Codon usage bias of human papillomavirus type 33 and 58: A comprehensive analysis.
J Basic Microbiol
; 64(5): e2300636, 2024 May.
Article
em En
| MEDLINE
| ID: mdl-38346260
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.
Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Papillomaviridae
/
Composição de Bases
/
Genoma Viral
/
Uso do Códon
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Papillomavirus Humano
Tipo de estudo:
Risk_factors_studies
Limite:
Female
/
Humans
País/Região como assunto:
Asia
Idioma:
En
Ano de publicação:
2024
Tipo de documento:
Article