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Home / Equine Research Bank / Virus Res / Codon usage bias of Venezuelan equine encephalitis virus and...
Virus research2023; 328; 199081; doi: 10.1016/j.virusres.2023.199081

Codon usage bias of Venezuelan equine encephalitis virus and its host adaption.

Abstract: Venezuelan equine encephalitis virus (VEEV) is an emerging zoonotic virus in the alphavirus genus. It can be transmitted to humans due to spillover from equid-mosquito cycles. The symptoms caused by VEEV include fever, headache, myalgia, nausea, and vomiting. It can also cause encephalitis in severe cases. The evolutionary features of VEEV are largely unknown. In this study, we comprehensively analyzed the codon usage pattern of VEEV by computing a variety of indicators, such as effective number of codons (ENc), codon adaptation index (CAI), relative synonymous codon usage (RSCU), on 130 VEEV coding sequences retrieved from GenBank. The results showed that the codon usage bias of VEEV is relatively low. ENc-GC3s plot, neutrality plot, and CAI-ENc correlation analyses supported that translational selection plays an important role in shaping the codon usage pattern of VEEV whereas the mutation pressure has a minor influence. Analysis of RSCU values showed that most of the preferred codons in VEEV are C/G-ended. Analysis of dinucleotide composition found that all CG- and UA-containing codons are not preferentially used. Phylogenetic analysis showed that VEEV isolates can be clustered into three genera and evolutionary force affects the codon usage pattern. Furthermore, a correspondence analysis (COA) showed that aromaticity and hydrophobicity as well as geographical distribution also have certain effects on the codon usage variation of VEEV, suggesting the possible involvement of translational selection. Overall, the codon usage of VEEV is comparatively slight and translational selection might be the main factor that shapes the codon usage pattern of VEEV. This study will promote our understanding about the evolution of VEEV and its host adaption, and might provide some clues for preventing the cross-species transmission of VEEV.
Copyright © 2023 The Authors. Published by Elsevier B.V. All rights reserved.
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Publication Date: 2023-03-03 PubMed ID: 36854361PubMed Central: PMC10194294DOI: 10.1016/j.virusres.2023.199081Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research article explored the codon usage pattern of the Venezuelan equine encephalitis virus (VEEV) and the possible factors that shape it, and found evidence that translational selections plays a significant role in its evolution and host adaptation.

Context and Objective of the Research

  • The Venezuelan equine encephalitis virus is an emerging zoonotic virus, which means it can be transmitted from animals (particularly equid-mosquito cycles) to humans.
  • The research aimed to understand VEEV’s evolutionary features, which are largely unknown, by analyzing its codon usage pattern.

Methodology

  • The researchers used 130 VEEV coding sequences from GenBank and computed a various indicators such as effective number of codons (ENc), codon adaptation index (CAI), and relative synonymous codon usage (RSCU).
  • They also conducted analysis of the ENc-GC3s plot, neutrality plot, CAI-ENc correlation, RSCU values and dinucleotide composition.

Findings

  • The results showed that the codon usage bias of VEEV is relatively low, and most of VEEV’s preferred codons are C/G-ended.
  • Analyses suggested that translational selection plays an important role in shaping the codon usage pattern of VEEV, while mutation pressure has less influence.
  • All CG- and UA-containing codons are not preferentially used by VEEV.
  • Phylogenetic analysis showed that VEEV isolates can be grouped into three genera and that evolutionary force impacts the codon usage pattern.
  • Correspondence analysis revealed that aromaticity and hydrophobicity along with geographical distribution also affect the codon usage variation of VEEV.

Significance

  • Understanding the codon usage pattern of VEEV can enhance knowledge about its evolution and its adaptation to hosts, which could provide insights for prevention strategies against cross-specie transmission of VEEV.

Cite This Article

APA
Wang H, Liu S, Lv Y, Wei W. (2023). Codon usage bias of Venezuelan equine encephalitis virus and its host adaption. Virus Res, 328, 199081. https://doi.org/10.1016/j.virusres.2023.199081

Publication

Virus research
ISSN: 1872-7492
NlmUniqueID: 8410979
Country: Netherlands
Language: English
Volume: 328
Pages: 199081
PII: 199081

Researcher Affiliations

Wang, Hongju
  • Kaifeng Key Laboratory of Infection and Biological Safety, School of Basic Medical Sciences, Henan University, Kaifeng, China.
Liu, Shijie
  • School of Clinical Medicine, Henan University, Kaifeng, China.
Lv, Yao
  • School of Clinical Medicine, Henan University, Kaifeng, China.
Wei, Wenqiang
  • Kaifeng Key Laboratory of Infection and Biological Safety, School of Basic Medical Sciences, Henan University, Kaifeng, China. Electronic address: weiwq168@163.com.

MeSH Terms

  • Animals
  • Humans
  • Codon Usage
  • Encephalitis Virus, Venezuelan Equine / genetics
  • Phylogeny
  • Selection, Genetic
  • Codon
  • Mutation
  • Evolution, Molecular

Conflict of Interest Statement

Declaration of Competing Interest All authors declare that they have no conflict of interest.

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