Abstract
Background Human papillomavirus 16 (HPV16) species group (alpha-9) of the Alphapapillomavirus genus contains HPV16, HPV31, HPV33, HPV35, HPV52, HPV58 and HPV67. These HPVs account for 75% of invasive cervical cancers worldwide. Viral variants of these HPVs differ in evolutionary history and pathogenicity. Moreover, a comprehensive nomenclature system for HPV variants is lacking, limiting comparisons between studies.MethodsDNA from cervical samples previously characterized for HPV type were obtained from multiple geographic regions to screen for novel variants. The complete 8 kb genomes of 120 variants representing the major and minor lineages of the HPV16-related alpha-9 HPV types were sequenced to capture maximum viral heterogeneity. Viral evolution was characterized by constructing phylogenic trees based on complete genomes using multiple algorithms. Maximal and viral region specific divergence was calculated by global and pairwise alignments. Variant lineages were classified and named using an alphanumeric system; the prototype genome was assigned to the A lineage for all types.ResultsThe range of genome-genome sequence heterogeneity varied from 0.6% for HPV35 to 2.2% for HPV52 and included 1.4% for HPV31, 1.1% for HPV33, 1.7% for HPV58 and 1.1% for HPV67. Nucleotide differences of approximately 1.0% - 10.0% and 0.5%–1.0% of the complete genomes were used to define variant lineages and sublineages, respectively. Each gene/region differs in sequence diversity, from most variable to least variable: noncoding region 1 (NCR1) /noncoding region 2 (NCR2) >upstream regulatory region (URR)> E6/E7 > E2/L2 > E1/L1.ConclusionsThese data define maximum viral genomic heterogeneity of HPV16-related alpha-9 HPV variants. The proposed nomenclature system facilitates the comparison of variants across epidemiological studies. Sequence diversity and phylogenies of this clinically important group of HPVs provides the basis for further studies of discrete viral evolution, epidemiology, pathogenesis and preventative/therapeutic interventions.
Highlights
Persistent infection of specific types of genital human papillomaviruses (HPVs) is the central cause of cervical cancer and its precursor, cervical intraepithelial neoplasia (CIN)
Human papillomavirus isolates of known types were obtained from previously characterized cervicovaginal exfoliated cells from a variety of studies performed in different geographic locations
We reasoned that this large set of clinical materials would capture a major portion of the genomic diversity of the Human papillomavirus 16 (HPV16)-related HPV types
Summary
Persistent infection of specific types of genital human papillomaviruses (HPVs) is the central cause of cervical cancer and its precursor, cervical intraepithelial neoplasia (CIN). A distinct papillomavirus (PV) ‘‘type’’ is established when the nucleotide sequence of the L1 gene of a cloned virus differs from that of any other characterized types by at least 10% [3,4]. Given that the HPV alpha-9 group plays such an important role in human cancer and variant lineages have different pathologic potentials, a comprehensive evolutionary study and classification system is needed. Human papillomavirus 16 (HPV16) species group (alpha-9) of the Alphapapillomavirus genus contains HPV16, HPV31, HPV33, HPV35, HPV52, HPV58 and HPV67. These HPVs account for 75% of invasive cervical cancers worldwide. A comprehensive nomenclature system for HPV variants is lacking, limiting comparisons between studies
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