Whole-Genome Analysis of HPV67: Phylogenetic Classification and Genomic Characterization

Human papillomavirus (HPV) is the most common sexually transmitted infection. In most cases, HPV infections will resolve without complications, however HPV is responsible for nearly all cases of cervical cancer. Phylogenetic analyses of HPVs show that HPV16, the most carcinogenic of all HPV types, is closely related to HPV67 which is rarely associated with cancer. This thesis curated a quality-controlled dataset of HPV67 whole genome samples to generate a phylogenetic tree, assign lineages, assess genetic diversity, and profile variants. Samples (n=149) showed a bias towards lineage B, with an absence of viral integration and co-infections with other HPV types. Variant analysis showed that E1 and E2 exhibited the highest frequency of amino acid-changing substitutions associated with phylogenetic clustering. E7 demonstrated a higher proportion of nonsynonymous substitutions and E1 showed more synonymous substitutions. E7 exhibited a dN/dS ratio of one (1), suggesting E7 may be more receptive to amino acid changes. Collectively, these findings help clarify HPV67’s limited role in carcinogenesis.