Phylogenetic Analyses of HPV53 and Prediction of B and T Cell Epitopes

To construct phylogenetic trees based on HPV53 full length sequences, and predict the physical and chemical parameters, secondary structure, B and T cell epitopes of HPV53 proteins(E1, E2, E4, E6, E7, L1, and L2).

The full-length sequences of HPV53 variants were retrieved from the National Center for Biotechnology Information(NCBI), and a phylogenetic tree was constructed to delineate variant lineages. The physical and chemical parameters of HPV53 proteins were analyzed by ProtParam. The secondary structure of proteins was analyzed using PSIPRED and SOPMA. The B and T cell epitopes for HPV53 proteins were predicted by the IEDB analysis server and the ABCpred server, respectively. Then, to select the potential dominant B and T cell epitopes, more parameters including flexibility, hydrophilicity, surface accessibility, antigenicity of predicted B and T cell epitopes were further predicted by bioinformatic methods such as VaxiJen. Finally, for homology analysis, the potential dominant B and T cell epitopes were compared with the 13 high-risk HPV subtypes using NCBI BLAST tool.

A total of 54 full-length HPV53 sequences were retrieved from the NCBI database, with 48 entries remaining after deduplication. These 48 HPV53 isolates from different countries/regions were clustered into three main evolutionary branches labeled as lineages A, B, and C. The physicochemical properties of three different HPV53 variants(representing A, B, and C lineages, respectively) were similar. The secondary structure of the E1, E6, and E7 proteins was predominantly α-helices, while E2, E4, L1, and L2 predominantly exhibited random coils. After prediction and screening, a total of 6 potential B-cell epitopes and 9 potential T-cell epitopes were identified on HPV53 proteins. Among these epitopes, B cell epitopes TTPIRPPPPPRPWAPT in E4 region, CYRCQHPLTPEEKQLH in E6 region, and T cell epitopes SGVHSYEEIPMQ in L2 region showed high homologous to HPV56(all > 90%).

Bioinformatics analysis and prediction revealed that HPV53 isolates could be clustered into three main evolutionary branches labeled as A, B, and C. These branches exhibited similar physicochemical properties, with minor differences in their secondary structure. Moreover, HPV53 viral proteins contained both B-cell and T-cell antigenic epitopes. These results lay the foundation for further research on vaccines and drugs based on HPV53-related peptides.