ArticleBioinformatics (Oxford, England)2015
Deep sequencing analysis of viral infection and evolution allows rapid and detailed characterization of viral mutant spectrum.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Enlarging viral mutation estimation: a view from the distribution of mutation rates.Microbiology (Reading, England) · 2026Article
- Mutation in enterovirus 71 nonstructural protein 3A increases genome replication fidelity and exhibits attenuated virulence in mice.Journal of virology · 2025Article
- Mutational landscapes of NITD008-resistant EV71 variants revealed through population sequencing.Virologica Sinica · 2025Article
- Algorithms for Short-Read Viral Haplotype Reconstruction: Challenges, Solutions, and Perspectives.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Embracing Complexity: What Novel Sequencing Methods Are Teaching Us About Herpesvirus Genomic Diversity.Annual review of virology · 2024Review
- Innate immune pathways act synergistically to constrain RNA virus evolution in Drosophila melanogaster.Nature ecology & evolution · 2022Article
- Experimental Evolution Reveals a Genetic Basis for Membrane-Associated Virus Release.Molecular biology and evolution · 2021Article
- Epidemiological data analysis of viral quasispecies in the next-generation sequencing era.Briefings in bioinformatics · 2021Review
- Experimental virus evolution in cancer cell monolayers, spheroids, and tissue explants.Virus evolution · 2021Article
- Strategy and Performance Evaluation of Low-Frequency Variant Calling for SARS-CoV-2 Using Targeted Deep Illumina Sequencing.Frontiers in microbiology · 2021Article
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- Application of Next-Generation Sequencing to Reveal How Evolutionary Dynamics of Viral Population Shape Dengue Epidemiology.Frontiers in microbiology · 2020Review
- Host nutritional status affects alphavirus virulence, transmission, and evolution.PLoS pathogens · 2019Article
- Membrane-Associated Enteroviruses Undergo Intercellular Transmission as Pools of Sibling Viral Genomes.Cell reports · 2019Article
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- Isolation of Highly Pathogenic H5N1 Influenza Viruses in 2009-2013 in Vietnam.Frontiers in microbiology · 2019Article
- Theoretical conditions for the coexistence of viral strains with differences in phenotypic traits: a bifurcation analysis.Royal Society open science · 2019Article
- Sixth European Seminar in Virology on Virus⁻Host Interaction at Single Cell and Organism Level.Viruses · 2018Article
- Seasonal Genetic Drift of Human Influenza A Virus Quasispecies Revealed by Deep Sequencing.Frontiers in microbiology · 2018Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationThe 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.
resultsApplying 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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.