ArticleJournal of virology2019
Sequencing Framework for the Sensitive Detection and Precise Mapping of Defective Interfering Particle-Associated Deletions across Influenza A and B Viruses.
Article in Journal of virology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
56 citing papers in PubMed, 1 synthesis or guideline pooled it, 76 citations in OpenAlex.
- Meta-analysis of genomic characteristics for antiviral influenza defective interfering particle prioritization.NAR genomics and bioinformatics · 2025Pooled it
- Influenza A deletion-containing viral genome production is altered by metabolites, metabolic signaling molecules, and cyanobacterial extracts.Applied and environmental microbiology · 2026Article
- Accounting for Defective Viral Genomes in viral consensus genome reconstruction, application to influenza virus.PLoS computational biology · 2026Article
- Longitudinal analysis of influenza A virus deletion-containing viral genomes reveals key determinants of co-evolutionary dynamics and interference.Nature communications · 2026Article
- Host genotype and sex shape influenza evolution and defective viral genomes.Nature communications · 2026Article
- Classification, functions, evolution, and applications of defective viral genomes.Frontiers in microbiology · 2026Review
- Deletion detection in SARS-CoV-2 genomes from COVID-19 patients: elimination of false positives.Virus evolution · 2026Article
- Host PI3K inhibition via anti-cancer drug alpelisib influences Influenza A non-infectious particles and deletion-containing viral genomes.Cell communication and signaling : CCS · 2025Article
- Phage-bacteria dynamics: The tragedy of the commons at hyperspeed.Current biology : CB · 2025Article
- Review
- Longitudinal analysis of influenza A virus deletion-containing viral genomes reveals key determinants of co-evolutionary dynamics and interference.bioRxiv : the preprint server for biology · 2025Article
- Live attenuated influenza vaccine with low proportions of defective interfering particles elicits robust immunogenicity and cross-protection.Nature communications · 2025Article
- Optimized high-throughput whole-genome sequencing workflow for surveillance of influenza A virus.Genome medicine · 2025Article
- Inflammatory, transcriptomic, and cell fate responses underlying the mammalian transmission of avian influenza viruses.Journal of virology · 2025Article
- Intersegment Recombination During Influenza A Virus Replication Gives Rise to a Novel Class of Defective Viral Genomes.Viruses · 2025Article
- Impact of inactivated vaccine on transmission and evolution of H9N2 avian influenza virus in chickens.NPJ vaccines · 2025Article
- High-throughput sequencing-based neutralization assay reveals how repeated vaccinations impact titers to recent human H1N1 influenza strains.Journal of virology · 2024Article
- Mathematical model calibrated toiScience · 2024Article
- Cryptic proteins translated from deletion-containing viral genomes dramatically expand the influenza virus proteome.Nucleic acids research · 2024Article
- High-throughput sequencing-based neutralization assay reveals how repeated vaccinations impact titers to recent human H1N1 influenza strains.bioRxiv : the preprint server for biology · 2024Article
Corrections and comments
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
The mechanisms and consequences of defective interfering particle (DIP) formation during influenza virus infection remain poorly understood. The development of next-generation sequencing (NGS) technologies has made it possible to identify large numbers of DIP-associated sequences, providing a powerful tool to better understand their biological relevance. However, NGS approaches pose numerous technical challenges, including the precise identification and mapping of deletion junctions in the presence of frequent mutation and base-calling errors, and the potential for numerous experimental and computational artifacts. Here, we detail an Illumina-based sequencing framework and bioinformatics pipeline capable of generating highly accurate and reproducible profiles of DIP-associated junction sequences. We use a combination of simulated and experimental control data sets to optimize pipeline performance and demonstrate the absence of significant artifacts. Finally, we use this optimized pipeline to reveal how the patterns of DIP-associated junction formation differ between different strains and subtypes of influenza A and B viruses and to demonstrate how these data can provide insight into mechanisms of DIP formation. Overall, this work provides a detailed roadmap for high-resolution profiling and analysis of DIP-associated sequences within influenza virus populations.
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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.