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Updated: Jan 29, 2026

Prediction of HIV-1 Coreceptor Usage Tropism by Sequence Analysis using a Genotypic Approach

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Published on: December 1, 2011

The Emerging JEV Genotype 5 Exhibits Distinct Codon Usage Characteristics.

Xiaoyu Gu¹, Ruichen Wang¹, Yuhong Yang¹

¹National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.

Pathogens (Basel, Switzerland)

|January 28, 2026

Summary

Japanese encephalitis virus (JEV) genotype 5 (G5) shows distinct codon usage, with lower GC content and stronger natural selection. This may enhance immune evasion and host adaptation, suggesting potential for efficient replication in humans.

Keywords:

Japanese encephalitis virus codon usage bias genotype 5 host adaptation

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Area of Science:

Virology
Molecular Evolution
Genomics

Background:

Japanese encephalitis virus (JEV) is a significant public health concern.
Understanding viral evolution is key to controlling JEV.
JEV exhibits genetic diversity with multiple genotypes.

Purpose of the Study:

To investigate the codon usage characteristics of JEV genotype 5 (G5).
To compare codon usage patterns of G5 with other JEV genotypes (G1-G4).
To elucidate the molecular evolutionary mechanisms of G5 JEV.

Main Methods:

Analysis of 339 complete JEV genome sequences.
Utilized Relative Synonymous Codon Usage (RSCU), Principal Component Analysis (PCA), Effective Number of Codons (ENC), and Codon Adaptation Index (CAI).
Included evolutionary, nucleotide composition, dinucleotide abundance, and neutrality plot analyses.

Main Results:

G5 forms a distinct evolutionary branch with lower GC content (50%) and GC3 (53%).
G5 exhibits preferential A/U-ended codon usage and stronger codon usage bias (mean ENC = 54.2).
Natural selection pressure is stronger on G5; it shows higher translational efficiency in human hosts.

Conclusions:

G5 JEV may enhance immune evasion and host adaptation through reduced CpG usage and optimized codon preference.
G5 JEV possesses potential for efficient replication in humans or other mammalian hosts.
Findings offer insights for JEV vaccine development.