Genetic variability and lineage phylogeny of human papillomavirus type-16 and -53 based on the E6, E7, and L1 genes in Southwest China

Abstract

Human papillomaviruses (HPVs) are circular double-stranded DNA viruses that are highly prevalent in the general population, and account for the cervical cancer burden in women worldwide. In this study, we analyzed HPV-16, the most prevalent type worldwide, and HPV-53, a possible high-risk type from infected women in Southwest China. To characterize mutations, intratypic variants, and genetic variability in the E6, E7, and L1 genes of HPV-16 (n=97) and HPV-53 (n=15), these genes were sequenced and submitted to GenBank. Phylogenetic trees were constructed using Bayesian trees, followed by secondary structure analysis and B-cell epitope prediction. Moreover, the selection pressures of the E6, E7, and L1 genes were estimated. In total, 27 novel variants of HPV-16 and 11 novel variants of HPV-53 were identified. In the HPV-16 E6-E7-L1 sequences, 73 nucleotide changes were observed with 40/73 being non-synonymous mutations (two in the alpha helix and five in the beta sheet) and 33/73 being synonymous. In the HPV-53 E6-E7-L1 sequences, 64 nucleotide changes were observed with 26/64 being non-synonymous mutations (three in the alpha helix and one in the beta sheet) and 38/64 being synonymous. Selective pressure analysis showed that most of these mutations did not reflect positive selection. The maximal divergence between any two variants within each gene of these two HPV types ranging from 0.94%(HPV-16 L1 gene)to 2.80%(HPV-53 E6 gene).Identifying new variants of HPV-16 and -53 from women in Southwest China may be helpful to design vaccines specifically for women in Southwest China and testing methods specifically for this region. The results of our study may contribute to future researches in diagnostic probes, vaccines improvement, or screening methods for a particular population.