Genome-wide association study of human papillomavirus infection and persistence in women living with HIV in Rwanda

Background We conducted an explorative genome-wide association study (GWAS) in East Africa to identify host genetic variants associated with the acquisition and persistence of human papillomavirus (HPV) infection. Methods We genotyped 385 Rwandan women living with HIV and selected host biomarker assay signals from genital swab samples using qPCR. We compared women who cleared HPV over a two-year interval (operationally defined as persistent infection), with those who did not. Exploratory gene-based aggregation analyses of rare and low-frequency variants represented on the genotyping array were also performed. Results In the primary cluster-stratified Cochran–Mantel–Haenszel analysis, rs13158830 within PPARGC1B exceeded the conventional genome-wide significance threshold for persistent HPV infection. The nearby MIR378A gene-expression assay signal was higher in HPV-positive women but did not distinguish clearance from persistence. Conclusions We identified an exploratory host genetic association with persistent HPV infection and several additional candidate loci. The lead rs13158830 signal remained evident in Fisher exact testing and PC-adjusted Firth regression, but the small number of carriers produced substantial uncertainty. These findings require replication in independent cohorts. Clinical trial registration Not applicable.