ArticleInfection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases2014
Characterization of the porcine epidemic diarrhea virus codon usage bias.
Article in Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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34 citing papers in PubMed.
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- Description of mitochondrial genomes and phylogenetic analysis of Megophthalminae (Hemiptera: Cicadellidae).Journal of insect science (Online) · 2024Article
- Relative synonymous codon usage and codon pair analysis of depression associated genes.Scientific reports · 2024Article
- A study on the codon usage bias of arenavirus common genes.Frontiers in microbiology · 2024Article
- Genetic background of adaptation of Crimean-Congo haemorrhagic fever virus to the different tick hosts.PloS one · 2024Article
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- Coronavirus accessory protein ORF3 biology and its contribution to viral behavior and pathogenesis.iScience · 2023Review
- Host adaptation of codon usage in SARS-CoV-2 from mammals indicates potential natural selection and viral fitness.Archives of virology · 2022Article
- Molecular and Structural Evolution of Porcine Epidemic Diarrhea Virus.Animals : an open access journal from MDPI · 2022Article
- Codon Usage and Context Analysis of Genes Modulated during SARS-CoV-2 Infection and Dental Inflammation.Vaccines · 2022Article
- Strategies and Patterns of Codon Bias in Molluscum Contagiosum Virus.Pathogens (Basel, Switzerland) · 2021Article
- Genes Common in Primary Immunodeficiencies and Cancer Display Overrepresentation of Codon CTG and Dominant Role of Selection Pressure in Shaping Codon Usage.Biomedicines · 2021Article
- Comprehensive analysis of synonymous codon usage patterns and influencing factors of porcine epidemic diarrhea virus.Archives of virology · 2021Article
- Article
- Study on the Characteristic Codon Usage Pattern in Porcine Epidemic Diarrhea Virus Genomes and Its Host Adaptation Phenotype.Frontiers in microbiology · 2021Article
- Biological Characteristics and Patterns of Codon Usage Evolution for the African Genotype Zika Virus.Viruses · 2020Article
- Analysis of preferred codon usage in the coronavirus N genes and their implications for genome evolution and vaccine design.Journal of virological methods · 2020Article
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10 authors.
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Abstract
Porcine epidemic diarrhea virus (PEDV) has been responsible for several recent outbreaks of porcine epidemic diarrhea (PED) and has caused great economic loss in the swine-raising industry. Considering the significance of PEDV, a systemic analysis was performed to study its codon usage patterns. The relative synonymous codon usage value of each codon revealed that codon usage bias exists and that PEDV tends to use codons that end in T. The mean ENC value of 47.91 indicates that the codon usage bias is low. However, we still wanted to identify the cause of this codon usage bias. A correlation analysis between the codon compositions (A3s, T3s, G3s, C3s, and GC3s), the ENC values, and the nucleotide contents (A%, T%, G%, C%, and GC%) indicated that mutational bias plays role in shaping the PEDV codon usage bias. This was further confirmed by a principal component analysis between the codon compositions and the axis values. Using the Gravy, Aroma, and CAI values, a role of natural selection in the PEDV codon usage pattern was also identified. Neutral analysis indicated that natural selection pressure plays a more important role than mutational bias in codon usage bias. Natural selection also plays an increasingly significant role during PEDV evolution. Additionally, gene function and geographic distribution also influence the codon usage bias to a degree.
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