novel opportunities for treatment and drug targets. In addition, viruses in environmental samples (e.g. water or soil samples) can be identified using eDNA/metagenomics approaches. The promise that recent developments in sequencing brings to the field of invertebrate virology are not devoid of technical challenges, including the need for better laboratory and bioinformatics strategies to sequence and assemble virus genomes within complex tissue or environmental samples, and the difficulties associated with the annotation of the large number of novel viruses being discovered.
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Affiliation(s)
- R van Aerle
- Centre for Environment, Fisheries, and Aquaculture Science (Cefas), Barrack Road, The Nothe, Weymouth, Dorset DT4 8UB, UK.
| | - E M Santos
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK.
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107
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Schlaberg R, Chiu CY, Miller S, Procop GW, Weinstock G. Validation of Metagenomic Next-Generation Sequencing Tests for Universal Pathogen Detection. Arch Pathol Lab Med 2017; 141:776-786. [PMID: 28169558 DOI: 10.5858/arpa.2016-0539-ra] [Citation(s) in RCA: 325] [Impact Index Per Article: 46.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT - Metagenomic sequencing can be used for detection of any pathogens using unbiased, shotgun next-generation sequencing (NGS), without the need for sequence-specific amplification. Proof-of-concept has been demonstrated in infectious disease outbreaks of unknown causes and in patients with suspected infections but negative results for conventional tests. Metagenomic NGS tests hold great promise to improve infectious disease diagnostics, especially in immunocompromised and critically ill patients. OBJECTIVE - To discuss challenges and provide example solutions for validating metagenomic pathogen detection tests in clinical laboratories. A summary of current regulatory requirements, largely based on prior guidance for NGS testing in constitutional genetics and oncology, is provided. DATA SOURCES - Examples from 2 separate validation studies are provided for steps from assay design, and validation of wet bench and bioinformatics protocols, to quality control and assurance. CONCLUSIONS - Although laboratory and data analysis workflows are still complex, metagenomic NGS tests for infectious diseases are increasingly being validated in clinical laboratories. Many parallels exist to NGS tests in other fields. Nevertheless, specimen preparation, rapidly evolving data analysis algorithms, and incomplete reference sequence databases are idiosyncratic to the field of microbiology and often overlooked.
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Affiliation(s)
- Robert Schlaberg
- From the Department of Pathology, University of Utah, and the Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah (Dr Schlaberg); the Departments of Laboratory Medicine and Medicine, University of California, San Francisco (Dr Chiu); the Departments of Pathology and Laboratory Medicine, University of California, San Francisco (Dr Miller); the Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio (Dr Procop); and The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut (Dr Weinstock)
| | - Charles Y Chiu
- From the Department of Pathology, University of Utah, and the Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah (Dr Schlaberg); the Departments of Laboratory Medicine and Medicine, University of California, San Francisco (Dr Chiu); the Departments of Pathology and Laboratory Medicine, University of California, San Francisco (Dr Miller); the Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio (Dr Procop); and The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut (Dr Weinstock)
| | - Steve Miller
- From the Department of Pathology, University of Utah, and the Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah (Dr Schlaberg); the Departments of Laboratory Medicine and Medicine, University of California, San Francisco (Dr Chiu); the Departments of Pathology and Laboratory Medicine, University of California, San Francisco (Dr Miller); the Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio (Dr Procop); and The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut (Dr Weinstock)
| | - Gary W Procop
- From the Department of Pathology, University of Utah, and the Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah (Dr Schlaberg); the Departments of Laboratory Medicine and Medicine, University of California, San Francisco (Dr Chiu); the Departments of Pathology and Laboratory Medicine, University of California, San Francisco (Dr Miller); the Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio (Dr Procop); and The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut (Dr Weinstock)
| | - George Weinstock
- From the Department of Pathology, University of Utah, and the Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah (Dr Schlaberg); the Departments of Laboratory Medicine and Medicine, University of California, San Francisco (Dr Chiu); the Departments of Pathology and Laboratory Medicine, University of California, San Francisco (Dr Miller); the Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio (Dr Procop); and The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut (Dr Weinstock)
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- From the Department of Pathology, University of Utah, and the Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah (Dr Schlaberg); the Departments of Laboratory Medicine and Medicine, University of California, San Francisco (Dr Chiu); the Departments of Pathology and Laboratory Medicine, University of California, San Francisco (Dr Miller); the Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio (Dr Procop); and The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut (Dr Weinstock)
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- From the Department of Pathology, University of Utah, and the Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah (Dr Schlaberg); the Departments of Laboratory Medicine and Medicine, University of California, San Francisco (Dr Chiu); the Departments of Pathology and Laboratory Medicine, University of California, San Francisco (Dr Miller); the Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio (Dr Procop); and The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut (Dr Weinstock)
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108
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Robinson KM, Crabtree J, Mattick JSA, Anderson KE, Dunning Hotopp JC. Distinguishing potential bacteria-tumor associations from contamination in a secondary data analysis of public cancer genome sequence data. MICROBIOME 2017; 5:9. [PMID: 28118849 PMCID: PMC5264480 DOI: 10.1186/s40168-016-0224-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 12/15/2016] [Indexed: 05/09/2023]
Abstract
BACKGROUND A variety of bacteria are known to influence carcinogenesis. Therefore, we sought to investigate if publicly available whole genome and whole transcriptome sequencing data generated by large public cancer genome efforts, like The Cancer Genome Atlas (TCGA), could be used to identify bacteria associated with cancer. The Burrows-Wheeler aligner (BWA) was used to align a subset of Illumina paired-end sequencing data from TCGA to the human reference genome and all complete bacterial genomes in the RefSeq database in an effort to identify bacterial read pairs from the microbiome. RESULTS Through careful consideration of all of the bacterial taxa present in the cancer types investigated, their relative abundance, and batch effects, we were able to identify some read pairs from certain taxa as likely resulting from contamination. In particular, the presence of Mycobacterium tuberculosis complex in the ovarian serous cystadenocarcinoma (OV) and glioblastoma multiforme (GBM) samples was correlated with the sequencing center of the samples. Additionally, there was a correlation between the presence of Ralstonia spp. and two specific plates of acute myeloid leukemia (AML) samples. At the end, associations remained between Pseudomonas-like and Acinetobacter-like read pairs in AML, and Pseudomonas-like read pairs in stomach adenocarcinoma (STAD) that could not be explained through batch effects or systematic contamination as seen in other samples. CONCLUSIONS This approach suggests that it is possible to identify bacteria that may be present in human tumor samples from public genome sequencing data that can be examined further experimentally. More weight should be given to this approach in the future when bacterial associations with diseases are suspected.
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MESH Headings
- Acinetobacter/genetics
- Bacteria/genetics
- Bacteria/isolation & purification
- Base Sequence
- Carcinoma/classification
- Carcinoma/genetics
- Carcinoma/microbiology
- Carcinoma, Ovarian Epithelial
- Chromosome Mapping
- Cystadenocarcinoma, Serous/genetics
- Cystadenocarcinoma, Serous/microbiology
- Databases, Genetic
- Genome, Bacterial
- Genome, Human
- Glioblastoma/genetics
- Glioblastoma/microbiology
- High-Throughput Nucleotide Sequencing
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/microbiology
- Microbiota
- Mycobacterium tuberculosis/genetics
- Neoplasms, Glandular and Epithelial/genetics
- Neoplasms, Glandular and Epithelial/microbiology
- Ovarian Neoplasms/genetics
- Ovarian Neoplasms/microbiology
- Pseudomonas/genetics
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Affiliation(s)
- Kelly M. Robinson
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD USA
| | - Jonathan Crabtree
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD USA
| | - John S. A. Mattick
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD USA
| | - Kathleen E. Anderson
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD USA
| | - Julie C. Dunning Hotopp
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD USA
- Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD USA
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109
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Borner J, Burmester T. Parasite infection of public databases: a data mining approach to identify apicomplexan contaminations in animal genome and transcriptome assemblies. BMC Genomics 2017; 18:100. [PMID: 28103801 PMCID: PMC5244568 DOI: 10.1186/s12864-017-3504-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 01/14/2017] [Indexed: 11/24/2022] Open
Abstract
Background Contaminations from various exogenous sources are a common problem in next-generation sequencing. Another possible source of contaminating DNA are endogenous parasites. On the one hand, undiscovered contaminations of animal sequence assemblies may lead to erroneous interpretation of data; on the other hand, when identified, parasite-derived sequences may provide a valuable source of information. Results Here we show that sequences deriving from apicomplexan parasites can be found in many animal genome and transcriptome projects, which in most cases derived from an infection of the sequenced host specimen. The apicomplexan sequences were extracted from the sequence assemblies using a newly developed bioinformatic pipeline (ContamFinder) and tentatively assigned to distinct taxa employing phylogenetic methods. We analysed 920 assemblies and found 20,907 contigs of apicomplexan origin in 51 of the datasets. The contaminating species were identified as members of the apicomplexan taxa Gregarinasina, Coccidia, Piroplasmida, and Haemosporida. For example, in the platypus genome assembly, we found a high number of contigs derived from a piroplasmid parasite (presumably Theileria ornithorhynchi). For most of the infecting parasite species, no molecular data had been available previously, and some of the datasets contain sequences representing large amounts of the parasite’s gene repertoire. Conclusion Our study suggests that parasite-derived contaminations represent a valuable source of information that can help to discover and identify new parasites, and provide information on previously unknown host-parasite interactions. We, therefore, argue that uncurated assembly data should routinely be made available in addition to the final assemblies. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3504-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Janus Borner
- Institute of Zoology, Biocenter Grindel, University of Hamburg, Martin-Luther-King-Platz 3, D-20146, Hamburg, Germany.
| | - Thorsten Burmester
- Institute of Zoology, Biocenter Grindel, University of Hamburg, Martin-Luther-King-Platz 3, D-20146, Hamburg, Germany.
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110
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Hjelmsø MH, Hellmér M, Fernandez-Cassi X, Timoneda N, Lukjancenko O, Seidel M, Elsässer D, Aarestrup FM, Löfström C, Bofill-Mas S, Abril JF, Girones R, Schultz AC. Evaluation of Methods for the Concentration and Extraction of Viruses from Sewage in the Context of Metagenomic Sequencing. PLoS One 2017; 12:e0170199. [PMID: 28099518 PMCID: PMC5242460 DOI: 10.1371/journal.pone.0170199] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 01/02/2017] [Indexed: 01/18/2023] Open
Abstract
Viral sewage metagenomics is a novel field of study used for surveillance, epidemiological studies, and evaluation of waste water treatment efficiency. In raw sewage human waste is mixed with household, industrial and drainage water, and virus particles are, therefore, only found in low concentrations. This necessitates a step of sample concentration to allow for sensitive virus detection. Additionally, viruses harbor a large diversity of both surface and genome structures, which makes universal viral genomic extraction difficult. Current studies have tackled these challenges in many different ways employing a wide range of viral concentration and extraction procedures. However, there is limited knowledge of the efficacy and inherent biases associated with these methods in respect to viral sewage metagenomics, hampering the development of this field. By the use of next generation sequencing this study aimed to evaluate the efficiency of four commonly applied viral concentrations techniques (precipitation with polyethylene glycol, organic flocculation with skim milk, monolithic adsorption filtration and glass wool filtration) and extraction methods (Nucleospin RNA XS, QIAamp Viral RNA Mini Kit, NucliSENS® miniMAG®, or PowerViral® Environmental RNA/DNA Isolation Kit) to determine the viriome in a sewage sample. We found a significant influence of concentration and extraction protocols on the detected viriome. The viral richness was largest in samples extracted with QIAamp Viral RNA Mini Kit or PowerViral® Environmental RNA/DNA Isolation Kit. Highest viral specificity were found in samples concentrated by precipitation with polyethylene glycol or extracted with Nucleospin RNA XS. Detection of viral pathogens depended on the method used. These results contribute to the understanding of method associated biases, within the field of viral sewage metagenomics, making evaluation of the current literature easier and helping with the design of future studies.
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Affiliation(s)
- Mathis Hjort Hjelmsø
- Research Group for Genomic Epidemiology, The National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
- * E-mail:
| | - Maria Hellmér
- Division of Microbiology and Production, The National Food Institute, Technical University of Denmark, Søborg, Denmark
| | - Xavier Fernandez-Cassi
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology, and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
| | - Natàlia Timoneda
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology, and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
- Institute of Biomedicine of the University of Barcelona, University of Barcelona, Barcelona, Catalonia, Spain
| | - Oksana Lukjancenko
- Research Group for Genomic Epidemiology, The National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Michael Seidel
- Institute of Hydrochemistry, Chair of Analytical Chemistry, Technical University of Munich, Munich, Germany
| | - Dennis Elsässer
- Institute of Hydrochemistry, Chair of Analytical Chemistry, Technical University of Munich, Munich, Germany
| | - Frank M. Aarestrup
- Research Group for Genomic Epidemiology, The National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Charlotta Löfström
- Division of Microbiology and Production, The National Food Institute, Technical University of Denmark, Søborg, Denmark
| | - Sílvia Bofill-Mas
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology, and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
| | - Josep F. Abril
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology, and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
- Institute of Biomedicine of the University of Barcelona, University of Barcelona, Barcelona, Catalonia, Spain
| | - Rosina Girones
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology, and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
| | - Anna Charlotte Schultz
- Division of Microbiology and Production, The National Food Institute, Technical University of Denmark, Søborg, Denmark
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111
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Tosar JP, Cayota A, Eitan E, Halushka MK, Witwer KW. Ribonucleic artefacts: are some extracellular RNA discoveries driven by cell culture medium components? J Extracell Vesicles 2017; 6:1272832. [PMID: 28326168 PMCID: PMC5328325 DOI: 10.1080/20013078.2016.1272832] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 11/29/2016] [Accepted: 12/09/2016] [Indexed: 12/25/2022] Open
Abstract
In a recently published study, Anna Krichevsky and colleagues raise the important question of whether results of in vitro extracellular RNA (exRNA) studies, including extracellular vesicle (EV) investigations, are confounded by the presence of RNA in cell culture medium components such as foetal bovine serum (FBS). The answer, according to their data, is a resounding “yes”. Even after lengthy ultracentrifugation to remove bovine EVs from FBS, the majority of exRNA in FBS remained. Although technical factors may affect the degree of depletion, residual EVs and exRNA in FBS could influence the conclusions of in vitro studies: certainly, for secreted RNA, and possibly also for cell-associated RNA. In this commentary, we critically examine some of the literature in this field, including a recent study from some of the authors of this piece, in light of the Wei et al. study and explore how cell culture-derived RNAs may affect what we think we know about EV RNAs. These findings hold particular consequence as the field moves towards a deeper understanding of EV–RNA associations and potential functions.
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Affiliation(s)
- Juan Pablo Tosar
- Functional Genomics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay; Nuclear Research Center, Faculty of Science, Universidad de la República, Montevideo, Uruguay
| | - Alfonso Cayota
- Functional Genomics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay; Department of Medicine, Faculty of Medicine, Universidad de la República, Montevideo, Uruguay
| | - Erez Eitan
- Laboratory of Neurosciences, National Institute on Aging, National Institutes of Health , Baltimore , MD , USA
| | - Marc K Halushka
- Department of Pathology, The Johns Hopkins University School of Medicine , Baltimore , MD , USA
| | - Kenneth W Witwer
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
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112
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Copy Number Heterogeneity of JC Virus Standards. J Clin Microbiol 2016; 55:824-831. [PMID: 27974546 PMCID: PMC5328450 DOI: 10.1128/jcm.02337-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 12/12/2016] [Indexed: 12/17/2022] Open
Abstract
Quantitative PCR is a diagnostic mainstay of clinical virology, and accurate quantitation of viral load among labs requires the use of international standards. However, the use of multiple passages of viral isolates to obtain sufficient material for international standards may result in genomic changes that complicate their use as quantitative standards. We performed next-generation sequencing to obtain single-nucleotide resolution and relative copy number of JC virus (JCV) clinical standards. Strikingly, the WHO international standard and the Exact v1/v2 prototype standards for JCV showed 8-fold and 4-fold variation in genomic coverage between different loci in the viral genome, respectively, due to large deletions in the large T antigen region. Intriguingly, several of the JCV standards sequenced in this study with large T antigen deletions were cultured in cell lines immortalized using simian virus 40 (SV40) T antigen, suggesting the possibility of transcomplementation in cell culture. Using a cutoff 5% allele fraction for junctional reads, 7 different rearrangements were present in the JC virus sequences present in the WHO standard across multiple library preparations and sequencing runs. Neither the copy number differences nor the rearrangements were observed in a clinical sample with a high copy number of JCV or a plasmid control. These results were also confirmed by the quantitative real-time PCR (qPCR), droplet digital PCR (ddPCR), and Sanger sequencing of multiple rearrangements. In summary, targeting different regions of the same international standard can result in up to an 8-fold difference in quantitation. We recommend the use of next-generation sequencing to validate standards in clinical virology.
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113
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Bullman S, Meyerson M, Kostic AD. Emerging Concepts and Technologies for the Discovery of Microorganisms Involved in Human Disease. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2016; 12:217-244. [PMID: 27959634 DOI: 10.1146/annurev-pathol-012615-044305] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Established infectious agents continue to be a major cause of human morbidity and mortality worldwide. However, the causative agent remains unknown for a wide range of diseases; many of these are suspected to be attributable to yet undiscovered microorganisms. The advent of unbiased high-throughput sequencing and bioinformatics has enabled rapid identification and molecular characterization of known and novel infectious agents in human disease. An exciting era of microbe discovery, now under way, holds great promise for the improvement of global health via the development of antimicrobial therapies, vaccination strategies, targeted public health measures, and probiotic-based preventions and therapies. Here, we review the history of pathogen discovery, discuss improvements and clinical applications for the detection of microbially associated diseases, and explore the challenges and strategies for establishing causation in human disease.
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Affiliation(s)
- Susan Bullman
- Dana-Farber Cancer Institute, Boston, Massachusetts 02215; , .,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Matthew Meyerson
- Dana-Farber Cancer Institute, Boston, Massachusetts 02215; , .,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142.,Harvard Medical School, Boston, Massachusetts 02115
| | - Aleksandar D Kostic
- Research Division, Joslin Diabetes Center, Boston, Massachusetts 02215; .,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115
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114
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Jackson EW, Bistolas KSI, Button JB, Hewson I. Novel Circular Single-Stranded DNA Viruses among an Asteroid, Echinoid and Holothurian (Phylum: Echinodermata). PLoS One 2016; 11:e0166093. [PMID: 27855181 PMCID: PMC5113903 DOI: 10.1371/journal.pone.0166093] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 10/21/2016] [Indexed: 11/24/2022] Open
Abstract
Echinoderms are prone to large population fluctuations that can be mediated by pervasive disease events. For the majority of echinoderm disease events the causative pathogen is unknown. Viruses have only recently been explored as potential pathogens using culture-independent techniques though little information currently exists on echinoderm viruses. In this study, ten circular ssDNA viruses were discovered in tissues among an asteroid (Asterias forbesi), an echinoid (Strongylocentrotus droebachiensis) and a holothurian (Parastichopus californicus) using viral metagenomics. Genome architecture and sequence similarity place these viruses among the rapidly expanding circular rep-encoding single stranded (CRESS) DNA viral group. Multiple genomes from the same tissue were no more similar in sequence identity to each other than when compared to other known CRESS DNA viruses. The results from this study are the first to describe a virus from a holothurian and continue to show the ubiquity of these viruses among aquatic invertebrates.
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Affiliation(s)
- Elliot W. Jackson
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
- * E-mail:
| | - Kalia S. I. Bistolas
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
| | - Jason B. Button
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
| | - Ian Hewson
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
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115
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Miller RR, Uyaguari-Diaz M, McCabe MN, Montoya V, Gardy JL, Parker S, Steiner T, Hsiao W, Nesbitt MJ, Tang P, Patrick DM. Metagenomic Investigation of Plasma in Individuals with ME/CFS Highlights the Importance of Technical Controls to Elucidate Contamination and Batch Effects. PLoS One 2016; 11:e0165691. [PMID: 27806082 PMCID: PMC5091812 DOI: 10.1371/journal.pone.0165691] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 10/17/2016] [Indexed: 12/24/2022] Open
Abstract
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a debilitating disease causing indefinite fatigue. ME/CFS has long been hypothesised to have an infectious cause; however, no specific infectious agent has been identified. We used metagenomics to analyse the RNA from plasma samples from 25 individuals with ME/CFS and compare their microbial content to technical controls as well as three control groups: individuals with alternatively diagnosed chronic Lyme syndrome (N = 13), systemic lupus erythematosus (N = 11), and healthy controls (N = 25). We found that the majority of sequencing reads were removed during host subtraction, thus there was very low microbial RNA content in the plasma. The effects of sample batching and contamination during sample processing proved to outweigh the effects of study group on microbial RNA content, as the few differences in bacterial or viral RNA abundance we did observe between study groups were most likely caused by contamination and batch effects. Our results highlight the importance of including negative controls in all metagenomic analyses, since there was considerable overlap between bacterial content identified in study samples and control samples. For example, Proteobacteria, Firmicutes, Actinobacteria, and Bacteriodes were found in both study samples and plasma-free negative controls. Many of the taxonomic groups we saw in our plasma-free negative control samples have previously been associated with diseases, including ME/CFS, demonstrating how incorrect conclusions may arise if controls are not used and batch effects not accounted for.
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Affiliation(s)
- Ruth R. Miller
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Miguel Uyaguari-Diaz
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Mark N. McCabe
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Vincent Montoya
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Jennifer L. Gardy
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Shoshana Parker
- Centre for Health Evaluation and Outcome Sciences, Vancouver, British Columbia, Canada
| | - Theodore Steiner
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - William Hsiao
- British Columbia Public Health Microbiology and Reference Laboratory, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Patrick Tang
- Department of Pathology, Sidra Medical and Research Center, Doha, Qatar
| | - David M. Patrick
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
- * E-mail:
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116
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Veldhoen N, Hobbs J, Ikonomou G, Hii M, Lesperance M, Helbing CC. Implementation of Novel Design Features for qPCR-Based eDNA Assessment. PLoS One 2016; 11:e0164907. [PMID: 27802293 PMCID: PMC5089736 DOI: 10.1371/journal.pone.0164907] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 09/22/2016] [Indexed: 11/18/2022] Open
Abstract
Environmental stewardship requires timely, accurate information related to the status of a given ecosystem and the species that occupy it. Recent advances in the application of the highly sensitive real-time quantitative polymerase chain reaction (qPCR) towards identification of constituents within environmental DNA (eDNA) now allow targeted detection of the presence of species-specific biological material within a localized geographic region. However, as with all molecular techniques predicated on the specificity and sensitivity of the PCR assay, careful validation of each eDNA qPCR assay in development must be performed both under controlled laboratory conditions and when challenged with field-derived eDNA samples. Such a step-wise approach forms the basis for incorporation of innovative qPCR design features that strengthen the implementation and interpretation of the eDNA assay. This includes empirical determination that the qPCR assay is refractory to the presence of human DNA and the use of a tripartite assay approach comprised of 1) a primer set targeting plant chloroplast that evaluates the presence of amplifiable DNA from field samples to increase confidence in a negative result, 2) an animal group primer set to increase confidence in the assay result, and 3) a species-specific primer set to assess presence of DNA from the target species. To demonstrate this methodology, we generated eDNA assays specific for the North American bullfrog (Lithobates (Rana) catesbeiana) and the Rocky Mountain tailed frog (Ascaphus montanus) and characterized each with respect to detection sensitivity and specificity with demonstrated performance in a field survey scenario. The qPCR design features presented herein address specific challenges of eDNA assays thereby increasing their interpretative power.
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Affiliation(s)
- Nik Veldhoen
- Department of Biochemistry and Microbiology, University of Victoria, P.O. Box 3055, STN CSC, Victoria, British Columbia, V8W 2Y2, Canada
| | - Jared Hobbs
- Hemmera Envirochem Inc., 303–1221 Broad Street, Victoria, British Columbia, V8W 2A4, Canada
| | - Georgios Ikonomou
- Department of Biochemistry and Microbiology, University of Victoria, P.O. Box 3055, STN CSC, Victoria, British Columbia, V8W 2Y2, Canada
| | - Michael Hii
- Department of Biochemistry and Microbiology, University of Victoria, P.O. Box 3055, STN CSC, Victoria, British Columbia, V8W 2Y2, Canada
| | - Mary Lesperance
- Department of Mathematics and Statistics, 3800 Finnerty Road, University of Victoria, Victoria, British Columbia, V8P 5C2, Canada
| | - Caren C. Helbing
- Department of Biochemistry and Microbiology, University of Victoria, P.O. Box 3055, STN CSC, Victoria, British Columbia, V8W 2Y2, Canada
- * E-mail:
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117
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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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118
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Bik EM. The Hoops, Hopes, and Hypes of Human Microbiome Research. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2016; 89:363-373. [PMID: 27698620 PMCID: PMC5045145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Recent developments in sequencing methods and bioinformatics analysis tools have greatly enabled the culture-independent analysis of complex microbial communities associated with environmental samples, plants, and animals. This has led to a spectacular increase in the number of studies on both membership and functionalities of these hitherto invisible worlds, in particular those of the human microbiome. The wide variety in available microbiome tools and platforms can be overwhelming, and making sound conclusions from scientific research can be challenging. Here, I will review 1) the methodological and analytic hoops a good microbiome study has to jump through, including DNA extraction and choice of bioinformatics tools, 2) the hopes this field has generated for diseases such as autism and inflammatory bowel diseases, and 3) some of the hypes that it has created, e.g., by confusing correlation and causation, and the recent pseudoscientific commercialization of microbiome research.
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Affiliation(s)
- Elisabeth M Bik
- Department of Medicine, Division of Infectious Diseases & Geographic Medicine, Stanford University
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119
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Berger JR, Wilson MR. Next-generation sequencing of tissue: A logical extension. NEUROLOGY-NEUROIMMUNOLOGY & NEUROINFLAMMATION 2016; 3:e261. [PMID: 27458600 PMCID: PMC4946770 DOI: 10.1212/nxi.0000000000000261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Joseph R Berger
- Department of Neurology (J.R.B.), Perelman School of Medicine, University of Pennsylvania, Philadelphia; and the Department of Neurology (M.R.W.), University of California San Francisco
| | - Michael R Wilson
- Department of Neurology (J.R.B.), Perelman School of Medicine, University of Pennsylvania, Philadelphia; and the Department of Neurology (M.R.W.), University of California San Francisco
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120
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Flygare S, Simmon K, Miller C, Qiao Y, Kennedy B, Di Sera T, Graf EH, Tardif KD, Kapusta A, Rynearson S, Stockmann C, Queen K, Tong S, Voelkerding KV, Blaschke A, Byington CL, Jain S, Pavia A, Ampofo K, Eilbeck K, Marth G, Yandell M, Schlaberg R. Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling. Genome Biol 2016; 17:111. [PMID: 27224977 PMCID: PMC4880956 DOI: 10.1186/s13059-016-0969-1] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 04/27/2016] [Indexed: 02/07/2023] Open
Abstract
Background High-throughput sequencing enables unbiased profiling of microbial communities, universal pathogen detection, and host response to infectious diseases. However, computation times and algorithmic inaccuracies have hindered adoption. Results We present Taxonomer, an ultrafast, web-tool for comprehensive metagenomics data analysis and interactive results visualization. Taxonomer is unique in providing integrated nucleotide and protein-based classification and simultaneous host messenger RNA (mRNA) transcript profiling. Using real-world case-studies, we show that Taxonomer detects previously unrecognized infections and reveals antiviral host mRNA expression profiles. To facilitate data-sharing across geographic distances in outbreak settings, Taxonomer is publicly available through a web-based user interface. Conclusions Taxonomer enables rapid, accurate, and interactive analyses of metagenomics data on personal computers and mobile devices. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-0969-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Steven Flygare
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Keith Simmon
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA
| | - Chase Miller
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Yi Qiao
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Brett Kennedy
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Tonya Di Sera
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Erin H Graf
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Keith D Tardif
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA
| | - Aurélie Kapusta
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Shawn Rynearson
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Chris Stockmann
- Department of Pediatrics, University of Utah, Salt Lake City, UT, USA
| | - Krista Queen
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Suxiang Tong
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Karl V Voelkerding
- Department of Pathology, University of Utah, Salt Lake City, UT, USA.,ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA
| | - Anne Blaschke
- Department of Pediatrics, University of Utah, Salt Lake City, UT, USA
| | - Carrie L Byington
- Department of Pediatrics, University of Utah, Salt Lake City, UT, USA
| | - Seema Jain
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Andrew Pavia
- Department of Pediatrics, University of Utah, Salt Lake City, UT, USA
| | - Krow Ampofo
- Department of Pediatrics, University of Utah, Salt Lake City, UT, USA
| | - Karen Eilbeck
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA.,USTAR Center for Genetic Discovery, Salt Lake City, UT, USA
| | - Gabor Marth
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA.,USTAR Center for Genetic Discovery, Salt Lake City, UT, USA
| | - Mark Yandell
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA. .,USTAR Center for Genetic Discovery, Salt Lake City, UT, USA.
| | - Robert Schlaberg
- Department of Pathology, University of Utah, Salt Lake City, UT, USA. .,ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA.
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121
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Viral metagenomics applied to blood donors and recipients at high risk for blood-borne infections. BLOOD TRANSFUSION = TRASFUSIONE DEL SANGUE 2016; 14:400-7. [PMID: 27136432 DOI: 10.2450/2016.0160-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 01/18/2016] [Indexed: 02/08/2023]
Abstract
BACKGROUND Characterisation of human-associated viral communities is essential for epidemiological surveillance and to be able to anticipate new potential threats for blood transfusion safety. In high-resource countries, the risk of blood-borne agent transmission of well-known viruses (HBV, HCV, HIV and HTLV) is currently considered to be under control. However, other unknown or unsuspected viruses may be transmitted to recipients by blood-derived products. To investigate this, the virome of plasma from individuals at high risk for parenterally and sexually transmitted infections was analysed by high throughput sequencing (HTS). MATERIALS AND METHODS Purified nucleic acids from two pools of 50 samples from recipients of multiple transfusions, and three pools containing seven plasma samples from either HBV-, HCV- or HIV-infected blood donors, were submitted to HTS. RESULTS Sequences from resident anelloviruses and HPgV were evidenced in all pools. HBV and HCV sequences were detected in pools containing 3.8×10(3) IU/mL of HBV-DNA and 1.7×10(5) IU/mL of HCV-RNA, respectively, whereas no HIV sequence was found in a pool of 150 copies/mL of HIV-RNA. This suggests a lack of sensitivity in HTS performance in detecting low levels of virus. In addition, this study identified other issues, including laboratory contaminants and the uncertainty of taxonomic assignment of short sequence. No sequence suggestive of a new viral species was identified. DISCUSSION This study did not identify any new blood-borne virus in high-risk individuals. However, rare and/or viruses present at very low titre could have escaped our protocol. Our results demonstrate the positive contribution of HTS in the detection of viral sequences in blood donations.
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122
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Schlottau K, Schulze C, Bilk S, Hanke D, Höper D, Beer M, Hoffmann B. Detection of a Novel Bovine Astrovirus in a Cow with Encephalitis. Transbound Emerg Dis 2016; 63:253-9. [PMID: 26948516 DOI: 10.1111/tbed.12493] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Indexed: 02/06/2023]
Abstract
Encephalitis can be caused by several infectious agents, including bacteria, fungi, parasites and viruses. In many cases, the causative agent cannot be identified, because the pathogens are unknown or detection methods are not routinely available. In our case, a 15-month-old cow developed central nervous disorders and died within 6 days after the onset of clinical signs. The histopathology revealed an acute encephalitis, predominantly in the brain stem, and a ganglionitis of the trigeminal ganglion with massive neuronal necroses in both the brain and the ganglion. However, a relevant panel of bacterial and viral infections of cattle could be routinely excluded. Therefore, a brain sample from the cow was analysed using a metagenomics approach with next-generation sequencing. A novel bovine astrovirus (BoAstV-BH89/14) could be identified using the analysis pipeline RIEMS, and the finding could be confirmed with a specific BoAstV RT-qPCR. The genome of the bovine astrovirus (BoAstV), belonging to the family Astroviridae in the genus Mamastrovirus, has a length of 6478 bp. Sequence identities between 71% to a sheep astrovirus and 69% to two recently described bovine astroviruses from the USA and Switzerland were ascertained. The latter were also connected to encephalitis cases in cattle. Like these, the new virus described here was detected in different brain sections using the specific BoAstV RT-qPCR and fluorescent in situ hybridization. In conclusion, while astroviruses so far were mainly found in relation to gastroenteritis in animals and humans, recently detected astrovirus infections were also related to encephalitis.
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Affiliation(s)
- K Schlottau
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - C Schulze
- Berlin-Brandenburg State Laboratory, Frankfurt (Oder), Germany
| | - S Bilk
- Berlin-Brandenburg State Laboratory, Frankfurt (Oder), Germany
| | - D Hanke
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - D Höper
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - M Beer
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - B Hoffmann
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
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123
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Oude Munnink BB, Cotten M, Canuti M, Deijs M, Jebbink MF, van Hemert FJ, Phan MVT, Bakker M, Jazaeri Farsani SM, Kellam P, van der Hoek L. A Novel Astrovirus-Like RNA Virus Detected in Human Stool. Virus Evol 2016; 2:vew005. [PMID: 27774298 PMCID: PMC4989881 DOI: 10.1093/ve/vew005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Several novel clades of astroviruses have recently been identified in human faecal samples. Here, we describe a novel astrovirus-like RNA virus detected in human stools, which we have tentatively named bastrovirus. The genome of this novel virus consists of 6,300 nucleotides organized in three open reading frames. Several sequence divergent strains were detected sharing 67–93 per cent nucleotide identity. Bastrovirus encodes a putative structural protein that is homologous to the capsid protein found in members of the Astroviridae family (45% amino acid identity). The virus also encodes a putative non-structural protein that is genetically distant from astroviruses but shares some homology to the non-structural protein encoded by members of the Hepeviridae family (28% amino acid identity). This novel bastrovirus is present in 8.7 per cent (35/400) of faecal samples collected from 300 HIV-1-positive and 100 HIV-1-negative individuals suggesting common occurrence of the virus. However, whether the source of the virus is infected human cells or other, for example, dietary, remains to be determined.
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Affiliation(s)
- Bas B. Oude Munnink
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Matthew Cotten
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK and
| | - Marta Canuti
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Martin Deijs
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Maarten F. Jebbink
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Formijn J. van Hemert
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - My V. T. Phan
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK and
| | - Margreet Bakker
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Seyed Mohammad Jazaeri Farsani
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Paul Kellam
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK and
- Division of Infection and Immunity, University College London, WC1E 6BT London, UK
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
- *Corresponding author: E-mail:
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124
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Munro AC, Houldcroft C. Human cancers and mammalian retroviruses: should we worry about bovine leukemia virus? Future Virol 2016. [DOI: 10.2217/fvl.16.5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Andrew C Munro
- School of Clinical Medicine, University of Cambridge, Long Road, Cambridge, CB2 0SP, UK
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125
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Walsh GM, Shih AW, Solh Z, Golder M, Schubert P, Fearon M, Sheffield WP. Blood-Borne Pathogens: A Canadian Blood Services Centre for Innovation Symposium. Transfus Med Rev 2016; 30:53-68. [PMID: 26962008 PMCID: PMC7126603 DOI: 10.1016/j.tmrv.2016.02.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 02/18/2016] [Indexed: 12/19/2022]
Abstract
Testing donations for pathogens and deferring selected blood donors have reduced the risk of transmission of known pathogens by transfusion to extremely low levels in most developed countries. Protecting the blood supply from emerging infectious threats remains a serious concern in the transfusion medicine community. Transfusion services can employ indirect measures such as surveillance, hemovigilance, and donor questioning (defense), protein-, or nucleic acid based direct testing (detection), or pathogen inactivation of blood products (destruction) as strategies to mitigate the risk of transmission-transmitted infection. In the North American context, emerging threats currently include dengue, chikungunya, and hepatitis E viruses, and Babesia protozoan parasites. The 2003 SARS and 2014 Ebola outbreaks illustrate the potential of epidemics unlikely to be transmitted by blood transfusion but disruptive to blood systems. Donor-free blood products such as ex vivo generated red blood cells offer a theoretical way to avoid transmission-transmitted infection risk, although biological, engineering, and manufacturing challenges must be overcome before this approach becomes practical. Similarly, next generation sequencing of all nucleic acid in a blood sample is currently possible but impractical for generalized screening. Pathogen inactivation systems are in use in different jurisdictions around the world, and are starting to gain regulatory approval in North America. Cost concerns make it likely that pathogen inactivation will be contemplated by blood operators through the lens of health economics and risk-based decision making, rather than in zero-risk paradigms previously embraced for transfusable products. Defense of the blood supply from infectious disease risk will continue to require innovative combinations of surveillance, detection, and pathogen avoidance or inactivation. A symposium on blood-borne pathogens was held September 26, 2015, in Toronto, Canada. Transmission-transmitted infections remain a threat to the blood supply. The residual risk from established pathogens is small; emerging agents are a concern. Next generation sequencing and donor-free blood are not yet practical approaches. Pathogen inactivation technology is being increasingly used around the world. Health economic concerns will likely guide future advances in this area.
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Affiliation(s)
- Geraldine M Walsh
- Centre for Innovation, Canadian Blood Services, Hamilton, Ottawa, and Vancouver, Canada
| | - Andrew W Shih
- Medical Services and Innovation, Canadian Blood Services, McMaster University, Hamilton, Canada; Pathology and Molecular Medicine, McMaster University, Hamilton, Canada
| | - Ziad Solh
- Medical Services and Innovation, Canadian Blood Services, McMaster University, Hamilton, Canada; Pathology and Molecular Medicine, McMaster University, Hamilton, Canada
| | - Mia Golder
- Centre for Innovation, Canadian Blood Services, Hamilton, Ottawa, and Vancouver, Canada
| | - Peter Schubert
- Centre for Innovation, Canadian Blood Services, Hamilton, Ottawa, and Vancouver, Canada; Centre for Blood Research, University of British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Canada
| | - Margaret Fearon
- Medical Services and Innovation, Canadian Blood Services, McMaster University, Hamilton, Canada; Pathology and Laboratory Medicine, University of Toronto, Canada
| | - William P Sheffield
- Centre for Innovation, Canadian Blood Services, Hamilton, Ottawa, and Vancouver, Canada; Pathology and Molecular Medicine, McMaster University, Hamilton, Canada.
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126
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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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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] [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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128
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Diverse circular replication-associated protein encoding viruses circulating in invertebrates within a lake ecosystem. INFECTION GENETICS AND EVOLUTION 2016; 39:304-316. [PMID: 26873065 DOI: 10.1016/j.meegid.2016.02.011] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 01/30/2016] [Accepted: 02/07/2016] [Indexed: 11/24/2022]
Abstract
Over the last five years next-generation sequencing has become a cost effective and efficient method for identifying known and unknown microorganisms. Access to this technique has dramatically changed the field of virology, enabling a wide range of environmental viral metagenome studies to be undertaken of organisms and environmental samples from polar to tropical regions. These studies have led to the discovery of hundreds of highly divergent single stranded DNA (ssDNA) virus-like sequences encoding replication-associated proteins. Yet, few studies have explored how viruses might be shared in an ecosystem through feeding relationships. Here we identify 169 circular molecules (160 CRESS DNA molecules, nine circular molecules) recovered from a New Zealand freshwater lake, that we have tentatively classified into 51 putatively novel species and five previously described species (DflaCV-3, -5, -6, -8, -10). The CRESS DNA viruses identified in this study were recovered from molluscs (Echyridella menzeisii, Musculium novaezelandiae, Potamopyrgus antipodarum and Physella acuta) and insect larvae (Procordulia grayi, Xanthocnemis zealandica, and Chironomus zealandicus) collected from Lake Sarah, as well as from the lake water and benthic sediments. Extensive diversity was observed across most CRESS DNA molecules recovered. The putative capsid protein of one viral species was found to be most similar to those of members of the Tombusviridae family, thus expanding the number of known RNA-DNA hybrid viruses in nature. We noted a strong association between the CRESS DNA viruses and circular molecules identified in the water and browser organisms (C. zealandicus, P. antipodarum and P. acuta), and between water sediments and undefended prey species (C. zealandicus). However, we were unable to find any significant correlation of viral assemblages to the potential feeding relationships of the host aquatic invertebrates.
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129
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A tale of two approaches: how metagenomics and proteomics are shaping the future of encephalitis diagnostics. Curr Opin Neurol 2016; 28:283-7. [PMID: 25923127 DOI: 10.1097/wco.0000000000000198] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
PURPOSE OF REVIEW We highlight how metagenomics and proteomics-based approaches are being applied to the problem of diagnosis in idiopathic encephalitis. RECENT FINDINGS Low cost, high-throughput next-generation sequencing platforms have enabled unbiased sequencing of biological samples. Rapid sequence-based computational algorithms then determine the source of all the nonhost (e.g., pathogen-derived) nucleic acids in a sample. This approach recently identified a case of neuroleptospirosis, resulting in a patient's dramatic clinical improvement with intravenous penicillin. Metagenomics also enabled the discovery of a neuroinvasive astrovirus in several patients. With regard to autoimmune encephalitis, advances in high throughput and efficient phage display of human peptides resulted in the discovery of autoantibodies against tripartite motif family members in a patient with paraneoplastic encephalitis. A complementary assay using ribosomes to display full-length human proteins identified additional autoantibody targets. SUMMARY Metagenomics and proteomics represent promising avenues of research to improve upon the diagnostic yield of current assays for infectious and autoimmune encephalitis, respectively.
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130
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Abstract
The characterization of the human blood-associated viral community (also called blood virome) is essential for epidemiological surveillance and to anticipate new potential threats for blood transfusion safety. Currently, the risk of blood-borne agent transmission of well-known viruses (HBV, HCV, HIV and HTLV) can be considered as under control in high-resource countries. However, other viruses unknown or unsuspected may be transmitted to recipients by blood-derived products. This is particularly relevant considering that a significant proportion of transfused patients are immunocompromised and more frequently subjected to fatal outcomes. Several measures to prevent transfusion transmission of unknown viruses have been implemented including the exclusion of at-risk donors, leukocyte reduction of donor blood, and physicochemical treatment of the different blood components. However, up to now there is no universal method for pathogen inactivation, which would be applicable for all types of blood components and, equally effective for all viral families. In addition, among available inactivation procedures of viral genomes, some of them are recognized to be less effective on non-enveloped viruses, and inadequate to inactivate higher viral titers in plasma pools or derivatives. Given this, there is the need to implement new methodologies for the discovery of unknown viruses that may affect blood transfusion. Viral metagenomics combined with High Throughput Sequencing appears as a promising approach for the identification and global surveillance of new and/or unexpected viruses that could impair blood transfusion safety.
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Affiliation(s)
- V Sauvage
- Département d'études des agents transmissibles par le sang, Institut national de la transfusion sanguine (INTS), Centre national de référence des hépatites virales B et C et du VIH en transfusion, 75015 Paris, France.
| | - M Eloit
- PathoQuest, bâtiment François-Jacob, 25, rue du Dr-Roux, 75015 Paris, France; Inserm U1117, Biology of Infection Unit, Laboratory of Pathogen Discovery, Institut Pasteur, 28, rue du Docteur-Roux, 75724 Paris, France
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131
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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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132
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Pathogen Discovery. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch7] [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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133
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Ng TFF, Zhang W, Sachsenröder J, Kondov NO, da Costa AC, Vega E, Holtz LR, Wu G, Wang D, Stine CO, Antonio M, Mulvaney US, Muench MO, Deng X, Ambert-Balay K, Pothier P, Vinjé J, Delwart E. A diverse group of small circular ssDNA viral genomes in human and non-human primate stools. Virus Evol 2015; 1:vev017. [PMID: 27774288 PMCID: PMC5014484 DOI: 10.1093/ve/vev017] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Viral metagenomics sequencing of fecal samples from outbreaks of acute gastroenteritis from the US revealed the presence of small circular ssDNA viral genomes encoding a replication initiator protein (Rep). Viral genomes were ∼2.5 kb in length, with bi-directionally oriented Rep and capsid (Cap) encoding genes and a stem loop structure downstream of Rep. Several genomes showed evidence of recombination. By digital screening of an in-house virome database (1.04 billion reads) using BLAST, we identified closely related sequences from cases of unexplained diarrhea in France. Deep sequencing and PCR detected such genomes in 7 of 25 US (28 percent) and 14 of 21 French outbreaks (67 percent). One of eighty-five sporadic diarrhea cases in the Gambia was positive by PCR. Twenty-two complete genomes were characterized showing that viruses from patients in the same outbreaks were closely related suggesting common origins. Similar genomes were also characterized from the stools of captive chimpanzees, a gorilla, a black howler monkey, and a lemur that were more diverse than the human stool-associated genomes. The name smacovirus is proposed for this monophyletic viral clade. Possible tropism include mammalian enteric cells or ingested food components such as infected plants. No evidence of viral amplification was found in immunodeficient mice orally inoculated with smacovirus-positive stool supernatants. A role for smacoviruses in diarrhea, if any, remains to be demonstrated.
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Affiliation(s)
- Terry Fei Fan Ng
- Blood Systems Research Institute, San Francisco, 270 Masonic Ave, San Francisco, CA 94118, USA, ; Department of laboratory Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Wen Zhang
- Blood Systems Research Institute, San Francisco, 270 Masonic Ave, San Francisco, CA 94118, USA, ; Department of Microbiology, School of Medicine, Jiangsu University, Jiangsu, Zhenjiang, China
| | - Jana Sachsenröder
- Blood Systems Research Institute, San Francisco, 270 Masonic Ave, San Francisco, CA 94118, USA, ; Federal Institute for Risk Assessment, Berlin, Germany
| | - Nikola O Kondov
- Blood Systems Research Institute, San Francisco, 270 Masonic Ave, San Francisco, CA 94118, USA
| | - Antonio Charlys da Costa
- Blood Systems Research Institute, San Francisco, 270 Masonic Ave, San Francisco, CA 94118, USA, ; Institute of Tropical Medicine, University of Sao Paulo, São Paulo, Brazil
| | - Everardo Vega
- NCIRD, Polio and Picornavirus Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Guang Wu
- Department of Molecular Microbiology, and
| | - David Wang
- Departments of Molecular Microbiology and Pathology & Immunology, Washington University in St. Louis, St. Louis, MO, USA
| | - Colin O Stine
- University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Usha S Mulvaney
- Blood Systems Research Institute, San Francisco, 270 Masonic Ave, San Francisco, CA 94118, USA
| | - Marcus O Muench
- Blood Systems Research Institute, San Francisco, 270 Masonic Ave, San Francisco, CA 94118, USA, ; Department of laboratory Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, 270 Masonic Ave, San Francisco, CA 94118, USA, ; Department of laboratory Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Katia Ambert-Balay
- National Reference Centre for enteric viruses, Dijon University Hospital, Dijon, France and
| | - Pierre Pothier
- National Reference Centre for enteric viruses, Dijon University Hospital, Dijon, France and
| | - Jan Vinjé
- NCIRD, National Calicivirus Laboratory, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, 270 Masonic Ave, San Francisco, CA 94118, USA, ; Department of laboratory Medicine, University of California at San Francisco, San Francisco, CA, USA
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134
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Kilianski A, Carcel P, Yao S, Roth P, Schulte J, Donarum GB, Fochler ET, Hill JM, Liem AT, Wiley MR, Ladner JT, Pfeffer BP, Elliot O, Petrosov A, Jima DD, Vallard TG, Melendrez MC, Skowronski E, Quan PL, Lipkin WI, Gibbons HS, Hirschberg DL, Palacios GF, Rosenzweig CN. Pathosphere.org: pathogen detection and characterization through a web-based, open source informatics platform. BMC Bioinformatics 2015; 16:416. [PMID: 26714571 PMCID: PMC4696252 DOI: 10.1186/s12859-015-0840-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 12/08/2015] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND The detection of pathogens in complex sample backgrounds has been revolutionized by wide access to next-generation sequencing (NGS) platforms. However, analytical methods to support NGS platforms are not as uniformly available. Pathosphere (found at Pathosphere.org) is a cloud - based open - sourced community tool that allows for communication, collaboration and sharing of NGS analytical tools and data amongst scientists working in academia, industry and government. The architecture allows for users to upload data and run available bioinformatics pipelines without the need for onsite processing hardware or technical support. RESULTS The pathogen detection capabilities hosted on Pathosphere were tested by analyzing pathogen-containing samples sequenced by NGS with both spiked human samples as well as human and zoonotic host backgrounds. Pathosphere analytical pipelines developed by Edgewood Chemical Biological Center (ECBC) identified spiked pathogens within a common sample analyzed by 454, Ion Torrent, and Illumina sequencing platforms. ECBC pipelines also correctly identified pathogens in human samples containing arenavirus in addition to animal samples containing flavivirus and coronavirus. These analytical methods were limited in the detection of sequences with limited homology to previous annotations within NCBI databases, such as parvovirus. Utilizing the pipeline-hosting adaptability of Pathosphere, the analytical suite was supplemented by analytical pipelines designed by the United States Army Medical Research Insititute of Infectious Diseases and Walter Reed Army Institute of Research (USAMRIID-WRAIR). These pipelines were implemented and detected parvovirus sequence in the sample that the ECBC iterative analysis previously failed to identify. CONCLUSIONS By accurately detecting pathogens in a variety of samples, this work demonstrates the utility of Pathosphere and provides a platform for utilizing, modifying and creating pipelines for a variety of NGS technologies developed to detect pathogens in complex sample backgrounds. These results serve as an exhibition for the existing pipelines and web-based interface of Pathosphere as well as the plug-in adaptability that allows for integration of newer NGS analytical software as it becomes available.
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Affiliation(s)
- Andy Kilianski
- Biosciences Division, Edgewood Chemical and Biological Center, 5183 Blackhawk Rd, Aberdeen Proving Ground, Edgewood, MD, 21010, USA.
| | | | - Shijie Yao
- OptiMetrics, Inc, Abingdon, MD, USA. .,Joint Genome Institute, Department of Energy, LBNL, Berkley, CA, USA.
| | - Pierce Roth
- Biosciences Division, Edgewood Chemical and Biological Center, 5183 Blackhawk Rd, Aberdeen Proving Ground, Edgewood, MD, 21010, USA. .,OptiMetrics, Inc, Abingdon, MD, USA.
| | | | | | | | - Jessica M Hill
- Biosciences Division, Edgewood Chemical and Biological Center, 5183 Blackhawk Rd, Aberdeen Proving Ground, Edgewood, MD, 21010, USA. .,OptiMetrics, Inc, Abingdon, MD, USA.
| | - Alvin T Liem
- Biosciences Division, Edgewood Chemical and Biological Center, 5183 Blackhawk Rd, Aberdeen Proving Ground, Edgewood, MD, 21010, USA. .,OptiMetrics, Inc, Abingdon, MD, USA.
| | - Michael R Wiley
- Center for Genome Sciences, United States Medical Research Institute of Infectious Diseases, Ft. Detrick, Frederick, MD, USA.
| | - Jason T Ladner
- Center for Genome Sciences, United States Medical Research Institute of Infectious Diseases, Ft. Detrick, Frederick, MD, USA.
| | - Bradley P Pfeffer
- Center for Genome Sciences, United States Medical Research Institute of Infectious Diseases, Ft. Detrick, Frederick, MD, USA.
| | - Oliver Elliot
- Department of Biomedical Informatics, Columbia University, New York, NY, USA.
| | - Alexandra Petrosov
- The Center for Infection and Immunity, Columbia University, New York, NY, USA.
| | - Dereje D Jima
- Walter Reed Army Institute of Research, Viral Diseases Branch, Silver Spring, MD, USA.
| | - Tyghe G Vallard
- Walter Reed Army Institute of Research, Viral Diseases Branch, Silver Spring, MD, USA.
| | - Melanie C Melendrez
- Walter Reed Army Institute of Research, Viral Diseases Branch, Silver Spring, MD, USA.
| | | | - Phenix-Lan Quan
- The Center for Infection and Immunity, Columbia University, New York, NY, USA.
| | - W Ian Lipkin
- The Center for Infection and Immunity, Columbia University, New York, NY, USA.
| | - Henry S Gibbons
- Biosciences Division, Edgewood Chemical and Biological Center, 5183 Blackhawk Rd, Aberdeen Proving Ground, Edgewood, MD, 21010, USA.
| | - David L Hirschberg
- The Center for Infection and Immunity, Columbia University, New York, NY, USA. .,Department of Interdisciplinary Arts and Sciences, University of Washington Tacoma, Tacoma, WA, USA.
| | - Gustavo F Palacios
- Center for Genome Sciences, United States Medical Research Institute of Infectious Diseases, Ft. Detrick, Frederick, MD, USA.
| | - C Nicole Rosenzweig
- Biosciences Division, Edgewood Chemical and Biological Center, 5183 Blackhawk Rd, Aberdeen Proving Ground, Edgewood, MD, 21010, USA.
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135
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Development of a candidate reference material for adventitious virus detection in vaccine and biologicals manufacturing by deep sequencing. Vaccine 2015; 34:2035-43. [PMID: 26709640 PMCID: PMC4823300 DOI: 10.1016/j.vaccine.2015.12.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/30/2015] [Accepted: 12/05/2015] [Indexed: 02/05/2023]
Abstract
Deep sequencing has potential as an improved adventitious virus screening method. 15 laboratories sequenced a common reagent containing 25 target viruses. 6 viruses were detected by all lab, the remainder were detected by 4–14 labs. A wide range of sample preparation and bioinformatics methods is currently used. A common reference material is essential to enable results to be compared.
Background Unbiased deep sequencing offers the potential for improved adventitious virus screening in vaccines and biotherapeutics. Successful implementation of such assays will require appropriate control materials to confirm assay performance and sensitivity. Methods A common reference material containing 25 target viruses was produced and 16 laboratories were invited to process it using their preferred adventitious virus detection assay. Results Fifteen laboratories returned results, obtained using a wide range of wet-lab and informatics methods. Six of 25 target viruses were detected by all laboratories, with the remaining viruses detected by 4–14 laboratories. Six non-target viruses were detected by three or more laboratories. Conclusion The study demonstrated that a wide range of methods are currently used for adventitious virus detection screening in biological products by deep sequencing and that they can yield significantly different results. This underscores the need for common reference materials to ensure satisfactory assay performance and enable comparisons between laboratories.
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Rowley AH, Wylie KM, Kim KYA, Pink AJ, Yang A, Reindel R, Baker SC, Shulman ST, Orenstein JM, Lingen MW, Weinstock GM, Wylie TN. The transcriptional profile of coronary arteritis in Kawasaki disease. BMC Genomics 2015; 16:1076. [PMID: 26679344 PMCID: PMC4683744 DOI: 10.1186/s12864-015-2323-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 12/15/2015] [Indexed: 12/31/2022] Open
Abstract
Background Kawasaki Disease (KD) can cause potentially life-threatening coronary arteritis in young children, and has a likely infectious etiology. Transcriptome profiling is a powerful approach to investigate gene expression in diseased tissues. RNA sequencing of KD coronary arteries could elucidate the etiology and the host response, with the potential to improve KD diagnosis and/or treatment. Methods Deep RNA sequencing was performed on KD (n = 8) and childhood control (n = 7) coronary artery tissues, revealing 1074 differentially expressed mRNAs. Non-human RNA sequences were subjected to a microbial discovery bioinformatics platform, and microbial sequences were analyzed by Metastats for association with KD. Results T lymphocyte activation, antigen presentation, immunoglobulin production, and type I interferon response were significantly upregulated in KD arteritis, while the tumor necrosis factor α pathway was not differentially expressed. Transcripts from known infectious agents were not specifically associated with KD coronary arteritis. Conclusions The immune transcriptional profile in KD coronary artery tissues has features of an antiviral immune response such as activated cytotoxic T lymphocyte and type I interferon-induced gene upregulation. These results provide new insights into the pathogenesis of KD arteritis that can guide selection of new immunomodulatory therapies for high-risk KD patients, and provide direction for future etiologic studies. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2323-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anne H Rowley
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, 310 E Superior Street, Morton 4-685B, Chicago, IL, 60611, USA. .,Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA. .,Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA.
| | - Kristine M Wylie
- Department of Pediatrics, Washington University School of Medicine, Saint Louis, MO, USA.,The McDonnell Genome Institute at Washington University, Washington University School of Medicine, Saint Louis, MO, USA
| | - Kwang-Youn A Kim
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Adam J Pink
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, 310 E Superior Street, Morton 4-685B, Chicago, IL, 60611, USA
| | - Amy Yang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Rebecca Reindel
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, 310 E Superior Street, Morton 4-685B, Chicago, IL, 60611, USA.,Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA.,Present address: AbbVie, Inc, North Chicago, IL, USA
| | - Susan C Baker
- Department of Microbiology/Immunology, Loyola University Stritch School of Medicine, Maywood, IL, USA
| | - Stanford T Shulman
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, 310 E Superior Street, Morton 4-685B, Chicago, IL, 60611, USA.,Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Jan M Orenstein
- Department of Pathology, George Washington University School of Medicine, Washington, DC, USA
| | - Mark W Lingen
- Department of Pathology, University of Chicago Pritzker School of Medicine, Chicago, IL, USA
| | - George M Weinstock
- The McDonnell Genome Institute at Washington University, Washington University School of Medicine, Saint Louis, MO, USA.,Present address: The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Todd N Wylie
- Department of Pediatrics, Washington University School of Medicine, Saint Louis, MO, USA.,The McDonnell Genome Institute at Washington University, Washington University School of Medicine, Saint Louis, MO, USA
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137
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Abstract
SummaryGenomics and whole genome sequencing (WGS) have the capacity to greatly enhance knowledge and understanding of infectious diseases and clinical microbiology. The growth and availability of bench-top WGS analysers has facilitated the feasibility of genomics in clinical and public health microbiology. Given current resource and infrastructure limitations, WGS is most applicable to use in public health laboratories, reference laboratories, and hospital infection control-affiliated laboratories. As WGS represents the pinnacle for strain characterisation and epidemiological analyses, it is likely to replace traditional typing methods, resistance gene detection and other sequence-based investigations (e.g., 16S rDNA PCR) in the near future. Although genomic technologies are rapidly evolving, widespread implementation in clinical and public health microbiology laboratories is limited by the need for effective semi-automated pipelines, standardised quality control and data interpretation, bioinformatics expertise, and infrastructure.
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138
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Greninger AL, Messacar K, Dunnebacke T, Naccache SN, Federman S, Bouquet J, Mirsky D, Nomura Y, Yagi S, Glaser C, Vollmer M, Press CA, Kleinschmidt-DeMasters BK, Klenschmidt-DeMasters BK, Dominguez SR, Chiu CY. Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing. Genome Med 2015; 7:113. [PMID: 26620704 PMCID: PMC4665321 DOI: 10.1186/s13073-015-0235-2] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 10/13/2015] [Indexed: 01/10/2023] Open
Abstract
Background Primary amoebic meningoencephalitis (PAM) is a rare, often lethal, cause of encephalitis, for which early diagnosis and prompt initiation of combination antimicrobials may improve clinical outcomes. Methods In this study, we sequenced a full draft assembly of the Balamuthia mandrillaris genome (44.2 Mb in size) from a rare survivor of PAM, and recovered the mitochondrial genome from six additional Balamuthia strains. We also used unbiased metagenomic next-generation sequencing (NGS) and SURPI bioinformatics analysis to diagnose an ultimately fatal case of Balamuthia mandrillaris encephalitis in a 15-year-old girl. Results and Discussion Comparative analysis of the mitochondrial genome and high-copy number genes from six additional Balamuthia mandrillaris strains demonstrated remarkable sequence variation, and the closest Balamuthia homologs corresponded to other amoebae, hydroids, algae, slime molds, and peat moss. Real-time NGS testing of hospital day 6 CSF and brain biopsy samples detected Balamuthia on the basis of high-quality hits to 16S and 18S ribosomal RNA sequences present in the National Center for Biotechnology Information (NCBI) nt reference database. The presumptive diagnosis of PAM by visualization of amoebae on brain biopsy histopathology and NGS analysis was subsequently confirmed at the US Centers for Disease Control and Prevention (CDC) using a Balamuthia-specific PCR assay. Retrospective analysis of a day 1 CSF sample revealed that more timely identification of Balamuthia by metagenomic NGS, potentially resulting in a better clinical outcome, would have required availability of the complete genome sequence. Conclusions These results underscore the diverse evolutionary origins of Balamuthia mandrillaris, provide new targets for diagnostic assay development, and will facilitate further investigations of the biology and pathogenesis of this eukaryotic pathogen. The failure to identify PAM from a day 1 sample without a fully sequenced Balamuthia genome in the database highlights the critical importance of whole-genome reference sequences for microbial detection by metagenomic NGS. Electronic supplementary material The online version of this article (doi:10.1186/s13073-015-0235-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexander L Greninger
- Department of Laboratory Medicine, University of California, 185 Berry Street, Box 0134, San Francisco, CA, 94107, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, 91407, USA
| | - Kevin Messacar
- Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, CO, USA
| | | | - Samia N Naccache
- Department of Laboratory Medicine, University of California, 185 Berry Street, Box 0134, San Francisco, CA, 94107, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, 91407, USA
| | - Scot Federman
- Department of Laboratory Medicine, University of California, 185 Berry Street, Box 0134, San Francisco, CA, 94107, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, 91407, USA
| | - Jerome Bouquet
- Department of Laboratory Medicine, University of California, 185 Berry Street, Box 0134, San Francisco, CA, 94107, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, 91407, USA
| | - David Mirsky
- Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, CO, USA
| | - Yosuke Nomura
- Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, CO, USA
| | - Shigeo Yagi
- California Department of Public Health, Richmond, CA, USA
| | | | | | - Craig A Press
- Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, CO, USA
| | | | | | - Samuel R Dominguez
- Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, CO, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, 185 Berry Street, Box 0134, San Francisco, CA, 94107, USA. .,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, 91407, USA. .,Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, CA, 94107, USA.
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139
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Luk KC, Berg MG, Naccache SN, Kabre B, Federman S, Mbanya D, Kaptué L, Chiu CY, Brennan CA, Hackett J. Utility of Metagenomic Next-Generation Sequencing for Characterization of HIV and Human Pegivirus Diversity. PLoS One 2015; 10:e0141723. [PMID: 26599538 PMCID: PMC4658132 DOI: 10.1371/journal.pone.0141723] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 10/12/2015] [Indexed: 02/06/2023] Open
Abstract
Given the dynamic changes in HIV-1 complexity and diversity, next-generation sequencing (NGS) has the potential to revolutionize strategies for effective HIV global surveillance. In this study, we explore the utility of metagenomic NGS to characterize divergent strains of HIV-1 and to simultaneously screen for other co-infecting viruses. Thirty-five HIV-1-infected Cameroonian blood donor specimens with viral loads of >4.4 log10 copies/ml were selected to include a diverse representation of group M strains. Random-primed NGS libraries, prepared from plasma specimens, resulted in greater than 90% genome coverage for 88% of specimens. Correct subtype designations based on NGS were concordant with sub-region PCR data in 31 of 35 (89%) cases. Complete genomes were assembled for 25 strains, including circulating recombinant forms with relatively limited data available (7 CRF11_cpx, 2 CRF13_cpx, 1 CRF18_cpx, and 1 CRF37_cpx), as well as 9 unique recombinant forms. HPgV (formerly designated GBV-C) co-infection was detected in 9 of 35 (25%) specimens, of which eight specimens yielded complete genomes. The recovered HPgV genomes formed a diverse cluster with genotype 1 sequences previously reported from Ghana, Uganda, and Japan. The extensive genome coverage obtained by NGS improved accuracy and confidence in phylogenetic classification of the HIV-1 strains present in the study population relative to conventional sub-region PCR. In addition, these data demonstrate the potential for metagenomic analysis to be used for routine characterization of HIV-1 and identification of other viral co-infections.
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Affiliation(s)
- Ka-Cheung Luk
- Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America
| | - Michael G Berg
- Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America
| | - Samia N Naccache
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America
| | - Beniwende Kabre
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America
| | - Scot Federman
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America
| | | | | | - Charles Y Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America.,Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, California, United States of America
| | - Catherine A Brennan
- Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America
| | - John Hackett
- Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America
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140
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Adams RI, Bateman AC, Bik HM, Meadow JF. Microbiota of the indoor environment: a meta-analysis. MICROBIOME 2015; 3:49. [PMID: 26459172 PMCID: PMC4604073 DOI: 10.1186/s40168-015-0108-3] [Citation(s) in RCA: 161] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 09/07/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND As modern humans, we spend the majority of our time in indoor environments. Consequently, environmental exposure to microorganisms has important implications for human health, and a better understanding of the ecological drivers and processes that impact indoor microbial assemblages will be key for expanding our knowledge of the built environment. In the present investigation, we combined recent studies examining the microbiota of the built environment in order to identify unifying community patterns and the relative importance of indoor environmental factors. Ultimately, the present meta-analysis focused on studies of bacteria and archaea due to the limited number of high-throughput fungal studies from the indoor environment. We combined 16S ribosomal RNA (rRNA) gene datasets from 16 surveys of indoor environments conducted worldwide, additionally including 7 other studies representing putative environmental sources of microbial taxa (outdoor air, soil, and the human body). RESULTS Combined analysis of subsets of studies that shared specific experimental protocols or indoor habitats revealed community patterns indicative of consistent source environments and environmental filtering. Additionally, we were able to identify several consistent sources for indoor microorganisms, particularly outdoor air and skin, mirroring what has been shown in individual studies. Technical variation across studies had a strong effect on comparisons of microbial community assemblages, with differences in experimental protocols limiting our ability to extensively explore the importance of, for example, sampling locality, building function and use, or environmental substrate in structuring indoor microbial communities. CONCLUSIONS We present a snapshot of an important scientific field in its early stages, where studies have tended to focus on heavy sampling in a few geographic areas. From the practical perspective, this endeavor reinforces the importance of negative "kit" controls in microbiome studies. From the perspective of understanding mechanistic processes in the built environment, this meta-analysis confirms that broad factors, such as geography and building type, structure indoor microbes. However, this exercise suggests that individual studies with common sampling techniques may be more appropriate to explore the relative importance of subtle indoor environmental factors on the indoor microbiome.
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Affiliation(s)
- Rachel I Adams
- Plant & Microbial Biology, University of California Berkeley, Berkeley, 94720, CA, USA.
| | - Ashley C Bateman
- Biology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, 97403, OR, USA.
| | - Holly M Bik
- UC Davis Genome Center, University of California, Davis, Davis, 95616, CA, USA.
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK.
| | - James F Meadow
- Biology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, 97403, OR, USA.
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141
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Smits SL, Bodewes R, Ruiz-González A, Baumgärtner W, Koopmans MP, Osterhaus ADME, Schürch AC. Recovering full-length viral genomes from metagenomes. Front Microbiol 2015; 6:1069. [PMID: 26483782 PMCID: PMC4589665 DOI: 10.3389/fmicb.2015.01069] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 09/17/2015] [Indexed: 12/17/2022] Open
Abstract
Infectious disease metagenomics is driven by the question: “what is causing the disease?” in contrast to classical metagenome studies which are guided by “what is out there?” In case of a novel virus, a first step to eventually establishing etiology can be to recover a full-length viral genome from a metagenomic sample. However, retrieval of a full-length genome of a divergent virus is technically challenging and can be time-consuming and costly. Here we discuss different assembly and fragment linkage strategies such as iterative assembly, motif searches, k-mer frequency profiling, coverage profile binning, and other strategies used to recover genomes of potential viral pathogens in a timely and cost-effective manner.
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Affiliation(s)
- Saskia L Smits
- Department of Viroscience, Erasmus Medical Center Rotterdam, Netherlands
| | - Rogier Bodewes
- Department of Viroscience, Erasmus Medical Center Rotterdam, Netherlands
| | - Aritz Ruiz-González
- Department of Zoology and Animal Cell Biology, University of the Basque Country (UPV/EHU) Vitoria-Gasteiz, Spain ; Systematics, Biogeography and Population Dynamics Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU) Vitoria-Gasteiz, Spain ; Conservation Genetics Laboratory, National Institute for Environmental Protection and Research Bologna, Italy
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover Hannover, Germany
| | - Marion P Koopmans
- Department of Viroscience, Erasmus Medical Center Rotterdam, Netherlands ; Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute for Public Health and the Environment Bilthoven, Netherlands
| | - Albert D M E Osterhaus
- Department of Viroscience, Erasmus Medical Center Rotterdam, Netherlands ; Center for Infection Medicine and Zoonoses Research Hannover, Germany
| | - Anita C Schürch
- Department of Viroscience, Erasmus Medical Center Rotterdam, Netherlands
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142
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Virome Analysis of Transfusion Recipients Reveals a Novel Human Virus That Shares Genomic Features with Hepaciviruses and Pegiviruses. mBio 2015; 6:e01466-15. [PMID: 26396247 PMCID: PMC4600124 DOI: 10.1128/mbio.01466-15] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
To investigate the transmission of novel infectious agents by blood transfusion, we studied changes in the virome composition of blood transfusion recipients pre- and posttransfusion. Using this approach, we detected and genetically characterized a novel human virus, human hepegivirus 1 (HHpgV-1), that shares features with hepatitis C virus (HCV) and human pegivirus (HPgV; formerly called GB virus C or hepatitis G virus). HCV and HPgV belong to the genera Hepacivirus and Pegivirus of the family Flaviviridae. HHpgV-1 was found in serum samples from two blood transfusion recipients and two hemophilia patients who had received plasma-derived clotting factor concentrates. In the former, the virus was detected only in the posttransfusion samples, indicating blood-borne transmission. Both hemophiliacs were persistently viremic over periods of at least 201 and 1,981 days. The 5′ untranslated region (UTR) of HHpgV-1 contained a type IV internal ribosome entry site (IRES), structurally similar to although highly divergent in sequence from that of HCV and other hepaciviruses. However, phylogenetic analysis of nonstructural genes (NS3 and NS5B) showed that HHpgV-1 forms a branch within the pegivirus clade distinct from HPgV and homologs infecting other mammalian species. In common with some pegivirus variants infecting rodents and bats, the HHpgV-1 genome encodes a short, highly basic protein upstream of E1, potentially possessing a core-like function in packaging RNA during assembly. Identification of this new human virus, HHpgV-1, expands our knowledge of the range of genome configurations of these viruses and may lead to a reevaluation of the original criteria by which the genera Hepacivirus and Pegivirus are defined. More than 30 million blood components are transfused annually in the United States alone. Surveillance for infectious agents in the blood supply is key to ensuring the safety of this critical resource for medicine and public health. Here, we report the identification of a new and highly diverse HCV/GB virus (GBV)-like virus from human serum samples. This new virus, human hepegivirus 1 (HHpgV-1), was found in serum samples from blood transfusion recipients, indicating its potential for transmission via transfusion products. We also found persistent long-term HHpgV-1 viremia in two hemophilia patients. HHpgV-1 is unique because it shares genetic similarity with both highly pathogenic HCV and the apparently nonpathogenic HPgV (GBV-C). Our results add to the list of human viruses and provide data to develop reagents to study virus transmission and disease association and for interrupting virus transmission and new human infections.
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143
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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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144
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Investigation of Human Cancers for Retrovirus by Low-Stringency Target Enrichment and High-Throughput Sequencing. Sci Rep 2015; 5:13201. [PMID: 26285800 PMCID: PMC4541070 DOI: 10.1038/srep13201] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 07/14/2015] [Indexed: 01/05/2023] Open
Abstract
Although nearly one fifth of all human cancers have an infectious aetiology, the causes for the majority of cancers remain unexplained. Despite the enormous data output from high-throughput shotgun sequencing, viral DNA in a clinical sample typically constitutes a proportion of host DNA that is too small to be detected. Sequence variation among virus genomes complicates application of sequence-specific, and highly sensitive, PCR methods. Therefore, we aimed to develop and characterize a method that permits sensitive detection of sequences despite considerable variation. We demonstrate that our low-stringency in-solution hybridization method enables detection of <100 viral copies. Furthermore, distantly related proviral sequences may be enriched by orders of magnitude, enabling discovery of hitherto unknown viral sequences by high-throughput sequencing. The sensitivity was sufficient to detect retroviral sequences in clinical samples. We used this method to conduct an investigation for novel retrovirus in samples from three cancer types. In accordance with recent studies our investigation revealed no retroviral infections in human B-cell lymphoma cells, cutaneous T-cell lymphoma or colorectal cancer biopsies. Nonetheless, our generally applicable method makes sensitive detection possible and permits sequencing of distantly related sequences from complex material.
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145
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Denesvre C, Dumarest M, Rémy S, Gourichon D, Eloit M. Chicken skin virome analyzed by high-throughput sequencing shows a composition highly different from human skin. Virus Genes 2015. [PMID: 26223320 DOI: 10.1007/s11262-015-1231-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recent studies show that human skin at homeostasis is a complex ecosystem whose virome include circular DNA viruses, especially papillomaviruses and polyomaviruses. To determine the chicken skin virome in comparison with human skin virome, a chicken swabs pool sample from fifteen indoor healthy chickens of five genetic backgrounds was examined for the presence of DNA viruses by high-throughput sequencing (HTS). The results indicate a predominance of herpesviruses from the Mardivirus genus, coming from either vaccinal origin or presumably asymptomatic infection. Despite the high sensitivity of the HTS method used herein to detect small circular DNA viruses, we did not detect any papillomaviruses, polyomaviruses, or circoviruses, indicating that these viruses may not be resident of the chicken skin. The results suggest that the turkey herpesvirus is a resident of chicken skin in vaccinated chickens. This study indicates major differences between the skin viromes of chickens and humans. The origin of this difference remains to be further studied in relation with skin physiology, environment, or virus population dynamics.
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Affiliation(s)
- Caroline Denesvre
- INRA, UMR1282, Infectious Diseases and Public Health, ISP, BIOlogy of Avian Viruses Team, 37380, Nouzilly, France.
| | - Marine Dumarest
- Institut Pasteur, Biology of Infection Unit, Inserm U1117, Pathogen Discovery Laboratory, 75015, Paris, France
| | - Sylvie Rémy
- INRA, UMR1282, Infectious Diseases and Public Health, ISP, BIOlogy of Avian Viruses Team, 37380, Nouzilly, France
| | - David Gourichon
- INRA, Pôle d'expérimentation avicole de Tours, 37380, Nouzilly, France
| | - Marc Eloit
- Institut Pasteur, Biology of Infection Unit, Inserm U1117, Pathogen Discovery Laboratory, 75015, Paris, France. .,PathoQuest, Paris, 25 rue du Dr Roux, 75015, Paris, France.
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146
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Gruber K. Here, there, and everywhere: From PCRs to next-generation sequencing technologies and sequence databases, DNA contaminants creep in from the most unlikely places. EMBO Rep 2015; 16:898-901. [PMID: 26150097 DOI: 10.15252/embr.201540822] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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147
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Aguiar ERGR, Olmo RP, Paro S, Ferreira FV, de Faria IJDS, Todjro YMH, Lobo FP, Kroon EG, Meignin C, Gatherer D, Imler JL, Marques JT. Sequence-independent characterization of viruses based on the pattern of viral small RNAs produced by the host. Nucleic Acids Res 2015; 43:6191-206. [PMID: 26040701 PMCID: PMC4513865 DOI: 10.1093/nar/gkv587] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/24/2015] [Indexed: 12/20/2022] Open
Abstract
Virus surveillance in vector insects is potentially of great benefit to public health. Large-scale sequencing of small and long RNAs has previously been used to detect viruses, but without any formal comparison of different strategies. Furthermore, the identification of viral sequences largely depends on similarity searches against reference databases. Here, we developed a sequence-independent strategy based on virus-derived small RNAs produced by the host response, such as the RNA interference pathway. In insects, we compared sequences of small and long RNAs, demonstrating that viral sequences are enriched in the small RNA fraction. We also noted that the small RNA size profile is a unique signature for each virus and can be used to identify novel viral sequences without known relatives in reference databases. Using this strategy, we characterized six novel viruses in the viromes of laboratory fruit flies and wild populations of two insect vectors: mosquitoes and sandflies. We also show that the small RNA profile could be used to infer viral tropism for ovaries among other aspects of virus biology. Additionally, our results suggest that virus detection utilizing small RNAs can also be applied to vertebrates, although not as efficiently as to plants and insects.
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Affiliation(s)
- Eric Roberto Guimarães Rocha Aguiar
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP 30270-901, Brazil CNRS-UPR9022, Institut de Biologie Moléculaire et Cellulaire, 67084 Strasbourg Cedex, France
| | - Roenick Proveti Olmo
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP 30270-901, Brazil CNRS-UPR9022, Institut de Biologie Moléculaire et Cellulaire, 67084 Strasbourg Cedex, France
| | - Simona Paro
- CNRS-UPR9022, Institut de Biologie Moléculaire et Cellulaire, 67084 Strasbourg Cedex, France
| | - Flavia Viana Ferreira
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP 30270-901, Brazil
| | - Isaque João da Silva de Faria
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP 30270-901, Brazil
| | - Yaovi Mathias Honore Todjro
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP 30270-901, Brazil
| | - Francisco Pereira Lobo
- Laboratório Multiusuário de Bioinformática, Embrapa Informática Agropecuária, Campinas, São Paulo, CEP 13083-886, Brazil
| | - Erna Geessien Kroon
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP 30270-901, Brazil
| | - Carine Meignin
- CNRS-UPR9022, Institut de Biologie Moléculaire et Cellulaire, 67084 Strasbourg Cedex, France Faculté des Sciences de la Vie, Université de Strasbourg, 67083 Strasbourg Cedex, France
| | - Derek Gatherer
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, Lancashire, LA1 4YQ, UK
| | - Jean-Luc Imler
- CNRS-UPR9022, Institut de Biologie Moléculaire et Cellulaire, 67084 Strasbourg Cedex, France Faculté des Sciences de la Vie, Université de Strasbourg, 67083 Strasbourg Cedex, France Institut d'Etudes Avancées de l'Université de Strasbourg (USIAS), 67084 Strasbourg Cedex, France
| | - João Trindade Marques
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP 30270-901, Brazil
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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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149
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Evaluation of Unbiased Next-Generation Sequencing of RNA (RNA-seq) as a Diagnostic Method in Influenza Virus-Positive Respiratory Samples. J Clin Microbiol 2015; 53:2238-50. [PMID: 25972420 DOI: 10.1128/jcm.02495-14] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 05/01/2015] [Indexed: 01/21/2023] Open
Abstract
Unbiased nontargeted metagenomic RNA sequencing (UMERS) has the advantage to detect known as well as unknown pathogens and, thus, can significantly improve the detection of viral, bacterial, parasitic, and fungal sequences in public health settings. In particular, conventional diagnostic methods successfully identify the putative pathogenic agent in only 30% to 40% of respiratory specimens from patients with acute respiratory illness. Here, we applied UMERS to 24 diagnostic respiratory specimens (bronchoalveolar lavage [BAL] fluid, sputum samples, and a swab) from patients with seasonal influenza infection and 5 BAL fluid samples from patients with pneumonia that tested negative for influenza to validate RNA sequencing as an unbiased diagnostic tool in comparison to conventional diagnostic methods. In addition to our comparison to PCR, we evaluated the potential to retrieve comprehensive influenza virus genomic information and the capability to detect known superinfecting pathogens. Compared to quantitative real-time PCR for influenza viral sequences, UMERS detected influenza viral sequences in 18 of 24 samples. Complete influenza virus genomes could be assembled from 8 samples. Furthermore, in 3 of 24 influenza-positive samples, additional viral pathogens could be detected, and 2 of 24 samples showed a significantly increased abundance of individual bacterial species known to cause superinfections during an influenza virus infection. Thus, analysis of respiratory samples from known or suspected influenza patients by UMERS provides valuable information that is relevant for clinical investigation.
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150
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Yang J, Hirschi KD, Farmer LM. Dietary RNAs: New Stories Regarding Oral Delivery. Nutrients 2015; 7:3184-99. [PMID: 25942490 PMCID: PMC4446746 DOI: 10.3390/nu7053184] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 04/10/2015] [Accepted: 04/27/2015] [Indexed: 12/17/2022] Open
Abstract
microRNAs (miRNAs), a class of small RNAs, are important regulators of various developmental processes in both plants and animals. Several years ago, a report showed the detection of diet-derived plant miRNAs in mammalian tissues and their regulation of mammalian genes, challenging the traditional functions of plant miRNAs. Subsequently, multiple efforts have attempted to replicate these findings, with the results arguing against the uptake of plant dietary miRNAs in healthy consumers. Moreover, several reports suggest the potential for "false positive" detection of plant miRNAs in human tissues. Meanwhile, some research continues to suggest both the presence and function of dietary miRNAs in mammalian tissues. Here we review the recent literature and discuss the strengths and weaknesses of emerging work that suggests the feasibility of dietary delivery of miRNAs. We also discuss future experimental approaches to address this controversial topic.
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Affiliation(s)
- Jian Yang
- United States Department of Agriculture/Agriculture Research Service, Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Kendal D Hirschi
- United States Department of Agriculture/Agriculture Research Service, Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA.
- Vegetable and Fruit Improvement Center, Texas A&M University, College Station, TX 77845, USA.
| | - Lisa M Farmer
- United States Department of Agriculture/Agriculture Research Service, Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA.
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