Table 1_Host and structure-specific codon usage of G genotype (VP7) among group A rotaviruses.xlsx

Rotavirus A (RVA) infects a relatively wide host range. Studying the evolutionary dynamics of viral genomes and the evolution of host adaptations can inform the development of epidemiological models of disease transmission. Moreover, comprehending the adaptive evolution of viruses in the host could provide insights into how viruses promote evolutionary advantages on a larger scale at host level. This study aims to determine whether host specificity in codon usage existed. We used the Clustal W function within MEGA X software to perform sequence alignment, followed by construction of a phylogenetic tree based on the maximum-likelihood method. Additionally, Codon W software and EMBOSS were utilized for analysis of codon usage bias index. We analyzed codon usage bias (CUB) of host-specific G genotype VP7 to elucidate the molecular-dynamic evolutionary pattern and reveal the adaptive evolution of VP7 at the host level. The CUB of RV VP7 exhibits significant difference between human and other species. This bias can be primarily attributed to natural selection. In addition, the β-barrel structural domain, which plays a crucial role in viral transmembrane entry into cells, demonstrates a stronger CUB. Our results provide novel insights into the evolutionary dynamics of RVs, cross-species transmission, and virus-host adaptation.

A型轮状病毒（Rotavirus A, RVA）的宿主范围相对广泛。研究病毒基因组的进化动态与宿主适应演化过程，可为疾病传播的流行病学模型构建提供理论依据。此外，解析病毒在宿主内的适应性演化，还可阐明病毒如何在宿主层面上更大尺度上获得进化优势的内在机制。本研究旨在探究密码子使用是否存在宿主特异性。我们采用MEGA X软件中的Clustal W工具完成序列比对，随后基于最大似然法构建系统发育树；同时借助Codon W软件与EMBOSS工具分析密码子使用偏性指数。我们针对宿主特异性G基因型VP7的密码子使用偏性（codon usage bias, CUB）进行分析，以阐明其分子动态演化模式，并揭示VP7在宿主层面的适应性演化。轮状病毒VP7的密码子使用偏性在人类与其他物种间存在显著差异，该偏性主要归因于自然选择。此外，在病毒跨膜进入细胞过程中发挥关键作用的β桶状结构域，其密码子使用偏性更强。本研究结果为轮状病毒的演化动态、跨物种传播以及病毒-宿主适应性机制提供了全新的研究视角。