Characteristics of synonymous codon usage bias in the beginning region of West Nile virus

Ma, Xiaoxia; Feng, Yuping; Liu, J.L.; Chen, L.; Zhao, Yongqing; Guo, Peng-hui; Guo, Jiahui; Ma, Liya; Ma, Zhiyong

doi:10.4238/2014.september.5.13

Cited by 2 publications

(1 citation statement)

References 36 publications

(32 reference statements)

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“…In this research, the majority of Flaviviridae viruses have a weak codon bias with the mean ENC value of 54.58. And this is in accordance with some earlier studies on codon usage bias of Tembusu virus and West Nile virus which has a low codon usage bias [16–18]. According to the calculation results of CodonW (Table 2), the content of A and G is the highest and RSCU analysis indicates that Flaviviridae viruses prefer A/U-ended codons.…”

Section: Discussionsupporting

confidence: 89%

Analysis of Synonymous Codon Usage Bias in Flaviviridae Virus

Yao

Chen

Tang

2019

BioMed Research International

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Background. Flaviviridae viruses are single-stranded, positive-sense RNA viruses, which threat human constantly mediated by mosquitoes, ticks, and sandflies. Considering the recent increase in the prevalence of the family virus and its risk potential, we investigated the codon usage pattern to understand its evolutionary processes and provide some useful data to develop the medications for most of Flaviviridae viruses. Results. The overall extent of codon usage bias in 65 Flaviviridae viruses is low with the average value of GC contents being 50.5% and the highest value being 55.9%; the lowest value is 40.2%. ENC values of Flaviviridae virus genes vary from 48.75 to 57.83 with a mean value of 55.56. U- and A-ended codons are preferred in the Flaviviridae virus. Correlation analysis shows that the positive correlation between ENC value and GC content at the third nucleotide positions was significant in this family virus. The result of analysis of ENC, neutrality plot analysis, and correlation analysis revealed that codon usage bias of all the viruses was affected mainly by natural selection. Meanwhile, according to correspondence analysis (CoA) based on RSCU and phylogenetic analysis, the Flaviviridae viruses mainly are made up of two groups, Group I (Yellow fever virus, Apoi virus, Tembusu virus, Dengue virus 1, and others) and Group II (West Nile virus lineage 2, Japanese encephalitis virus, Usutu virus, Kedougou virus, and others). Conclusions. All in, the bias of codon usage pattern is affected not only by compositional constraints but also by natural selection. Phylogenetic analysis also illustrates that codon usage bias of virus can serve as an effective means of evolutionary classification in Flaviviridae virus.

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Section: Discussionsupporting

confidence: 89%

Analysis of Synonymous Codon Usage Bias in Flaviviridae Virus

Yao

Chen

Tang

2019

BioMed Research International

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A small stretch of poor codon usage at the beginning of dengue virus open reading frame may act as a translational checkpoint

Yimyaem,

Jitobaom,

Auewarakul

2023

BMC Res Notes

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Objective Rare codons were previously shown to be enriched at the beginning of the dengue virus (DENV) open reading frame. However, the role of rare codons in regulating translation efficiency and replication of DENV remains unclear. The present study aims to clarify the significance of rare codon usage at the beginning of DENV transcripts using the codon adaptation index (CAI). Methodology CAIs of the whole starting regions of DENV transcripts as well as 18-codon sliding windows of the regions were analyzed. Results One of the intriguing findings is that those rare codons do not typically result in uniformly low CAI in the starting region with rare codons. However, it shows a notable local drop in CAI around the 50th codon in all dengue serotypes. This suggests that there may be a translational checkpoint at this site and that the rare codon usage upstream to this checkpoint may not be related to translational control.

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Characteristics of synonymous codon usage bias in the beginning region of West Nile virus

Cited by 2 publications

References 36 publications

Analysis of Synonymous Codon Usage Bias in Flaviviridae Virus

Analysis of Synonymous Codon Usage Bias in Flaviviridae Virus

A small stretch of poor codon usage at the beginning of dengue virus open reading frame may act as a translational checkpoint

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