title: Genetic variability in E6, E7, and L1 genes of human papillomavirus genotype 52 from Southwest China.
abstract: Human papillomavirus (HPV) is the major causative agent of cervical cancer, which accounts for the second highest cancer burden in women worldwide. HPV-52, the prevalent subtype in Asia, especially in southwest China, was analyzed in this study. To analyze polymorphisms, intratypic variants, and genetic variability in the E6-E7 (n=26) and L1 (n=53) genes of HPV-52, these genes were sequenced and the sequences were submitted to GenBank. Phylogenetic trees were constructed using the neighbor-joining and Kimura 2-parameters methods, followed by analysis of the diversity of secondary structure. Finally, we estimated the selection pressures acting on the E6-E7 and L1 genes. Fifty-one novel variants of HPV-52 L1, and two novel variants of HPV-52 E6-E7 were identified in this study. Thirty single nucleotide changes were observed in HPV-52 E6-E7 sequences with 19/30 non-synonymous mutations and 11/30 synonymous mutations (five in the alpha helix and five in the beta sheet). Fifty-five single nucleotide changes were observed in HPV-52 L1 sequences with 17/55 non-synonymous mutations (seven in the alpha helix and fourteen in the beta sheet) and 38/55 synonymous mutations. Selective pressure analysis predicted that most of these mutations reflect positive selection. Identifying new variants in HPV-52 may inform the rational design of new vaccines specifically for women in southwest China. Knowledge of genetic variation in HPV may be useful as an epidemiologic correlate of cervical cancer risk, or may even provide critical information for developing diagnostic probes.
authors.affiliation: Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education; Institute of Medical Genetics, College of Life Science, Sichuan University, China; Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan, Chongqing, China. Electronic address: zyw0417@gmail.com.
authors.forename: Yiwen
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education; Institute of Medical Genetics, College of Life Science, Sichuan University, China; Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan, Chongqing, China. Electronic address: 465220698@qq.com.
authors.forename: Man
authors.initials: M
authors.lastname: Cao
authors.affiliation: Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education; Institute of Medical Genetics, College of Life Science, Sichuan University, China; Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan, Chongqing, China. Electronic address: 442364812@qq.com.
authors.forename: Mengting
authors.initials: M
authors.lastname: Wang
authors.affiliation: Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education; Institute of Medical Genetics, College of Life Science, Sichuan University, China; Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan, Chongqing, China. Electronic address: brainding@scu.edu.cn.
authors.forename: Xianping
authors.initials: X
authors.lastname: Ding
authors.affiliation: Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education; Institute of Medical Genetics, College of Life Science, Sichuan University, China; Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan, Chongqing, China. Electronic address: 572175030@qq.com.
authors.forename: Yaling
authors.initials: Y
authors.lastname: Jing
authors.affiliation: Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education; Institute of Medical Genetics, College of Life Science, Sichuan University, China; Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan, Chongqing, China. Electronic address: 514373742@qq.com.
authors.forename: Zuyi
authors.initials: Z
authors.lastname: Chen
authors.affiliation: Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education; Institute of Medical Genetics, College of Life Science, Sichuan University, China; Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan, Chongqing, China. Electronic address: 553685346@qq.com.
authors.forename: Tengjiao
authors.initials: T
authors.lastname: Ma
authors.affiliation: Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education; Institute of Medical Genetics, College of Life Science, Sichuan University, China; Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan, Chongqing, China. Electronic address: 443742839@qq.com.
authors.forename: Honghan
authors.initials: H
authors.lastname: Chen
mesh_terms: D052685:Alphapapillomavirus / Q000235:genetics*; D000595:Amino Acid Sequence; D001483:Base Sequence; D002681:China; D004279:DNA, Viral / Q000235:genetics; D005260:Female; D006801:Humans; D008969:Molecular Sequence Data; D009856:Oncogene Proteins, Viral / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D017422:Sequence Analysis, DNA; D002583:Uterine Cervical Neoplasms / Q000821:virology
chemical_list: D004279:DNA, Viral; C574669:E6 protein, human papillomavirus type 52; C574670:E7 protein, human papillomavirus type 52; C574671:L1 protein, human papillomavirus type 52; D009856:Oncogene Proteins, Viral
keywords: HPV-52; Mutations; Phylogenetic analysis; Polymorphisms; Variants