ArticleRNA (New York, N.Y.)2020
RNA-seq accuracy and reproducibility for the mapping and quantification of influenza defective viral genomes.
Article in RNA (New York, N.Y.), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers, 1 of them a synthesis that pooled it.
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Who cites it
24 citing papers in PubMed, 1 synthesis or guideline pooled it, 30 citations in OpenAlex.
- Meta-analysis of genomic characteristics for antiviral influenza defective interfering particle prioritization.NAR genomics and bioinformatics · 2025Pooled it
- Accounting for Defective Viral Genomes in viral consensus genome reconstruction, application to influenza virus.PLoS computational biology · 2026Article
- Detailed single-cell mapping of the transcriptional response to a virus infection driven by copy-back viral genomes.PLoS pathogens · 2026Article
- Molecular characterization of arenavirus defective viral genomes reveals sequence features associated with their formation.Journal of virology · 2026Article
- Detailed single-cell mapping of the transcriptional response to a virus infection driven by copy-back viral genomes.bioRxiv : the preprint server for biology · 2026Article
- Classification, functions, evolution, and applications of defective viral genomes.Frontiers in microbiology · 2026Review
- 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
- Review
- Population dynamics of defective viral genomes of tomato black ring virus during host-to-host transmission.Journal of virology · 2024Article
- Evaluating storage conditions and enhancement strategies on viral biomarker recovery for WBE applications.Water science and technology : a journal of the International Association on Water Pollution Research · 2024Article
- Influenza A genomic diversity during human infections underscores the strength of genetic drift and the existence of tight transmission bottlenecks.Virus evolution · 2024Article
- VODKA2: a fast and accurate method to detect non-standard viral genomes from large RNA-seq data sets.RNA (New York, N.Y.) · 2023Article
- Generation and Functional Analysis of Defective Viral Genomes during SARS-CoV-2 Infection.mBio · 2023Article
- ViReMa: a virus recombination mapper of next-generation sequencing data characterizes diverse recombinant viral nucleic acids.GigaScience · 2023Article
- Transient RNA structures cause aberrant influenza virus replication and innate immune activation.Science advances · 2022Article
- Article
- Accumulation of copy-back viral genomes during respiratory syncytial virus infection is preceded by diversification of the copy-back viral genome population followed by selection.Virus evolution · 2022Article
- Article
Corrections and comments
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Authors and funding
10 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Like most RNA viruses, influenza viruses generate defective viral genomes (DVGs) with large internal deletions during replication. There is accumulating evidence supporting a biological relevance of such DVGs. However, further understanding of the molecular mechanisms that underlie the production and biological activity of DVGs is conditioned upon the sensitivity and accuracy of detection methods, that is, next-generation sequencing (NGS) technologies and related bioinformatics algorithms. Although many algorithms were developed, their sensitivity and reproducibility were mostly assessed on simulated data. Here, we introduce DG-seq, a time-efficient pipeline for DVG detection and quantification, and a set of biological controls to assess the performance of not only our bioinformatics algorithm but also the upstream NGS steps. Using these tools, we provide the first rigorous comparison of the two commonly used sample processing methods for RNA-seq, with or without a PCR preamplification step. Our data show that preamplification confers a limited advantage in terms of sensitivity and introduces size- but also sequence-dependent biases in DVG quantification, thereby providing a strong rationale to favor preamplification-free methods. We further examine the features of DVGs produced by wild-type and transcription-defective (PA-K635A or PA-R638A) influenza viruses, and show an increased diversity and frequency of DVGs produced by the PA mutants compared to the wild-type virus. Finally, we demonstrate a significant enrichment in DVGs showing direct, A/T-rich sequence repeats at the deletion breakpoint sites. Our findings provide novel insights into the mechanisms of influenza virus DVG production.
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Registered trials
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.