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During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
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Codon Usage of Hepatitis E Viruses: A Comprehensive Analysis.

Bingzhe Li1, Han Wu1, Ziping Miao2

  • 1Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China.

Frontiers in Microbiology
|July 8, 2022
PubMed
Summary
This summary is machine-generated.

Hepatitis E virus (HEV) exhibits codon usage bias influenced by natural selection and mutation pressure, varying across genotypes. Understanding these patterns offers insights into HEV evolution and its zoonotic nature.

Keywords:
codon usageeffective codon numberhepatitis E virusrelatively synonymous codon usagezoonotic pathogen

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Area of Science:

  • Virology
  • Genomics
  • Evolutionary Biology

Background:

  • Hepatitis E virus (HEV) is an emerging zoonotic pathogen with diverse species and genotypes.
  • The codon usage bias of HEV and its underlying drivers remain largely unclear.

Purpose of the Study:

  • To characterize the codon usage patterns of various HEV genotypes.
  • To identify the primary factors influencing codon usage bias in HEV.

Main Methods:

  • Analysis of complete coding sequences (ORF1, ORF2, ORF3) from seven HEV genotypes.
  • Application of Relative Synonymous Codon Usage (RSCU) and Principal Component Analysis (PCA).
  • Utilized dinucleotide abundance, Parity Rule 2 (PR2), Effective Number of Codons (ENC)-plot, and neutrality analysis.

Main Results:

  • Six of seven HEV genotypes showed a tendency to use codons ending in G/C.
  • Significant variation in codon usage bias was observed across human, zoonotic, and animal HEV genotypes, and within specific genotypes (HEV-4, HEV-8, HEV-C1).
  • Natural selection was identified as the predominant force shaping HEV codon usage bias, with mutation pressure also playing a role in certain genotypes.

Conclusions:

  • Codon usage bias in HEV is a complex phenomenon driven primarily by natural selection, with contributions from mutation pressure.
  • Findings provide valuable insights into the evolutionary mechanisms of HEV and its genetic characteristics.