Genetic variation analyses of human papillomavirus 39 and prediction of T and B Cell epitopes
10.3760/cma.j.cn112866-20241205-00170
- VernacularTitle:人乳头瘤病毒39型遗传变异分析及T细胞与B细胞抗原表位预测
- Author:
Yuxiao ZHANG
1
;
Yijuan YANG
;
Li WANG
;
Sihan LAN
;
Jing YU
;
Jie HE
;
Hongping ZHANG
;
Min FENG
Author Information
1. 中国医学科学院北京协和医学院医学生物学研究所，昆明 650118
- Publication Type:Journal Article
- Keywords:
Human papillomavirus type 39;
Genetic variation analyses;
T cell;
B cell;
Epitope prediction
- From:
Chinese Journal of Experimental and Clinical Virology
2025;39(1):9-17
- CountryChina
- Language:Chinese
-
Abstract:
Objective:This study aimed to analyze the genetic variation of the human papillomavirus (HPV) type 39 genomes and to predict and screen the dominant T-cell and B-cell epitopes of the viral early proteins (E1, E2, E6, E7) and late proteins (L1, L2).Methods:A total of 70 full-length sequences of HPV39 variants were retrieved from the clinical samples and the National Center for Biotechnology Information (NCBI) to construct a phylogenetic tree, analyze genetic polymorphisms, and predict the physicochemical properties of the viral proteins. Next, T-cell and B-cell epitopes were predicted using IEDB and ABCpred, and potential dominant epitopes were further selected based on parameters such as the secondary structure of the epitope region, peptide flexibility, hydrophilicity, surface accessibility and antigenicity. Finally, a homology analysis of the potential dominant epitopes was performed with 12 high-risk HPV types.Results:HPV39 variants from different sources can be clustered into two lineages (A and B), each exhibiting distinct mutation patterns. The mutation rate was the highest in E7 and the lowest in E1 among the different viral genes. However, these nucleotide/amino acid mutations did not significantly impact the physicochemical properties of the viral proteins. After prediction and screening, 5 and 6 potential dominant B-cell epitopes were identified in both L1 and L2, respectively. E1, E2, E6, and E7 yielded 18, 10, 4, and 1 potential dominant HLA-I restricted T-cell epitopes, respectively. Additionally, E1, E2, and E6 yielded 7, 3, and 2 potential dominant HLA-II restricted T-cell epitopes, respectively. Homology analysis indicated that T-cell dominant epitopes in E1, E2, and E6, as well as B-cell epitopes in L2, showed high homology (93%-100%) with HPV68, HPV33, HPV45, and HPV59.Conclusions:Bioinformatics analysis and prediction revealed that HPV39 variants can be clustered into two main evolutionary branches, A and B, each exhibiting a specific mutation pattern. The viral proteins contain potential dominant T-cell and B-cell epitopes that can be further investigated, providing valuable theoretical support for the development of HPV39-related peptide-based vaccines and therapeutics.
