HPV16 whole genome minority variants in persistent infections from young Dutch women

Chronic infections by one of the oncogenic human papillomaviruses (HPVs) are responsible for near 5% of the global cancer burden and HPV16 is the type most often found in cancers. HPV genomes display unexpected levels of variation when deep-sequenced. Minority variants may reveal HPV genomic instability and HPV-related carcinogenic transformation of host cells. Here we investigate HPV16 genome variation using a whole-HPV genome deep sequencing protocol (TaME-seq) on 36 pre-clinical HPV16 cervical infections from a population of young Dutch women. One infection was followed over a three-year period, eight were followed over a two-year period, three were followed over a one-year period and four infections had a single sampling point. Using a 1% variant frequency cutoff, we find on average 48 minority variants (MVs) per HPV16 genome and 1737 MVs in total when sequencing coverage was >100×. In contrast to other studies detecting APOBEC-related C>T mutation profiles in pre-cancerous and cancer samples, we find the other transition mutation T>C to be the most common in pre-clinical samples. Our results suggest that the relative mutagenic footprint of HPV16 genomes may differ between pre-clinical infections and transforming lesions. In addition, we identify a number of minority variants that have previously been associated with higher incidence of high grade lesions (CIN3+) in a population study. These findings may provide a starting point for future studies exploring causality between emerging HPV genomic variants and cancer development.