Human papillomavirus type 68 prevalence and genetic variability based on E6/E7 genes in Sichuan

Abstract

Background:Cervical cancer is one of the malignant tumors threatening women's health worldwide, only second to breast cancer. 99.7% cervical cancer was found to be associated with high-risk HPV (HR-HPV) persistent infections. HPV68 is a common HR-HPV, closely related to cervical cancer.Methods:Cell samples were collected by cervical scraped for HPV detecting and typing, and HPV 68 positive samples were selected out. Important E6, E7 genes of HPV 68 were sequenced and analyzed for the study of HPV 68 genetic polymorphisms. Phylogenetic tree of E6-E7 was constructed by Maximum likelihood method of MEGA v7.0 software. The selection pressure sites of HPV68 E6, E7 were predicted by codeml in the PAML 4.8. The secondary structure and three-dimensional structure of HPV68 E6, E7 were analyzed by PSIPRED server and SWISS-MODEL respectively. T-cell and B-cell antigen epitopes of HPV68 E6, E7 were predicted by immune epitope Database Analysis (IEDB) resource and ABCpred server respectivelyResults:a total of 10650 cell samples were collected for detecting and typing, and 2939 (27.60%, 2939/10650) positive samples were detected, 174 (5.92%, 174/2939) were HPV68; 150 HPV68 E6-E7 were successful amplified and analyzed, 32 nucleotide mutations were observed in this study, 50% (16/32) were non-synonymous mutations; among them, 4 non-synonymous mutations were detected in E6 gene (one in the Coil and three in the Strand), 12 were in E7 gene (four in the alpha helix, two in the Coil and six in the Strand). Phylogenetic analysis of HPV68 E6-E7 suggested that C was the most frequent HPV68 lineage in Sichuan China. 82-90SESVYATTL, 85-93VYATTLETI, 13-21KLPDLCRTL and 67-81-SCIKFYAKIRELRYY, 68-82CIKFYAKIRELRYYS, 66-80QSCIKFYAKIRELRY were the most potential HPV68 E6 HLA-Ⅰ, HLA-Ⅱepitopes respectively; and B-cell epitopes were 138-153CRHCWTSKREDRRRTR, 82-97SESVYATTLETITNTK. 92-101LLFMDSLNFV, 45-53AVNHHQHQL and 20-35EIEPVDLVCHEQLGDS were the most potential HPV68 E7 HLA-Ⅰand B-cell epitopes. 3 HPV68 E6 positive selection sites and 5 HPV68 E7 were detected, and they all had a certain influence on the proteins structure and epitopes affinity.Conclusion:Non-synonymous mutations of HPV 68 located in positive selection sites resulted in differences in protein structure and epitopes affinity, that may affect the pathogenicity and adaptability of HPV68 to the environment. HPV68 data enrichment is of great significance for understanding the inherent geographical and biological differences of HPV68 in china; and targeting potential epitopes for therapeutic vaccines may improve the effective of vaccines design for specific populations.