Vaginal microbiome dynamics and HPV clearance

Almost every cervical cancer begins with a human papillomavirus infection that fails to clear. Most infections do clear, on their own, within a couple of years — so the question that matters clinically is not who becomes infected but who stays infected, and why.

This thesis asks whether the vaginal microbiome is part of that answer: whether the composition of the bacterial community present at infection is a biological variable in whether HPV is cleared or persists.

What I do on it

I lead the longitudinal and cross-sectional analyses of vaginal microbiome composition as a biological correlate of HPV clearance, in a cohort of female sex workers in Nairobi, Kenya — a population carrying a disproportionate share of both HPV and cervical cancer burden.

That covers the pipeline end to end:

• amplicon sequencing bioinformatics, from raw reads to community composition
• the statistical analysis and data visualisation, in R
• contributing to the wet-lab side, including DNA extraction and molecular assays

Status

Two manuscripts are in preparation from this work — one longitudinal, following microbiome signatures against HPV persistence over time, and one cross-sectional, on the association between community composition and HPV prevalence. An abstract has been accepted for poster presentation at EUROGIN 2026 in Vienna.