Changes in intra-host genetic diversity according to lesion severity in longitudinal HPV16 samples.

Human papillomavirus type 16 (HPV16) is the most common cause of cervical cancer, but most infections are transient and with lesions not progressing to cancer. There is a lack of specific biomarkers for diagnosis and risk stratification. This study aimed to explore the intra-host HPV16 genomic variation in longitudinal samples from HPV16-infected women with different cervical lesion severity (normal, low-grade, and high-grade). The TaME-seq deep sequencing protocol was used to generate whole genome HPV16 sequences of 102 samples collected over time from 40 individuals. Single nucleotide variants (SNVs) and intra-host single nucleotide variants (iSNVs) were identified in the viral genomes. A majority of individuals had a unique set of SNVs and these SNVs were stable over time. Overall, the number of iSNVs and APOBEC3-induced iSNVs were significantly lower in high-grade relative to normal and low-grade samples, respectively. A significant increase in the number of APOBEC3-induced iSNVs over time was observed for normal samples when compared to high-grade. Our results provide new insight into the dynamics of HPV16 within-hosts evolution. Low number of iSNVs and APOBEC3-induced iSNVs, characteristics of high-grade lesions, could potentially serve as biomarkers to guide triage of HPV-induced cervical precancerous lesions.