Dataset Information

Deep sequencing analysis of viral infection and evolution allows rapid and detailed characterization of viral mutant spectrum.

ABSTRACT:

Motivation

The study of RNA virus populations is a challenging task. Each population of RNA virus is composed of a collection of different, yet related genomes often referred to as mutant spectra or quasispecies. Virologists using deep sequencing technologies face major obstacles when studying virus population dynamics, both experimentally and in natural settings due to the relatively high error rates of these technologies and the lack of high performance pipelines. In order to overcome these hurdles we developed a computational pipeline, termed ViVan (Viral Variance Analysis). ViVan is a complete pipeline facilitating the identification, characterization and comparison of sequence variance in deep sequenced virus populations.

Results

Applying ViVan on deep sequenced data obtained from samples that were previously characterized by more classical approaches, we uncovered novel and potentially crucial aspects of virus populations. With our experimental work, we illustrate how ViVan can be used for studies ranging from the more practical, detection of resistant mutations and effects of antiviral treatments, to the more theoretical temporal characterization of the population in evolutionary studies.

Availability and implementation

Freely available on the web at http://www.vivanbioinfo.org

Contact

: nshomron@post.tau.ac.il

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Isakov O

PROVIDER: S-EPMC4481840 | biostudies-literature | 2015 Jul

REPOSITORIES: biostudies-literature

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Publications

Deep sequencing analysis of viral infection and evolution allows rapid and detailed characterization of viral mutant spectrum.

Isakov Ofer O Bordería Antonio V AV Golan David D Hamenahem Amir A Celniker Gershon G Yoffe Liron L Blanc Hervé H Vignuzzi Marco M Shomron Noam N

Bioinformatics (Oxford, England) 20150219 13

<h4>Motivation</h4>The study of RNA virus populations is a challenging task. Each population of RNA virus is composed of a collection of different, yet related genomes often referred to as mutant spectra or quasispecies. Virologists using deep sequencing technologies face major obstacles when studying virus population dynamics, both experimentally and in natural settings due to the relatively high error rates of these technologies and the lack of high performance pipelines. In order to overcome ...[more]

PMID: 25701575

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Dataset Information

Deep sequencing analysis of viral infection and evolution allows rapid and detailed characterization of viral mutant spectrum.

Motivation

Results

Availability and implementation

Contact

Supplementary information

Publications

Deep sequencing analysis of viral infection and evolution allows rapid and detailed characterization of viral mutant spectrum.

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