A population-based prospective study of carcinogenic human papillomavirus variant lineages, viral persistence, and cervical neoplasia

Abstract

Human papillomavirus (HPV) types differ profoundly in cervical carcinogenicity. For the most carcinogenic type HPV16, variant lineages representing further evolutionary divergence also differ in cancer risk. Variants of the remaining 10 to 15 carcinogenic HPV types have not been well studied. In the first prospective, population-based study of HPV variants, we explored whether, on average, the oldest evolutionary branches within each carcinogenic type predicted different risks of >2-year viral persistence and/or precancer and cancer [cervical intraepithelial neoplasia grade 3+ (CIN3+)]. We examined the natural history of HPV variants in the 7-year, 10,049-woman Guanacaste Cohort Study, using a nested case-control design. Infections were assigned to a variant lineage determined by phylogenetic parsimony methods based on URR/E6 sequences. We used the Fisher's combination test to evaluate significance of the risk associations, cumulating evidence across types. Globally, for HPV types including HPV16, the P value was 0.01 for persistence and 0.07 for CIN3+. Excluding HPV16, the P values were 0.04 and 0.37, respectively. For HPV16, non-European viral variants were significantly more likely than European variants to cause persistence [odds ratio (OR), 2.6; P = 0.01] and CIN3+ (OR, 2.4; P = 0.004). HPV35 and HPV51 variant lineages also predicted CIN3+. HPV variants generally differ in risk of persistence. For some HPV types, especially HPV16, variant lineages differ in risk of CIN3+. The findings indicate that continued evolution of HPV types has led to even finer genetic discrimination linked to HPV natural history and cervical cancer risk. Larger viral genomic studies are warranted, especially to identify the genetic basis for HPV16's unique carcinogenicity.

Figure 1

Bayesian tree of 99 human papillomavirus types inferred from the concatenated amino acids and nucleotide sequences of 6 ORFs (E6, E7, E1, E2, L2 and L1). MrBayes v3.1.2 (44,45) with 10,000,000 cycles for the Markov chain Monte Carlo algorithm was used to generate phylogenetic trees. For Bayesian tree construction, the computer program ModelTest v3.7 (46) was used to identify the best evolutionary model; the identified gamma model was set for among-site rate variation and allowed all substitution rates of aligned sequence to be different. The ORF sequence was left blank if unavailable. HPV species groups were generally classified according to the classification system for PVs by de Villiers et al. (6). All high risk mucosal HPV types cluster together within the alpha PV genus, highlighted with bold lines. The broken lines represent skin HPV types.

Figure 2

Study Population. The cases and controls for the analysis were drawn from the population-based prospective Proyecto Epidemiologico Guanacaste, which included a random sample of approximately 1/6 of the adult women in the province. During the enrollment phase, we attempted to enroll all women with invasive cancer diagnosed in the province during the same time period. As such, this project it represents a true population-wide study of the different outcomes of type-specific HPV infections and variants. The analysis is based on individual viral types and, therefore, women could contribute to more than one type-specific analysis.