ArticleNucleic acids research2007
Codon conservation in the influenza A virus genome defines RNA packaging signals.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 100 papers.
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Who cites it
100 citing papers in PubMed, 182 citations in OpenAlex.
- Deep learning predicts potential reassortments of avian H5N1 with human influenza viruses.National science review · 2025Article
- Concentration-dependent formation of intersegment interactions in the viral inclusions of influenza A virus infected cells.iScience · 2025Article
- High-throughput single-virion DNA-PAINT reveals structural diversity, cooperativity, and flexibility during selective packaging in influenza.Nucleic acids research · 2025Article
- Article
- Locations and structures of influenza A virus packaging-associated signals and other functional elements via an in silico pipeline for predicting constrained features in RNA viruses.PLoS computational biology · 2024Article
- Review
- Mechanisms and consequences of mRNA destabilization during viral infections.Virology journal · 2024Review
- Co-evolution of immunity and seasonal influenza viruses.Nature reviews. Microbiology · 2023Review
- Influenza virus transcription and progeny production are poorly correlated in single cells.eLife · 2023Article
- A novel approach to finding conserved features in low-variability gene alignments characterises RNA motifs in SARS-CoV and SARS-CoV-2.Scientific reports · 2023Article
- Sequential disruption of SPLASH-identified vRNA-vRNA interactions challenges their role in influenza A virus genome packaging.Nucleic acids research · 2023Article
- In vivo secondary structural analysis of Influenza A virus genomic RNA.Cellular and molecular life sciences : CMLS · 2023Article
- CpG dinucleotide enrichment in the influenza A virus genome as a live attenuated vaccine development strategy.PLoS pathogens · 2023Article
- Comprehensive in virio structure probing analysis of the influenza A virus identifies functional RNA structures involved in viral genome replication.Computational and structural biotechnology journal · 2023Article
- Rotavirus RNA chaperone mediates global transcriptome-wide increase in RNA backbone flexibility.Nucleic acids research · 2022Article
- Programmable antivirals targeting critical conserved viral RNA secondary structures from influenza A virus and SARS-CoV-2.Nature medicine · 2022Article
- Contribution of RNA-RNA Interactions Mediated by the Genome Packaging Signals for the Selective Genome Packaging of Influenza A Virus.Journal of virology · 2022Article
- In silico analysis of local RNA secondary structure in influenza virus A, B and C finds evidence of widespread ordered stability but little evidence of significant covariation.Scientific reports · 2022Article
- Synergistic Effect between 3'-Terminal Noncoding and Adjacent Coding Regions of the Influenza A Virus Hemagglutinin Segment on Template Preference.Journal of virology · 2021Article
- Selective Genome Packaging Mechanisms of Influenza A Viruses.Cold Spring Harbor perspectives in medicine · 2021Review
40 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 3 institutions in 3 countries.
Funding
Abstract
Genome segmentation facilitates reassortment and rapid evolution of influenza A virus. However, segmentation complicates particle assembly as virions must contain all eight vRNA species to be infectious. Specific packaging signals exist that extend into the coding regions of most if not all segments, but these RNA motifs are poorly defined. We measured codon variability in a large dataset of sequences to identify areas of low nucleotide sequence variation independent of amino acid conservation in each segment. Most clusters of codons showing very little synonymous variation were located at segment termini, consistent with previous experimental data mapping packaging signals. Certain internal regions of conservation, most notably in the PA gene, may however signify previously unidentified functions in the virus genome. To experimentally test the bioinformatics analysis, we introduced synonymous mutations into conserved codons within known packaging signals and measured incorporation of the mutant segment into virus particles. Surprisingly, in most cases, single nucleotide changes dramatically reduced segment packaging. Thus our analysis identifies cis-acting sequences in the influenza virus genome at the nucleotide level. Furthermore, we propose that strain-specific differences exist in certain packaging signals, most notably the haemagglutinin gene; this finding has major implications for the evolution of pandemic viruses.
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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.