Abstract：
Cervical cancer is closely linked to specific strains of human papillomavirus (HPV), notably HPV-33 and HPV-58, which exhibit a significant prevalence among women in China. Nevertheless, the codon usage bias in HPV-33 and HPV-58 is not well comprehended. The objective of this research is to analyze the codon usage patterns HPV-33 and HPV-58, pinpoint the primary factors that influence codon preference. The overall preference for codon usage in two HPV genotypes is not significant. Both HPV genotypes exhibit a preference for codons that end with A/U. The GC3 content for HPV-33 is 25.43% ± 0.35%, and for HPV-58, it is 29.44% ± 0.57%. Out of the 26 favored codons in HPV-33 and HPV-58 (relative synonymous codon usage (RSCU) > 1), 25 conclude with A/U. Principal component analysis (PCA) shows a tight clustering of the entire genome sequences of HPV-33 and HPV-58, suggesting a similarity in their RSCU preferences. Moreover, an examination of dinucleotide abundance indicated that translation selection influenced the development of a distinctive dinucleotide usage pattern in HPV-33 and HPV-58. Additionally, a combined analysis involving an effective number of codons plot, parity rule 2, and neutrality analysis demonstrated that, for HPV-33 and HPV-58, the primary determinant influencing codon usage preference is natural selection. HPV-33 and HPV-58 exhibit a restricted set of favored codons in common with humans, potentially mitigating competition for translation resources. Our discoveries could provide valuable perspectives on the evolutionary patterns and codon usage preferences of HPV-33 and HPV-58 viruses, contributing to the development and application of relevant HPV subtype vaccines.
摘要：
宫颈癌与人乳头瘤病毒（HPV）的特定菌株密切相关，特别是HPV-33和HPV-58，在中国女性中表现出显著的患病率。然而，HPV-33和HPV-58中的密码子使用偏差没有得到很好的理解。这项研究的目的是分析密码子使用模式HPV-33和HPV-58，找出影响密码子偏好的主要因素。两种HPV基因型对密码子使用的总体偏好并不显著。两种HPV基因型都表现出对A/U结尾的密码子的偏好。HPV-33的GC3含量为25.43%±0.35%，HPV-58为29.44%±0.57%。在HPV-33和HPV-58的26个有利密码子中（相对同义密码子使用（RSCU）>1），25以A/U结束主成分分析（PCA）显示了HPV-33和HPV-58的整个基因组序列的紧密聚类，表明它们的RSCU偏好相似。此外，对二核苷酸丰度的检查表明，翻译选择影响了HPV-33和HPV-58中独特的二核苷酸使用模式的发展。此外,涉及有效密码子数量图的组合分析，平价规则2和中立分析表明，对于HPV-33和HPV-58,影响密码子使用偏好的主要决定因素是自然选择.HPV-33和HPV-58表现出与人类共有的一组有限的有利密码子，有可能减轻翻译资源的竞争。我们的发现可以为HPV-33和HPV-58病毒的进化模式和密码子使用偏好提供有价值的观点。促进HPV亚型相关疫苗的开发和应用。
