Viral Metagenomics
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Viral Metagenomics
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Author : Vitantonio Pantaleo
language : en
Publisher: Springer Nature
Release Date : 2023-12-07
Viral Metagenomics written by Vitantonio Pantaleo and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-12-07 with Medical categories.
This second edition volume expands on the previous edition with discussions about the latest viral metagenomics aspects covering a range of different specimens such as soil, freshwater, wastewater, fecal samples, blood plasma, clinical tissues, fungi, and herbarium samples. Chapters also look at different viral groups including archaeal viruses, eukaryotic viruses, phages, mycoviruses, and circular DNA viruses. Techniques required for studying the three viral metagenomic steps of samples processing, library construction, and analysis of data are also discussed. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Vital Metagenomics: Methods and Protocols, Second Edition is a valuable resource for researchers who are interested in learning more about this important and developing field.
Virus Discovery By Metagenomics The Im Possibilities
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Author : Bas E. Dutilh
language : en
Publisher: Frontiers Media SA
Release Date : 2017-10-25
Virus Discovery By Metagenomics The Im Possibilities written by Bas E. Dutilh and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-10-25 with categories.
Since the late 1800s, the discovery of new viruses was a gradual process. Viruses were described one by one using a suite of techniques such as (electron) microscopy and viral culture. Investigators were usually interested in a disease state within an organism, and expeditions in viral ecology were rare. The advent of metagenomics using high-throughput sequencing has revolutionized not only the rate of virus discovery, but also the nature of the discoveries. For example, the viral ecology and etiology of many human diseases are being characterized, non-pathogenic viral commensals are ubiquitous, and the description of environmental viromes is making progress. This Frontiers in Virology Research Topic showcases how metagenomic and bioinformatic approaches have been combined to discover, classify and characterize novel viruses.
Viral Metagenomics In Host Associated Systems
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Author :
language : en
Publisher:
Release Date : 2010
Viral Metagenomics In Host Associated Systems written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010 with categories.
Viruses are the most abundant and diverse entities on earth. Exploration of viral diversity has traditionally been limited by the lack of common marker genes, however, the advent of viral metagenomics has made it possible to characterize global viral communities. Viruses in host-associated systems, such as human and animal tissues, are of special interest as they may be causative agents of disease. Additionally, changes in the total viral consortium may be indicative of host health status, with opportunists and pathogens replacing normal viral flora in the disease state. This dissertation presents an introduction to viral metagenomics and explores use in both human and animal associated systems. Methods in viral metagenomics, including both molecular biology and bioinformatics are reviewed as well as viral metagenomic studies to date. The metagenomic signature technique is explored as a method to characterize metagenomes and to screen for contaminating host genomic DNA sequences in viral metagenomes. Three experimental studies are presented to demonstrate the utility of metagenomics in healthy and diseased individuals. A case study of oropharyngeal viruses revealed the presence of phage-encoded virulence genes in healthy individuals, and also provided the first ever characterization of oropharyngeal viral communities. In the second study, viral communities from the airways of individuals with and without cystic fibrosis (CF) were compared. There was a striking difference in metabolic functions encoded by phage in CF versus Non-CF individuals. Regardless of which taxa were present, CF-associated phage shared a common core metabolism that reflected the disease state and aberrant airway physiology. Viral communities in healthy and diseased fish were compared in the third study. In contrast to the airway viromes, fish-associated viromes were found to differ taxonomically but not in metabolic function in the disease state. Together these studies demonstrate the power of viral metagenomics for discovery and for deciphering how viral communities change in the face of disease.
Virus Discovery By Metagenomics The Im Possibilities
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Author :
language : en
Publisher:
Release Date : 2017
Virus Discovery By Metagenomics The Im Possibilities written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017 with categories.
Since the late 1800s, the discovery of new viruses was a gradual process. Viruses were described one by one using a suite of techniques such as (electron) microscopy and viral culture. Investigators were usually interested in a disease state within an organism, and expeditions in viral ecology were rare. The advent of metagenomics using high-throughput sequencing has revolutionized not only the rate of virus discovery, but also the nature of the discoveries. For example, the viral ecology and etiology of many human diseases are being characterized, non-pathogenic viral commensals are ubiquitous, and the description of environmental viromes is making progress. This Frontiers in Virology Research Topic showcases how metagenomic and bioinformatic approaches have been combined to discover, classify and characterize novel viruses.
Viral Metagenomics
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Author :
language : en
Publisher:
Release Date : 2007
Viral Metagenomics written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2007 with categories.
The purpose of this report is to design and develop a tool for analysis of raw sequence read data from viral metagenomics experiments. The tool should compare read sequences of known viral nucleic acid sequence data and enable a user to attempt to determine, with some degree of confidence, what virus groups may be present in the sample. This project was conducted in two phases. In phase 1 we surveyed the literature and examined existing metagenomics tools to educate ourselves and to more precisely define the problem of analyzing raw read data from viral metagenomic experiments. In phase 2 we devised an approach and built a prototype code and database. This code takes viral metagenomic read data in fasta format as input and accesses all complete viral genomes from Kpath for sequence comparison. The system executes at the UNIX command line, producing output that is stored in an Oracle relational database. We provide here a description of the approach we came up with for handling un-assembled, short read data sets from viral metagenomics experiments. We include a discussion of the current MetaView code capabilities and additional functionality that we believe should be added, should additional funding be acquired to continue the work.
Viral Metagenomics For Swine Health
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Author : Brandi Feehan
language : en
Publisher:
Release Date : 2022
Viral Metagenomics For Swine Health written by Brandi Feehan and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022 with categories.
Viral metagenomic sequencing describes an unbiased technique to identify viruses present in a sample. The rise of metagenomics, through next generation sequencing (NGS) and bioinformatics, has aided disease epidemiology, diagnostics, and vaccine development for the swine industry. Metagenomic techniques originated from labor intensive functional screening which NGS overcame by significantly increase the data output. Although, with this increase of data, computational methods were needed to elucidate biological significance. Therefore, bioinformatics made NGS relevant for viral metagenomics targeting swine health. Viral metagenomics for the swine industry involves uncovering molecular characteristics to aid in the development of vaccines, diagnostics, and therapeutics. We utilized metagenomics to identify a novel mammalian orthorubulavirus 5 (PIV5) while attempting to isolate porcine rotavirus B (RVB). During cell passaging, the responsible technician fell ill with symptoms of a respiratory infection. On passage four, cells exhibited the cytopathic effect of syncytia formation and were sent for NGS which identified a human PIV5 strain, named Moskva. The resulting genome demonstrated an 87% nucleotide identity to a human PIV5 strain. The original cell culture and pig fecal samples were negative for Moskva by qRT-PCR. Moskva formed a distinct clade from other PIV5 strains in a whole genome based phylogenetic tree. Comparing the two major surface glycoproteins, fusion (F) and hemagglutinin-neuraminidase (HN), amongst human PIV5 strains, Moskva had 32 and 31 amino acid substitutions, respectively. The novel PIV5 strain proved that further research is needed to determine prevalence of PIV5 in different mammalian hosts and geographical locations; in addition, the effects of amino acid substitutions in the viral surface proteins F and HN of the Moskva strain, especially with relevance to human health, need to be determined. Viral metagenomics was further applied to investigate Betaarterivirus suid 2 (PRRSV-2), the causative agent of porcine reproductive and respiratory syndrome (PRRS). PRRSV-2 detection and genome assembly through NGS approaches indicated that current PRRSV-2 analytic methods for NGS were insufficient. Nearly half of the PRRSV-2 qRT-PCR positive samples were unsuccessfully assembled using NGS. Read classification detected a novel porcine virus, a lentivirus, which was found especially as a coinfecting agent with PRRSV-2. While PRRSV-2 glycoprotein 5 (GP5) has been used historically for phylogenetic analysis, five of the ten PRRSV-2 genes illustrated increased nucleotide diversity when compared to GP5, indicating that other PRRSV-2 genes could be suitable candidates to demonstrate PRRSV-2 diversity. Comparatively, both the whole genome and GP5 phylogenetic trees lacked clustering patterns relative to temporal or geographical distribution, which also indicated the need for the use of a different PRRSV-2 gene for phylogenetic analysis. The use of a representative gene for PRRSV-2 classification is crucial to more accurately comprehend PRRSV-2 diversity and its implications for PRRSV-2 evolution, distribution, and virulence.
Viral Metagenomics
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Author : Vitantonio Pantaleo
language : en
Publisher: Humana
Release Date : 2019-03-17
Viral Metagenomics written by Vitantonio Pantaleo and has been published by Humana this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-03-17 with Science categories.
This volume explores the use of viral metagenomics to diagnose known viruses for plant and food production, human and animal health, and identifying viral vectors like insects. The chapters in this book cover topics, such as sRNAs isolation from tissues of grapevines and woody plants, high-resolution screening of arthropod and plant viral communities, identifying new pathogens in fish, detecting viruses in mycorrhizal fungi and their orchid host, and insect virus discovery through metagenomic and cell culture-based approaches. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and comprehensive, Viral Metagenomics: Methods and Protocols is a valuable resource for researchers and specialists who are interested in learning more about this evolving field.
Enhancing Virus Surveillance Through Metagenomics
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Author : Karyna Rosario-Cora
language : en
Publisher:
Release Date : 2010
Enhancing Virus Surveillance Through Metagenomics written by Karyna Rosario-Cora and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010 with categories.
ABSTRACT: Monitoring viruses circulating in the human population and the environment is critical for protecting public and ecosystem health. The goal of this dissertation was to incorporate a viral metagenomic approach into virus surveillance efforts (both clinical and water quality control programs) to enhance traditional virus detection methods. Clinical surveillance programs are designed to identify and monitor etiological agents that cause disease. However, the ability to identify viruses may be compromised when novel or unsuspected viruses are causing infection since traditional virus detection methods target specific known pathogens. Here we describe the successful application of viral metagenomics in a clinical setting using samples from symptomatic patients collected through the Enterovirus Surveillance (EVS) program in the Netherlands (Appendix A). Despite extensive PCR-based testing, the viruses in a small percentage of these samples (n = 7) remained unidentified for more than 10 years after collection. Viral metagenomics allowed the identification of viruses in all seven samples within a week using minimal sequencing, thus rapidly filling the diagnostic gap. The unexplained samples contained BK polyomavirus, Herpes simplex virus, Newcastle disease virus and the recently discovered Saffold viruses (SAFV) which dominated the unexplained samples (n = 4). This study demonstrated that metagenomic analyses can be added as a routine tool to investigate unidentified viruses in clinical samples in a public-health setting. In addition, metagenomic data gathered for SAFV was used to complete four genotype 3 SAFV (SAFV-3) genomes through primer walking, doubling the number of SAFV-3 full genomic sequences in public databases. In addition to monitoring viruses in symptomatic patients, it is also important to monitor viruses in wastewater (raw and treated) to protect the environment from biological contamination and prevent further spread of pathogens. To gain a comprehensive understanding of viruses that endure wastewater treatment, viral metagenomics was used to survey the total DNA and RNA viral community in reclaimed water (the reusable end-product of wastewater treatment) (Appendix B). Phages (viruses that infect bacteria) dominated the DNA viral community while eukaryotic viruses similar to known plant and insect viruses dominated RNA metagenomic libraries suggesting that highly stable viruses may be disseminated through this alternative water supply. A plant virus, the Pepper mild mottle virus (PMMoV), was identified as a potential indicator of wastewater contamination based on metagenomic data and quantitative PCR assays (Appendix C). The metagenomic analysis also revealed a wealth of novel single-stranded DNA (ssDNA) viruses in reclaimed water. Further investigation of sequences with low-level similarities to known ssDNA viruses led to the completion of ten novel ssDNA genomes from reclaimed water and marine environments (Appendix D). Unique genome architectures and phylogenetic analysis suggest that these ssDNA viruses belong to new viral genera and/or families. To further explore the ecology of the novel ssDNA viruses, a strategy was developed to take metagenomic analysis to the next level by combining expression analysis and immunotechnology (Appendix E). This dissertation made a significant contribution to current microbiological data regarding wastewater by uncovering viruses that endure the wastewater treatment and identifying a new viral bioindicator.
A Viral Metagenomic Approach To Study Taxonomic And Functional Diversity Of Viral Communities From The Environment To Humans
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Author : Laura Fancello
language : en
Publisher:
Release Date : 2013
A Viral Metagenomic Approach To Study Taxonomic And Functional Diversity Of Viral Communities From The Environment To Humans written by Laura Fancello and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013 with categories.
Viruses are the most abundant and diverse organisms but little is known about their diversity. Recently, viral metagenomics has allowed performing broad unselective exploration of uncultivated viral communities, bypassing the limits of classical viral detection tools. However, most viral metagenomes are generated from temperate regions (for environmental studies) or from modern stool samples, sera/blood and naso-/oro- pharyngeal samples (for human-associated studies). Therefore, the purpose of my thesis is to study viral communities in the least investigated environments or human samples, using viral metagenomics.The first part of my thesis is a review of the main computational tools for the analysis of viral metagenomes. The second part of my thesis presents the first viromes generated from the Sahara desert. In the third part, I investigate human-associated viral communities: i) the first virome from a human coprolite; ii) the first viromes generated from human pericardial fluids, in idiopathic pericarditis cases; ii) a functional-level investigation of previously described viral metagenomes from cystic fibrosis patient sputa that focuses on antimicrobial resistance genes carried by bacteriophages to better understand the emergence of multidrug-resistance bacteria in the airways of cystic fibrosis patients.This thesis work provides original data on unexplored viral communities and shows the potential of viral metagenomics to give insights on viral diversity, reveal the presence of expected and unexpected viruses and decipher their role in the ecosystem.
Targeted Enrichment And Viral Metagenomics In The Detection Of Livestock And Wildlife Viruses
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Author : Amber Papineau
language : en
Publisher:
Release Date : 2019
Targeted Enrichment And Viral Metagenomics In The Detection Of Livestock And Wildlife Viruses written by Amber Papineau and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019 with categories.
This thesis focuses on metagenomic viral detection based on high-throughput sequencing. Metagenomics sequencing results in a mixture of sequences, including viral, host and other non-target sequences. Metagenomic viral detection can lack sensitivity due to the low incidence of viral sequences in these mixtures. For this reason, enrichment methods are often employed in metagenomic viral detection. Targeted enrichment is a method based on the hybridization of probes designed to enrich the desired target from a mixture. ViroCap is a method of targeted enrichment designed for vertebrate viruses. It has previously been validated to aid in the detection of viruses from human samples. The second chapter of this thesis describes the evaluation of ViroCap in 10 wildlife and livestock hosts. Enrichment was calculated on a blinded panel of 24 animal and zoonotic viral species. The average enrichment of percent-viral-reads across the 22 viral families tested was 182-fold. Depth of coverage increased 123 times and breadth of coverage increased by 43%. In addition, 6 unexpected viruses were detected. Chapter 3 of this thesis describes the results of the use of viral metagenomics and ViroCap enrichment in a diagnostic disease investigation. ViroCap enrichment and metagenomic high-throughput sequencing revealed the presence of 4 viruses in a mass die-off of Canada and Snow geese, including avian metapneumovirus and avian adeno-associated virus. In addition, the entire genome sequence of a novel species of Gammacoronavirus is described. The first sequence information of goose adenovirus in Canada is also described. Chapter 4 describes the fecal virome of arctic and red foxes. 6 viral families were detected with the use of ViroCap targeted enrichment. A diversity of divergent circoviruses and parvoviruses are described. In addition, numerous avian influenza and canine kobuvirus subtypes were also detected in the feces of several arctic foxes. In conjunction with the description of wildlife viromes, this thesis establishes the utility of targeted enrichment in the detection of livestock and wildlife viruses.