ArticlePloS one2014
Genome-wide analysis of codon usage and influencing factors in chikungunya viruses.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 78 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
78 citing papers in PubMed.
- Transgene sequence codon optimization and composition determines replication competence of self-amplifying RNA.Molecular therapy : the journal of the American Society of Gene Therapy · 2026Article
- Whole-Genome Analysis of LSDV Isolates from the 2019 and 2023 Outbreaks in Israel Points to Undetected Circulation and Recombination Events.Veterinary sciences · 2026Article
- Analysis of Codon Usage Bias in theThe Canadian journal of infectious diseases & medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale · 2026Article
- Codon usage bias of low-risk human papillomavirus types 6 and 11.Antonie van Leeuwenhoek · 2025Article
- Decoding codon usage in human papillomavirus type 59.Virus genes · 2025Article
- Analysis of synonymous codon usage bias of Lassa virus.Virus research · 2025Article
- Codon Usage Bias: A Potential Factor Affecting VGLUT Developmental Expression and Protein Evolution.Molecular neurobiology · 2025Article
- Decoding Codon Usage Patterns in High-Risk Human Papillomavirus Genomes: A Comprehensive Analysis.Current microbiology · 2025Article
- Article
- Comprehensive Analysis of Codon Usage Bias in Human Papillomavirus Type 51.Polish journal of microbiology · 2024Article
- SARS-CoV-2 Displays a Suboptimal Codon Usage Bias for Efficient Translation in Human Cells Diverted by Hijacking the tRNA Epitranscriptome.International journal of molecular sciences · 2024Article
- Dengue virus preferentially uses human and mosquito non-optimal codons.Molecular systems biology · 2024Article
- Compositional Features and Codon Usage Pattern of Genes Associated with Parkinson's Disease.Molecular neurobiology · 2024Article
- Comprehensive Genomics Investigation of Neboviruses Reveals Distinct Codon Usage Patterns and Host Specificity.Microorganisms · 2024Article
- Fitness difference between two synonymous mutations of Phytophthora infestans ATP6 gene.BMC ecology and evolution · 2024Article
- Relative synonymous codon usage and codon pair analysis of depression associated genes.Scientific reports · 2024Article
- Comparative analysis of codon usage patterns in the chloroplast genomes of nine forage legumes.Physiology and molecular biology of plants : an international journal of functional plant biology · 2024Article
- Genetic background of adaptation of Crimean-Congo haemorrhagic fever virus to the different tick hosts.PloS one · 2024Article
- 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
- Codon usage bias analysis of the gene encoding NADArchives of microbiology · 2023Article
18 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
3 authors.
Funding
Abstract
Chikungunya virus (CHIKV) is an arthropod-borne virus of the family Togaviridae that is transmitted to humans by Aedes spp. mosquitoes. Its genome comprises a 12 kb single-strand positive-sense RNA. In the present study, we report the patterns of synonymous codon usage in 141 CHIKV genomes by calculating several codon usage indices and applying multivariate statistical methods. Relative synonymous codon usage (RSCU) analysis showed that the preferred synonymous codons were G/C and A-ended. A comparative analysis of RSCU between CHIKV and its hosts showed that codon usage patterns of CHIKV are a mixture of coincidence and antagonism. Similarity index analysis showed that the overall codon usage patterns of CHIKV have been strongly influenced by Pan troglodytes and Aedes albopictus during evolution. The overall codon usage bias was low in CHIKV genomes, as inferred from the analysis of effective number of codons (ENC) and codon adaptation index (CAI). Our data suggested that although mutation pressure dominates codon usage in CHIKV, patterns of codon usage in CHIKV are also under the influence of natural selection from its hosts and geography. To the best of our knowledge, this is first report describing codon usage analysis in CHIKV genomes. The findings from this study are expected to increase our understanding of factors involved in viral evolution, and fitness towards hosts and the environment.
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.