Human papillomaviruses: genetic basis of carcinogenicity

Abstract

Persistent infection by specific oncogenic human papillomaviruses (HPVs) is established as the necessary cause of cervix cancer. DNA sequence differences between HPV genomes determine whether an HPV has the potential to cause cancer. Of the more than 100 HPV genotypes characterized at the genetic level, at least 15 are associated, to varying degrees, with cervical cancer. Classification based on nucleotide similarity places nearly all HPVs that infect the cervicovaginal area within the alpha-PV genus. Within this genus, phylogenetic trees inferred from the entire viral genome cluster all cancer-causing types together, suggesting the existence of a common ancestor for the oncogenic HPVs. However, in separate trees built from the early open reading frames (ORFs; i.e. E1, E2, E6, E7) or the late ORFs (i.e. L1, L2), the carcinogenic potential sorts with the early region of the genome, but not the late region. Thus, genetic differences within the early region specify the pathogenic potential of alpha-HPV infections. Since the HPV genomes are monophyletic and sites are highly correlated across the genome, diagnosis of oncogenic types and non-oncogenic types can be accomplished using any region across the genome. Here we review our current understanding of the evolutionary history of the oncogenic HPVs, in particular, we focus on the importance of viral genome heterogeneity and discuss the genetic basis for the oncogenic phenotype in some but not all alpha-PVs.

Fig. 1

The structure and organization of an HPV genome (adapted from [57]). A schematic picture of a representative α-HPV genome is shown. The reference HPV-16 genome is a circular, double-stranded 7,908 bp molecule. The 3 major regions of the genome contain the upstream regulatory region (URR), the early (E) gene region, and the late (L) gene region. Also shown is the region of the genome conserved in most cancers with integrated HPV genomes.

Fig. 2

Phylogenetic tree of the mucosal/genital α-HPVs. A ‘total evidence’ phylogenetic tree was inferred from maximum parsimony, neighbor joining and Bayesian methods (for details see [10]). The tree shown is from the Bayesian analysis inferred from alignment of protein and nucleotide sequences of 6 concatenated ORFs (E6, E7, E1, E2, L2 and L1). Bovine PV type 1 was used as the out-group taxa. The numbers to the right represent the species group (e.g. ‘α9’ contains HPVs 16, 31, 35, 58, 33, 67 and 52). At least 3 ancestral papillomaviruses are responsible for the current heterogeneous groups of genital HPV genomes including LR1/NOT1 (α10, α8, α1 and α13), LR2/NOT2 (α2, α3, α4, α15) and HR/OT (α5, α6, α7, α9 and α11), the later joined by bold lines represents the clade that contains all known HPV types associated with cervix cancer. HR = High-risk; OT = oncogenic type; LR = low-risk; NOT = non-oncogenic type.

Fig. 3

Trees from early and late genes show phylogenetic incongruence. Phylogenetic trees were inferred using Bayesian methods [11]. The early gene tree (left) was calculated from E1, E2, E6 and E7 concatenated nucleotide alignments, while the late gene tree (right) was derived from combined L1 and L2 nucleotide sequence data. The α-papillomavirus group designations are shown on their respective leaf branches adjacent to the name of the HPV type as shown in the center. All types within the HR/OT clade are shown and representative viruses were chosen from each of the other α-HPV species groups.

Fig. 4

Phylogeny and sequence dissimilarity plots of HPV-16 variants. a A phylogenetic tree indicating the intratypic relationships of HPV-16. b The nucleotide sequence dissimilarities of HPV16 variants inferred from the complete genomes and the L1. The tree was inferred from the concatenated amino acids and nucleotide sequences of 8 ORFs (E1, E2, E4, E5, E6, E7, L1 and L2). For the dissimilarity plots, each HPV-16 variant sequence was analyzed against all other sequences and plotted. The open circles represent HPV-16 European (E) variants; triangles represent non-European variants consisting of African-1 (Af-1), African-2 (Af-2) or Asian-American (As-Am). The relationship of the European HPV-16 variants is indicated with a solid line and the non-European HPV-16 variants with a broken line. The European HPV-16 variants show less divergence as a group than the non-European HPV-16 variants. Each type is 0% different to itself.

Fig. 5

Prevalence (a), persistence (b) and progression (c) in a population-based study. Approximately 10,000 women representing a random population of women from Guanacaste, Costa Rica were followed for 5–7 years in a natural history study of HPV and cervix neoplasia as described [10, 55]. a Prevalence of HPV types at the baseline visit. b Percent persistence of an HPV type detected at baseline. c Percent of persistent infections progressing to CIN3/cancer. HPV types are divided into 3 categories: oncogenic, non-oncogenic and questionable. Since the study was a true population-based cohort, prevalence is shown as number of infections that is proportional to cross-sectional prevalence. The 3 panels demonstrate that oncogenic, non-oncogenic and other types have similar rates of prevalence and persistence, but only oncogenic types, given persistence, progress to CIN3/cancer. This data provides evidence that it is not simply persistence that determines pathogenicity, but persistence with an oncogenic HPV that is critical.