title: Genetic variability of HPV-58 E6 and E7 genes in Southwest China.
abstract: HPV accounts for most of incidence of cervical cancer. Genetic variations of E6 and E7 may be associated with the development of cervical cancer in specific geographic regions. HPV-58 has been found to be a relatively prevalent high-risk HPV among southwest Chinese women. To explore gene intratypic variations and polymorphisms of HPV-58 E6 and E7 genes originating in Southwest China, a total of 2000 scraped cell samples were collected for DNA extraction and HPV typing. Then, the E6 and E7 genes of HPV-58 (n=22) were sequenced and compared to others submitted to GenBank, followed by an analysis of the diversity of secondary structure by DNASTAR software. Phylogenetic trees were then constructed by Neighbor-Joining and the Kimura 2-parameters methods, followed by an analysis of selection pressures acting on the E6/E7 genes by PAML software. 22 were HPV-58 positive among 215 high-risk types' samples. The nucleotide variation rate of E6 was 86.36% (19/22) among the 22 HPV-58 E6 sequences studied. 4 single nucleotide changes were identified among the E6 sequences with 3/4 synonymous mutations (C187T, A260C, C307T) and 1/4 non-synonymous mutations (A388C, from Lys to Asn, in alpha helix). The most common mutations of E6 genes are the C307T and A388C. 8 single nucleotide changes were identified among the HPV-58 E7 sequences with 2/8 synonymous mutations (T726C, T744G) and 6/8 non-synonymous mutations (G599A, C632T, G694A, G760A, G761A, T803C). The nucleotide variation rate of E7 was 72.73% (17/22). The most common mutations of E7 genes are C632T, G694A, T744G, G760A (from Gly to Ser, in turn), G761A and T803C. The phylogenetic analyses demonstrate that all HPV-58 E6/E7 variants identified belonged to the Southeast Asia lineage. There was no evidence of positive selection in the sequence alignment of HPV-58 E6 and E7 genes.
authors.affiliation: Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China; Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming 650118, PR China.
authors.forename: Lijuan
authors.initials: L
authors.lastname: Yang
authors.affiliation: The Third Affiliated Hospital of Kunming Medical University, Yunnan Provincial Tumor Hospital, Kunming 650118, PR China.
authors.forename: Hongying
authors.initials: H
authors.lastname: Yang
authors.affiliation: Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China; Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming 650118, PR China.
authors.forename: Junying
authors.initials: J
authors.lastname: Chen
authors.affiliation: Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China; Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming 650118, PR China.
authors.forename: Xinwei
authors.initials: X
authors.lastname: Huang
authors.affiliation: Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China; Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming 650118, PR China.
authors.forename: Yue
authors.initials: Y
authors.lastname: Pan
authors.affiliation: Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China; Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming 650118, PR China.
authors.forename: Duo
authors.initials: D
authors.lastname: Li
authors.affiliation: Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China; Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming 650118, PR China.
authors.forename: Xiaojie
authors.initials: X
authors.lastname: Ding
authors.affiliation: The First Affiliated Hospital of Kunming Medical University, Kunming 650032, PR China.
authors.forename: Kun
authors.initials: K
authors.lastname: Wu
authors.affiliation: Southwest Guizhou Vocational and Technical College for Nationalities, Xingyi 562400, PR China.
authors.forename: Xinan
authors.initials: X
authors.lastname: Shi
authors.affiliation: Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China; Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming 650118, PR China.
authors.forename: Juanjuan
authors.initials: J
authors.lastname: Fu
authors.affiliation: Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China; Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming 650118, PR China.
authors.forename: Haijing
authors.initials: H
authors.lastname: Shi
authors.affiliation: Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China; Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming 650118, PR China.
authors.forename: Shaohui
authors.initials: S
authors.lastname: Ma
authors.affiliation: Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China; Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming 650118, PR China. Electronic address: msun08@yahoo.com.
authors.forename: Qiangming
authors.initials: Q
authors.lastname: Sun
mesh_terms: D002681:China; D005260:Female; D014644:Genetic Variation; D006801:Humans; D008969:Molecular Sequence Data; D058889:Molecular Typing; D059645:Mutation Rate; D027383:Papillomaviridae / Q000145:classification / Q000235:genetics*; D030361:Papillomavirus Infections / Q000453:epidemiology / Q000821:virology*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics*
chemical_list: D014764:Viral Proteins
keywords: Cervical cancer; E6 gene; E7 gene; HPV-58; Variation