Sequence variation of human papillomavirus Type 31 long control region: Phylogenetic and functional implications

Abstract

About one-third of human papillomavirus (HPV) types infect the anogenital tract. High-risk genital HPV types (such as HPV 16, 18, 31, 33, and 35) are linked causally to the development of cervical cancer. The long control region (LCR) of the HPV genome regulates the replication and transcription of the viral genome. In this study, the functional significance of nucleotide sequence variation within the LCR of HPV 31 was investigated. The LCR was amplified by polymerase chain reaction (PCR) from 41 HPV 31 positive cervical samples of Hungarian women. A phylogenetic tree constructed from the nucleotide sequences of the LCR variants revealed the presence of three intratypic variant lineages of HPV 31, in accordance with previous results. In order to explore the functional consequences of sequence variation in the LCR of HPV 31, selected LCR variants were cloned into a luciferase reporter vector, transfected into C33-A cells and tested in luciferase reporter assays. Significant differences were found between the transcriptional activities of HPV 31 LCR variants belonging to different variant lineages. As the LCR is governing the transcription of the E6 and E7 oncogenes, the differences in the transcriptional activities of LCR variants may be associated with differences in their oncogenic potential.

CpG methylation in human papillomavirus (HPV) type 31 long control region (LCR) in cervical infections associated with cytological abnormalities

“…In HPV-31 LCR, there are 12 CpG sites, seven of them in E2 binding sites (E2BS) [13]. The majority of our samples had hypomethylated CpGs both in the 5 0 LCR/ enhancer and in the promoter regions without significant variation between patient groups, and these results are consistent with the observation of previous studies investigating HPV-31 [14,15].…”

“…Quantitative DNA methylation analysis by next-generation sequencing focused on CpG sites in the whole HPV-31 LCR (from nt 7066 to 97) and the 5 0 -end of the E6 gene. The methylation Single nucleotide changes and deletions characteristic of HPV-31 variants from different lineages were found in the sequenced LCR fragments, and in 16 specimens the results of the next-generation sequencing of bisulfite-modified DNA were concordant with previously reported results obtained by non-modified Sanger sequencing [13]. As the bisulfite modification does not affect 30 of the 39 lineagespecific SNPs, it allowed us to identify the HPV-31 lineages.…”

Genetic variability in E5, E6, E7 and L1 genes of human papillomavirus type 31

“…As above, in the present study the variant lineage A of HPV-31 was the most commonly detected variant, followed by C. However, the present study also observed the presence of variant lineage B, which has not been previously reported from Southern China. The results of one previous study by Ferenczi et al (36) differ substantially from the above; when 41 HPV-31 positive specimens were collected from Italian females, the proportions of A, B and C variants were 4.9, 29.3 and 65.8%, respectively (36). Therefore, geographic variation and ethnic differences cannot be ignored.…”

The Distribution and Common Amino Acid Polymorphisms of Human Papillomavirus (HPV)-31 Variants in 2700 Women from Northern China

“…Chagas et al in brazil enrolled 35 HPV-31 positive specimens from women with abnormal cytology, and reported the proportion of A, B and C variants were 57.2%, 5.7% and 37.1%,respectively [7]. Ferenczi et al collected 41 HPV-31 positive specimens in Italy from women undergoing colposcopical examination for malignant or premalignant disease, and found the proportion of A, B and C variants were 4.9%, 29.3% and 65.8%, respectively [8]. But results from hospital-based studies have limited representation, for the presence of lesions may confound the real distribution of variants in general population.…”