Metagenomics and the molecular identification of novel viruses

Bexfield, Nick; Kellam, Paul

doi:10.1016/j.tvjl.2010.10.014

Cited by 81 publications

(65 citation statements)

References 115 publications

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“…On the basis of these results, the probability of false-negative results in this analysis is believed to be low. Indeed, Bexfield and Kellam (38) performed an elegant simulation to estimate the probability of detecting viral sequences based on the viral genome transcript sequence frequency and the number of sequence reads generated.…”

Section: Discussionmentioning

confidence: 99%

Landscape of DNA Virus Associations across Human Malignant Cancers: Analysis of 3,775 Cases Using RNA-Seq

Khoury¹,

Tannir

Williams³

et al. 2013

J Virol

198

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Elucidation of tumor-DNA virus associations in many cancer types has enhanced our knowledge of fundamental oncogenesis mechanisms and provided a basis for cancer prevention initiatives. RNA-Seq is a novel tool to comprehensively assess such associations. We interrogated RNA-Seq data from 3,775 malignant neoplasms in The Cancer Genome Atlas database for the presence of viral sequences. Viral integration sites were also detected in expressed transcripts using a novel approach. The detection capacity of RNA-Seq was compared to available clinical laboratory data. Human papillomavirus (HPV) transcripts were detected using RNA-Seq analysis in head-and-neck squamous cell carcinoma, uterine endometrioid carcinoma, and squamous cell carcinoma of the lung. Detection of HPV by RNA-Seq correlated with detection by in situ hybridization and immunohistochemistry in squamous cell carcinoma tumors of the head and neck. Hepatitis B virus and Epstein-Barr virus (EBV) were detected using RNA-Seq in hepatocellular carcinoma and gastric carcinoma tumors, respectively. Integration sites of viral genes and oncogenes were detected in cancers harboring HPV or hepatitis B virus but not in EBV-positive gastric carcinoma. Integration sites of expressed viral transcripts frequently involved known coding areas of the host genome. No DNA virus transcripts were detected in acute myeloid leukemia, cutaneous melanoma, low-and high-grade gliomas of the brain, and adenocarcinomas of the breast, colon and rectum, lung, prostate, ovary, kidney, and thyroid. In conclusion, this study provides a large-scale overview of the landscape of DNA viruses in human malignant cancers. While further validation is necessary for specific cancer types, our findings highlight the utility of RNA-Seq in detecting tumor-associated DNA viruses and identifying viral integration sites that may unravel novel mechanisms of cancer pathogenesis.

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Section: Discussionmentioning

confidence: 99%

Landscape of DNA Virus Associations across Human Malignant Cancers: Analysis of 3,775 Cases Using RNA-Seq

Khoury¹,

Tannir

Williams³

et al. 2013

J Virol

198

View full text Add to dashboard Cite

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“…characterization (Ambrose and Clewley 2006;Delwart 2007;Bexfield and Kellam 2010). Some of the more commonly used sequence-independent strategies are briefly described in the following sections as well as a number of different sequencing technologies.…”

Section: Step Two -Sequence-independent Amplificationmentioning

confidence: 99%

“…The use of hybridization-based approaches, such as microarray and subtractive hybridization, can be found in other reviews (Ambrose and Clewley 2006;Delwart 2007;Bexfield and Kellam 2010;Tang and Chiu 2010). It also discusses shortly how to follow up on the findings and what the different possible viral metagenomic applications in veterinary science are.…”

Section: Introductionmentioning

confidence: 99%

Viral metagenomics as an emerging and powerful tool in veterinary medicine

Blomström

2011

Veterinary Quarterly

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New diseases continue to emerge in both human and animal populations, and the importance of animals, as reservoirs for viruses that can cause zoonoses are evident. Thus, an increased knowledge of the viral flora in animals, both in healthy and diseased individuals, is important both for animal and human health. Viral metagenomics is a culture-independent approach that is used to investigate the complete viral genetic populations of a sample. This review describes and discusses the different possible steps of a viral metagenomic study utilizing sequence-independent amplification, high-throughput sequencing, and bioinformatics to identify viruses. With this technology, multiple viruses can be detected simultaneously and novel and highly divergent viruses can be discovered and genetically characterized for the first time. This review also briefly discusses the applications of viral metagenomics in veterinary science and lists some of the viruses discovered within this field.

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“…Sometimes viral etiology cannot be characterized by traditional culture and molecular methods [6]. Scarce techniques, such as depictive modification investigation or arbitrary sequencing of plasmid libraries of nuclease resilient drivels of viral genomes [7], take lead in the previous to the discovery of several viruses, counting polyomavirus [8].…”

Section: Introductionmentioning

confidence: 99%

Next-generation sequencing technologies as emergent tools and their challenges in viral diagnostic

Singh¹

2018

biomedicalresearch

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Next-Generation Sequencing (NGS) has the range of high-throughput quickly adapted into the countless facet of viral diagnostic research. This method has been extensively applying in full genome sequencing, genetic diversity identification, transcriptomic routine diagnostic work patient care and management, and the new understanding of the interactions between viral and host transcriptome, to promote virus research. An exciting era of viral exploration has begun and will set us new challenges to understand the role of newly discovered viral diversity in both disease and health. In this review, discuss about the preparation of viral nucleic acid templates for sequencing, assay formats underlying next-generation sequencing systems, methods for imaging and base calling, quality control, data processing pipelines and bioinformatics approaches for sequence alignment, variant calling and suggestions for selecting suitable tools. Also discuss of the most important advances that the new sequencing technologies have brought to the fields of clinical virology and challenges behind it.

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Metagenomics and the molecular identification of novel viruses

Cited by 81 publications

References 115 publications

Landscape of DNA Virus Associations across Human Malignant Cancers: Analysis of 3,775 Cases Using RNA-Seq

Landscape of DNA Virus Associations across Human Malignant Cancers: Analysis of 3,775 Cases Using RNA-Seq

Viral metagenomics as an emerging and powerful tool in veterinary medicine

Next-generation sequencing technologies as emergent tools and their challenges in viral diagnostic

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