ArticleGenome biology and evolution2015
Cancer, Warts, or Asymptomatic Infections: Clinical Presentation Matches Codon Usage Preferences in Human Papillomaviruses.
Article in Genome biology and evolution, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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.
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Who cites it
11 citing papers in PubMed.
- Translational regulation of human papillomavirus mRNAs in carcinogenesis: old questions and new insights.Frontiers in cell and developmental biology · 2025Review
- Why HPV16? Why, now, HPV42? How the discovery of HPV42 in rare cancers provides an opportunity to challenge our understanding about the transition between health and disease for common members of the healthy microbiota.FEMS microbiology reviews · 2024Review
- A small stretch of poor codon usage at the beginning of dengue virus open reading frame may act as a translational checkpoint.BMC research notes · 2023Article
- Article
- Variability in Codon Usage in Coronaviruses Is Mainly Driven by Mutational Bias and Selective Constraints on CpG Dinucleotide.Viruses · 2021Article
- Article
- Papillomaviruses infecting cetaceans exhibit signs of genome adaptation following a recombination event.Virus evolution · 2020Article
- Genome Plasticity in Papillomaviruses and De Novo Emergence of E5 Oncogenes.Genome biology and evolution · 2019Article
- HPV disease transmission protection and control.Microbial cell (Graz, Austria) · 2016Review
- Assessing parallel gene histories in viral genomes.BMC evolutionary biology · 2016Article
- Role of the host restriction factor APOBEC3 on papillomavirus evolution.Virus evolution · 2015Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Viruses rely completely on the hosts' machinery for translation of viral transcripts. However, for most viruses infecting humans, codon usage preferences (CUPrefs) do not match those of the host. Human papillomaviruses (HPVs) are a showcase to tackle this paradox: they present a large genotypic diversity and a broad range of phenotypic presentations, from asymptomatic infections to productive lesions and cancer. By applying phylogenetic inference and dimensionality reduction methods, we demonstrate first that genes in HPVs are poorly adapted to the average human CUPrefs, the only exception being capsid genes in viruses causing productive lesions. Phylogenetic relationships between HPVs explained only a small proportion of CUPrefs variation. Instead, the most important explanatory factor for viral CUPrefs was infection phenotype, as orthologous genes in viruses with similar clinical presentation displayed similar CUPrefs. Moreover, viral genes with similar spatiotemporal expression patterns also showed similar CUPrefs. Our results suggest that CUPrefs in HPVs reflect either variations in the mutation bias or differential selection pressures depending on the clinical presentation and expression timing. We propose that poor viral CUPrefs may be central to a trade-off between strong viral gene expression and the potential for eliciting protective immune response.
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Registered trials
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