ArticleNucleic acids research2018
Structural divergence creates new functional features in alphavirus genomes.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers, 1 of them a synthesis that pooled it.
What it found
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Who cites it
45 citing papers in PubMed, 1 synthesis or guideline pooled it, 67 citations in OpenAlex.
- The life cycle of the alphaviruses: From an antiviral perspective.Antiviral research · 2023Pooled it
- Review
- A conserved in-frame stop codon acts as a multipotent defense mechanism in alphaviruses.Science advances · 2026Article
- SHAPE-MaP-Based Assessment of the Structure of Citrus Tristeza Virus Long Non-Coding RNA.Viruses · 2026Article
- Diverse database and machine learning model to narrow the generalization gap in RNA structure prediction.Science advances · 2026Article
- The ability of alphavirus replicases to synthesize non-viral type I interferon-inducing RNAs correlates with viral RNA synthesis and has a diverse impact on virus replication and pathogenicity.Journal of virology · 2026Article
- The Sindbis virus nsP3 opal codon protects viral RNA and fitness by maintaining replication spherule integrity.bioRxiv : the preprint server for biology · 2025Article
- Article
- Eastern equine encephalitis virus: Pathogenesis, immune response, and clinical manifestations.Infectious medicine · 2025Review
- RNA architecture of porcine deltacoronavirus genome inside virions detected by vRIC-seq.Scientific data · 2024Article
- The molecular dissection of TRIM25's RNA-binding mechanism provides key insights into its antiviral activity.Nature communications · 2024Article
- RNA structures within Venezuelan equine encephalitis virus E1 alter macrophage replication fitness and contribute to viral emergence.PLoS pathogens · 2024Article
- Chikungunya Virus RNA Secondary Structures Impact Defective Viral Genome Production.Microorganisms · 2024Article
- RNA structures within Venezuelan equine encephalitis virus E1 alter macrophage replication fitness and contribute to viral emergence.bioRxiv : the preprint server for biology · 2024Article
- Unraveling the complex interplay: immunopathology and immune evasion strategies of alphaviruses with emphasis on neurological implications.Frontiers in cellular and infection microbiology · 2024Review
- The RNA helicase DDX39A binds a conserved structure in chikungunya virus RNA to control infection.Molecular cell · 2023Article
- Structural analysis of MALAT1 long noncoding RNA in cells and in evolution.RNA (New York, N.Y.) · 2023Article
- Structure-first identification of RNA elements that regulate dengue virus genome architecture and replication.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Article
- RNA secondary structure packages evaluated and improved by high-throughput experiments.Nature methods · 2022Article
Corrections and comments
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Authors and funding
11 authors at 2 institutions in 1 country.
Funding
Abstract
Alphaviruses are mosquito-borne pathogens that cause human diseases ranging from debilitating arthritis to lethal encephalitis. Studies with Sindbis virus (SINV), which causes fever, rash, and arthralgia in humans, and Venezuelan equine encephalitis virus (VEEV), which causes encephalitis, have identified RNA structural elements that play key roles in replication and pathogenesis. However, a complete genomic structural profile has not been established for these viruses. We used the structural probing technique SHAPE-MaP to identify structured elements within the SINV and VEEV genomes. Our SHAPE-directed structural models recapitulate known RNA structures, while also identifying novel structural elements, including a new functional element in the nsP1 region of SINV whose disruption causes a defect in infectivity. Although RNA structural elements are important for multiple aspects of alphavirus biology, we found the majority of RNA structures were not conserved between SINV and VEEV. Our data suggest that alphavirus RNA genomes are highly divergent structurally despite similar genomic architecture and sequence conservation; still, RNA structural elements are critical to the viral life cycle. These findings reframe traditional assumptions about RNA structure and evolution: rather than structures being conserved, alphaviruses frequently evolve new structures that may shape interactions with host immune systems or co-evolve with viral proteins.
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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.