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Phylogenetic analysis and antigenic epitope prediction for E6 and E7 of Alpha-papillomavirus 9 in Taizhou, China
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Phylogenetic analysis and antigenic epitope prediction for E6 and E7 of Alpha-papillomavirus 9 in Taizhou, China
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Phylogenetic analysis and antigenic epitope prediction for E6 and E7 of Alpha-papillomavirus 9 in Taizhou, China
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Journal Article
Phylogenetic analysis and antigenic epitope prediction for E6 and E7 of Alpha-papillomavirus 9 in Taizhou, China
2024
Overview
Background
Alpha-papillomavirus 9 (α-9) is a member of the human papillomavirus (HPV) α genus, causing 75% invasive cervical cancers worldwide. The purpose of this study was to provide data for effective treatment of HPV-induced cervical lesions in Taizhou by analysing the genetic variation and antigenic epitopes of α-9 HPV E6 and E7.
Methods
Cervical exfoliated cells were collected for HPV genotyping. Positive samples of the α-9 HPV single type were selected for
E6
and
E7
gene sequencing. The obtained nucleotide sequences were translated into amino acid sequences (protein primary structure) using MEGA X, and positive selection sites of the amino acid sequences were evaluated using PAML. The secondary and tertiary structures of the E6 and E7 proteins were predicted using PSIPred, SWISS-MODEL, and PyMol. Potential T/B-cell epitopes were predicted by Industrial Engineering Database (IEDB).
Results
From 2012 to 2023, α-9 HPV accounted for 75.0% (7815/10423) of high-risk HPV-positive samples in Taizhou, both alone and in combination with other types. Among these, single-type-positive samples of α-9 HPV were selected, and the entire
E6
and
E7
genes were sequenced, including 298 HPV16, 149 HPV31, 185 HPV33, 123 HPV35, 325 HPV52, and 199 HPV58 samples. Compared with reference sequences, 34, 12, 10, 2, 17, and 17 nonsynonymous nucleotide mutations were detected in HPV16, 31, 33, 35, 52, and 58, respectively. Among all nonsynonymous nucleotide mutations, 19 positive selection sites were selected, which may have evolutionary significance in rendering α-9 HPV adaptive to its environment. Immunoinformatics predicted 57 potential linear and 59 conformational B-cell epitopes, many of which are also predicted as CTL epitopes.
Conclusion
The present study provides almost comprehensive data on the genetic variations, phylogenetics, positive selection sites, and antigenic epitopes of α-9 HPV E6 and E7 in Taizhou, China, which will be helpful for local HPV therapeutic vaccine development.
Publisher
BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
Subject
/ Alphapapillomavirus - genetics
/ Alphapapillomavirus - immunology
/ Analysis
/ Animal Genetics and Genomics
/ Antigens
/ B cells
/ Biomedical and Life Sciences
/ China
/ E7 gene
/ Epitopes
/ Epitopes, B-Lymphocyte - genetics
/ Epitopes, B-Lymphocyte - immunology
/ Epitopes, T-Lymphocyte - genetics
/ Epitopes, T-Lymphocyte - immunology
/ Female
/ Genes
/ Genomes
/ Humans
/ Microbial Genetics and Genomics
/ Mutation
/ Oncogene Proteins, Viral - genetics
/ Oncogene Proteins, Viral - immunology
/ Papillomavirus E7 Proteins - genetics
/ Papillomavirus E7 Proteins - immunology
/ Papillomavirus Infections - virology
/ Peptides
/ Proteins
/ T cells
/ Vaccines
