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. 2025 Jun 12:16:1544577.
doi: 10.3389/fgene.2025.1544577. eCollection 2025.

Genetic and codon usage analyses reveal the evolution of the seoul virus

Yamei Wei  1   2 , Yanan Cai  1   2 , Xu Han  2 , Zhanying Han  2 , Yanbo Zhang  2 , Yonggang Xu  2 , Caixiao Jiang  2 , Qi Li  1   2
Affiliations

Genetic and codon usage analyses reveal the evolution of the seoul virus

Yamei Wei et al. Front Genet. .

Abstract

Introduction: Seoul virus (Orthohantavirus seoulense, SEOV), a member of the Hantaviridae, causes hemorrhagic fever with renal syndrome (HFRS) through rodent hosts. However, its molecular evolutionary dynamics and codon usage patterns remain poorly understood.

Methods: This study integrated coding sequences from GenBank and previously acquired SEOV strains to systematically analyze genetic evolution and codon usage bias.

Results: It revealed that SEOV evolved seven clades (A-G) with distinct amino acid variation sites and geographic clustering. Recombination events were identified during evolution, alongside purifying and positive selection on specific sites (e.g., codon 259 in the S segment and codon 11 in the M segment). The three viral segments (L, M, and S) exhibited weak codon usage bias, predominantly driven by natural selection, with host adaptation significantly influencing evolutionary trajectories. The S segment demonstrated the strongest pathogenicity due to its closer codon usage alignment with Homo sapiens (H. sapiens) and Rattus norvegicus (R. norvegicus), whereas the L segment showed the lowest host adaptation. Divergent codon preferences among clades highlighted adaptive strategies in host-virus interactions.

Conclusion: These findings elucidate the evolutionary mechanisms of SEOV and provide a theoretical foundation for live attenuated vaccine design and region-specific viral control strategies.

Keywords: codon usage bias; evolution; genetic; hantavirus; phylogenetic; seoul virus.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Phylogenetic tree of SEOV reconstructed by ML. Clades A to G and sequences from different locations have different colors. Bootstrap values for major nodes are shown.
FIGURE 2
FIGURE 2
Specific amino acid mutation sites at the evolutionary branch level. The specific amino acid mutation sites in clades A to G have different colors. The numbers below indicate the positions of amino acid mutation sites in their corresponding encoded proteins.
FIGURE 3
FIGURE 3
COA analysis of SEOV. The first 2D coordinate was used to plot the codon positions.
FIGURE 4
FIGURE 4
Factors contributing to bias in SEOV codon usage. In the ENC plot, the curve is the expectation curve for each sequence position in the SEOV. PR2 analysis: A value of 0.5 or 0.5 indicates that the effects of mutational pressure and natural selection, respectively, did not cause bias. Neutral plot: Regression plots with slopes closer to 1 indicate greater mutation pressure.
FIGURE 5
FIGURE 5
Adaptation of SEOV to the host. Different clades are represented by different colors.
See this image and copyright information in PMC

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