ArticlePloS one2019
Identification and quantification of defective virus genomes in high throughput sequencing data using DVG-profiler, a novel post-sequence alignment processing algorithm.
Article in PloS one, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 33 citations in OpenAlex.
- Identification of fidelity-determined residues of Porcine reproductive and respiratory syndrome virus through structural alignment.Virulence · 2026Article
- Accounting for Defective Viral Genomes in viral consensus genome reconstruction, application to influenza virus.PLoS computational biology · 2026Article
- Molecular characterization of arenavirus defective viral genomes reveals sequence features associated with their formation.Journal of virology · 2026Article
- Bioinformatics identification of copyback and multihost-adapted defective viral genomes in dengue virus.Frontiers in cellular and infection microbiology · 2026Article
- Deletion detection in SARS-CoV-2 genomes from COVID-19 patients: elimination of false positives.Virus evolution · 2026Article
- Classification, functions, evolution, and applications of defective viral genomes.Frontiers in microbiology · 2026Review
- ELViS: an R package for estimating copy number levels of viral genomic segments at base-resolution.Bioinformatics (Oxford, England) · 2025Article
- Defective but promising: evaluating the utility of currently available bioinformatic pipelines for detecting defective viral genomes in RNA-Seq data.The Journal of general virology · 2025Article
- Validation of diverse and previously untraceable Sendai virus copyback viral genomes by direct RNA sequencing.Journal of virology · 2025Article
- Intersegment Recombination During Influenza A Virus Replication Gives Rise to a Novel Class of Defective Viral Genomes.Viruses · 2025Article
- Identification, functional analysis, and clinical applications of defective viral genomes.Frontiers in microbiology · 2025Review
- The ageing virus hypothesis: Epigenetic ageing beyond the Tree of Life.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- Population dynamics of defective viral genomes of tomato black ring virus during host-to-host transmission.Journal of virology · 2024Article
- Quantifying defective and wild-type viruses from high-throughput RNA sequencing.Bioinformatics (Oxford, England) · 2024Article
- Intra-Host Citrus Tristeza Virus Populations during Prolonged Infection Initiated by a Well-Defined Sequence Variant inViruses · 2024Article
- Expanding Possibilities for Foreign Gene Expression by Cucumber Green Mottle Mosaic Virus Genome-Based Bipartite Vector System.Plants (Basel, Switzerland) · 2024Article
- Antiviral responses versus virus-induced cellular shutoff: a game of thrones between influenza A virus NS1 and SARS-CoV-2 Nsp1.Frontiers in cellular and infection microbiology · 2024Review
- VODKA2: a fast and accurate method to detect non-standard viral genomes from large RNA-seq data sets.RNA (New York, N.Y.) · 2023Article
- High-resolution mapping reveals the mechanism and contribution of genome insertions and deletions to RNA virus evolution.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Review
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Authors and funding
11 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Most viruses are known to spontaneously generate defective viral genomes (DVG) due to errors during replication. These DVGs are subgenomic and contain deletions that render them unable to complete a full replication cycle in the absence of a co-infecting, non-defective helper virus. DVGs, especially of the copyback type, frequently observed with paramyxoviruses, have been recognized to be important triggers of the antiviral innate immune response. DVGs have therefore gained interest for their potential to alter the attenuation and immunogenicity of vaccines. To investigate this potential, accurate identification and quantification of DVGs is essential. Conventional methods, such as RT-PCR, are labor intensive and will only detect primer sequence-specific species. High throughput sequencing (HTS) is much better suited for this undertaking. Here, we present an HTS-based algorithm called DVG-profiler to identify and quantify all DVG sequences in an HTS data set generated from a virus preparation. DVG-profiler identifies DVG breakpoints relative to a reference genome and reports the directionality of each segment from within the same read. The specificity and sensitivity of the algorithm was assessed using both in silico data sets as well as HTS data obtained from parainfluenza virus 5, Sendai virus and mumps virus preparations. HTS data from the latter were also compared with conventional RT-PCR data and with data obtained using an alternative algorithm. The data presented here demonstrate the high specificity, sensitivity, and robustness of DVG-profiler. This algorithm was implemented within an open source cloud-based computing environment for analyzing HTS data. DVG-profiler might prove valuable not only in basic virus research but also in monitoring live attenuated vaccines for DVG content and to assure vaccine lot to lot consistency.
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