Viral Genomics and Bioinformatics (original) (raw)
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Scrutinizing Virus Genome Termini by High-Throughput Sequencing
PLoS ONE, 2014
Analysis of genomic terminal sequences has been a major step in studies on viral DNA replication and packaging mechanisms. However, traditional methods to study genome termini are challenging due to the time-consuming protocols and their inefficiency where critical details are lost easily. Recent advances in next generation sequencing (NGS) have enabled it to be a powerful tool to study genome termini. In this study, using NGS we sequenced one iridovirus genome and twenty phage genomes and confirmed for the first time that the high frequency sequences (HFSs) found in the NGS reads are indeed the terminal sequences of viral genomes. Further, we established a criterion to distinguish the type of termini and the viral packaging mode. We also obtained additional terminal details such as terminal repeats, multi-termini, asymmetric termini. With this approach, we were able to simultaneously detect details of the genome termini as well as obtain the complete sequence of bacteriophage genomes. Theoretically, this application can be further extended to analyze larger and more complicated genomes of plant and animal viruses. This study proposed a novel and efficient method for research on viral replication, packaging, terminase activity, transcription regulation, and metabolism of the host cell.
InTech eBooks, 2012
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High-Throughput Sequencing: Advantages Beyond Virus Identification
Grapevine Viruses: Molecular Biology, Diagnostics and Management, 2017
The application of high-throughput sequencing (HTS) in plant virology research had an immense influence on our perspective of disease etiology. The technology opened a new avenue of exploration that is unbiased and at an unparalleled level of sensitivity. Initially, HTS was used for virus discovery with the greatest success up until now being the discovery of Grapevine red blotch-associated virus (GRBaV) and Grapevine Pinot gris virus (GPGV). Most of the early studies constructed HTS libraries from either an enriched dsRNA extract or the small RNA fraction, but other nucleic acids have also been used. The expansion of virus databases and improved bioinformatic tools would suggest that HTS will be implemented as a sensitive virus detection tool more routinely. The discovery of the complex grapevine virome challenges the concept of what can be considered as a healthy vine although offering new opportunities to the implementation of certification schemes and exchanges of plant propagation materials. In this chapter the history of HTS in grapevine virus research is reviewed followed by the exploration of the different strategies used for the discovery of new viruses and new variants of known viruses. The concept of a "background" virome is introduced and explored within the context of its interaction with the host and the impact this might have on certification of healthy plant material. The chapter is concluded with some thoughts on the future of HTS in grapevine virus research.
Curation of viral genomes: challenges, applications and the way forward
BMC Bioinformatics, 2006
Background: Whole genome sequence data is a step towards generating the 'parts list' of life to understand the underlying principles of Biocomplexity. Genome sequencing initiatives of human and model organisms are targeted efforts towards understanding principles of evolution with an application envisaged to improve human health. These efforts culminated in the development of dedicated resources. Whereas a large number of viral genomes have been sequenced by groups or individuals with an interest to study antigenic variation amongst strains and species. These independent efforts enabled viruses to attain the status of 'best-represented taxa' with the highest number of genomes. However, due to lack of concerted efforts, viral genomic sequences merely remained as entries in the public repositories until recently.
Bioinformatics Tool for Identification of Virulent Sequence in Viral Genome.
Computer society of India conference
A virus is a small infectious agent that can replicate only inside the living cells of an organism. Viruses can infect all types of organisms, from animals and plants to bacteria. The most commonly used laboratory methods for the detection of viruses and virus components in biological samples can be broadly divided into 3 categories – those that measure virus infectivity, those that examine viral serology (that is, host antibody responses to the virus), and those that rely on molecular methods. Current tests for determining viral load generally rely on a technique called polymerase chain reaction (PCR) and other is DNA microarray technology. However both methods are costly and time consuming. Thus the need for easy, quick and cost-effective technique is essential to find the viral sequence. Use of Bioinformatics for developing a tool using simple computer program helped to analyze, identify and extract the virulent sequence from viral genome.
viruSITE—integrated database for viral genomics
Database, 2016
Viruses are the most abundant biological entities and the reservoir of most of the genetic diversity in the Earth's biosphere. Viral genomes are very diverse, generally short in length and compared to other organisms carry only few genes. viruSITE is a novel database which brings together high-value information compiled from various resources. viruSITE covers the whole universe of viruses and focuses on viral genomes, genes and proteins. The database contains information on virus taxonomy, host range, genome features, sequential relatedness as well as the properties and functions of viral genes and proteins. All entries in the database are linked to numerous information resources. The above-mentioned features make viruSITE a comprehensive knowledge hub in the field of viral genomics. The web interface of the database was designed so as to offer an easy-to-navigate, intuitive and user-friendly environment. It provides sophisticated text searching and a taxonomy-based browsing system. viruSITE also allows for an alternative approach based on sequence search. A proprietary genome browser generates a graphical representation of viral genomes. In addition to retrieving and visualising data, users can perform comparative genomics analyses using a variety of tools.
Evolution of selective-sequencing approaches for virus discovery and virome analysis
Virus research, 2017
Recent advances in sequencing technologies have transformed the field of virus discovery and virome analysis. Once, mostly confined to the traditional Sanger sequencing based individual virus discovery, is now entirely replaced by high throughput sequencing (HTS) based virus metagenomics that can be used to characterize the nature and composition of entire viromes. To better harness the potential of HTS for study of viromes, sample preparation methodologies used different refinements to exclude amplification of non-viral components that can overshadow low-titer viruses. These virus-sequence enrichment approaches mostly focused on the sample preparation methods, like enzymatic digestion of non-viral nucleic acids and size exclusion of non-viral constituents by column filtration, ultrafiltration or density centrifugation. However, recently an approach of virus-sequence enrichment called virome-capture sequencing, focused on the amplification or HTS library preparation stage, was shown...