ArticlePloS one2013
CpG usage in RNA viruses: data and hypotheses.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
66 citing papers in PubMed, 121 citations in OpenAlex.
- Increased or decreased numbers of CpG dinucleotide motifs in the genome of influenza A virus do not affectJournal of virology · 2026Article
- Genomic features associated with sustained mammalian transmission of avian influenza A viruses.Nature microbiology · 2026Article
- The Emerging JEV Genotype 5 Exhibits Distinct Codon Usage Characteristics.Pathogens (Basel, Switzerland) · 2026Article
- Construction of Attenuated Viruses by Changing the UpA Dinucleotide Frequency.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Impact of the Zinc Antiviral Protein on the Genomic Composition of RNA Viruses Infecting Vertebrates.Molecular biology and evolution · 2025Article
- Article
- Exploring laccase: a sustainable enzymatic solution for the paper recycling domain.Archives of microbiology · 2024Review
- Innate immune regulations and various siRNA modalities.Drug delivery and translational research · 2023Review
- Codon usage bias analysis of the gene encoding NADArchives of microbiology · 2023Article
- Different Patterns of Codon Usage and Amino Acid Composition across Primate Lentiviruses.Viruses · 2023Article
- The virome of the invasive Asian bush mosquitoVirus evolution · 2023Article
- Selective Depletion of ZAP-Binding CpG Motifs in HCV Evolution.Pathogens (Basel, Switzerland) · 2022Article
- Codon Usage Provides Insights into the Adaptive Evolution of Mycoviruses in Their Associated Fungi Host.International journal of molecular sciences · 2022Article
- Intracellular mono-ADP-ribosyltransferases at the host-virus interphase.Cellular and molecular life sciences : CMLS · 2022Review
- Assessing in vivo mutation frequencies and creating a high-resolution genome-wide map of fitness costs of Hepatitis C virus.PLoS genetics · 2022Article
- Article
- Synonymous Codon Pattern of Cowpea Mild Mottle Virus Sheds Light on Its Host Adaptation and Genome Evolution.Pathogens (Basel, Switzerland) · 2022Article
- The low abundance of CpG in the SARS-CoV-2 genome is not an evolutionarily signature of ZAP.Scientific reports · 2022Article
- CpG content in the Zika virus genome affects infection phenotypes in the adult brain and fetal lymph nodes.Frontiers in immunology · 2022Article
- Zinc-finger antiviral protein-mediated inhibition of porcine epidemic diarrhea virus growth is antagonized by the coronaviral nucleocapsid protein.Frontiers in microbiology · 2022Article
6 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
7 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
CpG repression in RNA viruses has been known for decades, but a reasonable explanation has not yet been proposed to explain this phenomenon. In this study, we calculated the CpG odds ratio of all RNA viruses that have available genome sequences and analyzed the correlation with their genome polarity, base composition, synonymous codon usage, phylogenetic relationship, and host. The results indicated that the viral base composition, synonymous codon usage and host selection were the dominant factors that determined the CpG bias in RNA viruses. CpG usage variation between the different viral groups was caused by different combinations of these pressures, which also differed from each other in strength. The consistent under-representation of CpG usage in -ssRNA viruses is determined predominantly by base composition, which may be a consequence of the U/A preferred mutation bias of -ssRNA viruses, whereas the CpG usage of +ssRNA viruses is affected greatly by their hosts. As a result, most +ssRNA viruses mimic their hosts' CpG usage. Unbiased CpG usage in dsRNA viruses is most likely a result of their dsRNA genome, which allows the viruses to escape from the host-driven CpG elimination pressure. CpG was under-represented in all reverse-transcribing viruses (RT viruses), suggesting that DNA methylation is an important factor affecting the CpG usage of retroviruses. However, vertebrate-infecting RT viruses may also suffer host' CpG elimination pressure that also acts on +ssRNA viruses, which results in further under-representation of CpG in the vertebrate-infecting RT viruses.
Indexed as
Identifiers
What OpenQuestion holds
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.