Longitudinal analysis of high-risk HPV infections reveals within-host viral genome changes over time

Abstract

Persistent infection with high-risk (HR)-HPV causes cervical cancer, however, it is unclear why most infections resolve while a minority progress. We deep sequenced the HPV genomes of 1,228 HR-HPV-positive serial samples from 351 women with persistent infections (2–10 serial samples per woman over 1–8 years), including 279 controls and 72 precancer/cancer cases, to assess HR-HPV genome changes during infection and relation to infection outcomes. Seventy-seven percent of persistent infections (45–97% by HPV type) were infections with the same exact viral genome isolate; for HPV16, only 52% were persistent with the same isolate. This may suggest some infections include a type-specific isolate switch or new isolate infection during persistence. We additionally observed within-host change to the HPV genome estimated as gradual changes to intrahost single nucleotide variant (iSNV) frequency, and changes varied by HPV type, with HPV33 infections showing the most iSNV changes. Cases exhibited fewer viral genome changes during infection compared to controls (OR = 0.31, 95% CI = 0.1 – 0.86, p = 0.019), suggesting a more stable and clonal viral genome in cases. By viral gene, E7 had fewer nonsynonymous mutations in the cases compared to controls that cleared within 2 years of infection (p = 0.012), which confirms the importance of E7 conservation and suggests mutations to E7 reduce persistence associated with progression. There was a similar pattern in E4 (p = 0.013), while E5 had more changes in the cases (p = 0.008). A subset of 28 infections had an intervening HPV-negative sample between HPV-positive visits; 93% of these infections had the same exact viral genome isolate in the samples before and after the negative, consistent with subclinical persistence and subsequent re-detection. Our data suggests that HR-HPV type-persistence can include a collection of viral isolates, and viral mutations during infection, particularly in E7, reduce HR-HPV persistence and thus carcinogenic potential. Author summary: Cervical cancer is the fourth most common cancer in women worldwide and is caused by persistent infection with high-risk types of human papillomavirus. Although most infections are cleared naturally, a small number persist and can progress to precancer and cancer. It remains unclear why certain infections progress while others do not. In this study, we followed women over time and analyzed repeated samples from the same infections to examine how the viral genome changes within an individual during infection. We found that the infections that subsequently progressed to precancer or cancer had significantly more stable viral genomes, whereas infections that did not progress showed greater genetic variation over time. We also observed differences in specific viral genes between persistence associated with progression and infections that cleared. These findings suggest that changes within the viral genome during infection can influence disease outcome. By highlighting the importance of tracking viral genetic variation over time, our work provides new insight into HPV infections and suggests that monitoring viral genome stability could help improve risk assessment and prevention strategies.

Original publication: PLOS Pathogens (2026-07-15). Source. Source DOI: 10.1371/journal.ppat.1014362.