Genetic variability and lineage phylogeny of human papillomavirus type 45 based on E6 and E7 genes in Southwest China

• Published in: Virus research 2018-08, Vol.255, p.85-89
• Main Authors: Cui, Fangying, Zhang, Zhuo, Xu, Jianju, Ding, Xianping, Mu, Xuemei, Wan, Qiuling, Tan, Liping, Fang, Liyuan, Chen, Zuyi
• Format: Article
• Language: English
• Subjects: Alphapapillomavirus - classification; Alphapapillomavirus - genetics; Alphapapillomavirus - isolation & purification; Base Sequence; China - epidemiology; DNA, Viral - genetics; Female; Genetic Variation; Human papillomavirus; Humans; Mutation; Oncogene Proteins, Viral - genetics; Papillomavirus E7 Proteins - genetics; Papillomavirus Infections - epidemiology; Papillomavirus Infections - genetics; Phylogeny; Polymorphism; Prevalence; Selection, Genetic; Sequence Analysis, DNA
• ISSN: 0168-1702; 1872-7492
• DOI: 10.1016/j.virusres.2018.07.003

•The genetic variation of HPV45 E6 and E7 in Chinese women.•The phylogenetic tree was reconstructed.•The selection pressures of the E6 and E7 genes were estimated.•Identify geographical origin explaining the differential prevalence of HPV45 sublineages. The current study investigated nucleotide variability and phylogeny in high-risk HPV45 collected from Chinese women. Fifty-one samples positive for single infections of HPV45 were collected for DNA extraction and HPV typing. The E6 and E7 genes of HPV45 were sequenced, and then the phylogenetic tree was reconstructed by the maximum likelihood method implemented in IQ-TREE under the HKY nucleotide substitution model. The selection pressures of the E6 and E7 genes were estimated using PAML software. Eleven nucleotide polymorphism sites were observed in the HPV45 E6 sequences, with 6 synonymous (C134T, T163C, A284C, T341C, T482C, A497G) and 5 non-synonymous (A124C, C157T, T162A, G259T, G487A) mutations. Six nucleotide polymorphism sites were observed in the E7 sequences, with 5 non-synonymous (G600A, A603C, A769C, G808T, G832T) and 1 synonymous (A718C) mutation. Our investigation suggests that B2 was the most frequent HPV45 sublineage in Southwest China, followed by A2; no A1 or A3 variants were detected. Selective pressure analysis showed that these mutations could reflect positive selection in HPV45 E6 and E7 genes.