Whole genome sequencing and evolutionary analysis of human papillomavirus type 16 in central China

Abstract

Human papillomavirus type 16 plays a critical role in the neoplastic transformation of cervical cancers. Molecular variants of HPV16 existing in different ethnic groups have shown substantial phenotypic differences in pathogenicity, immunogenicity and tumorigenicity. In this study, we sequenced the entire HPV16 genome of 76 isolates originated from Anyang, central China. Phylogenetic analysis of these sequences identified two major variants of HPV16 in the Anyang area, namely the European prototype (E(p)) and the European Asian type (E(As)). These two variants show a high degree of divergence between groups, and the E(p) comprised higher genetic diversity than the E(As). Analysis with two measurements of genetic diversity indicated that viral population size was relatively stable in this area in the past. Codon based likelihood models revealed strong statistical support for adaptive evolution acting on the E6 gene. Bayesian analysis identified several important amino acid positions that may be driving adaptive selection in the HPV 16 population, including R10G, D25E, L83V, and E113D in the E6 gene. We hypothesize that the positive selection at these codons might be a contributing factor responsible for the phenotypic differences in carcinogenesis and immunogenicity among cervical cancers in China based on the potential roles of these molecular variants reported in other studies.

Figure 1. Maximum Likelihood phylogenetic tree for 76 HPV16 samples from Anyang.

This tree is constructed using whole genome sequences and bootstrap scores larger than 70% are displayed. The tree itself is shown in bold, the sample IDs are linked through dashed lines. EPs are the European Prototypes and EAs are the European Asian types.

Figure 2. Sliding window plot of genetic diversity across the HPV genome.

Window size is set as 250 bp and step size = 50 bp. The solid arrows indicate the two regions in the E1 gene that failed in the PCR reactions. The dashed arrow indicates the region in E2 gene that failed in some of the specimens. Theta_w is the Watternson's estimate of genetic diversity which is based on the number of polymorphic sites , and theta_piis the Tajima's estimate of genetic diversity relying on average pairwise differences .