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Background  Persistent infection with high-risk human papillomavirus (hrHPV) is a critical step in cervical carcinogenesis. We report on type-specific hrHPV persistence, clearance and incidence among screen-positive Rwandan women living with HIV (WLWH).    Methods  This was a nested analysis from a large cervical cancer screening study of ~ 5000 Rwandan WLWH. Women who tested positive for hrHPV and/or visual inspection with acetic acid were referred to colposcopy. For a subset of women ( n  = 298) who were ≥ 6 months delayed in receiving colposcopy, we tested their screening and colposcopy visit specimens using the AmpFire HPV genotyping assay that tests 14 hrHPV types (16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, and 68) individually.    Results  The mean, median (interquartile range [IQR]) and range of time between the screening and colposcopy visits were 644, 650 (490–820.5) and 197–1161 days, respectively. Mean, median (IQR) and range of age at the screening visit were 38, 37 (34–43) and 30–54 years, respectively. Two-hundred eighty-three (95.0%) had CD4 count (cells per mm 3 ) data available at baseline with mean, median (IQR) and range of 592, 513 (346–717) and 0–7290, respectively. Two-hundred thirty-five WLWH were positive for at least one hrHPV type at the screening visit, of whom 50.2% had at least one HPV type-specific infection persist; 37.2% of all HPV infections detected at the screening visit persisted. Compared to all other HPV types in aggregate, HPV16 (vs. non-HPV16 types) (47.7%,  p  = 0.03) and HPV33 (vs. non-HPV33 types) (56.7%, p = 0.03) were significantly more likely, and HPV39 (vs. non-HPV39 types) (6.7%,  p  = 0.01), HPV51 (vs. non-HPV51 types) (15.6%,  p  < 0.01), and HPV66 (vs. non-HPV66 types (17.9%,  p  = 0.04) were significantly less likely, to persist. Lower CD4 counts were associated with having any persistent hrHPV infection (p trend  = 0.04) and multiple persistent hrHPV infections (p trend  = 0.04).    Conclusion  There is a significant proportion of WLWH with persistent hrHPV infection, emphasizing the need to vaccinate them against HPV prior to becoming sexually active.    Supplementary Information  The online version contains supplementary material available at 10.1186/s13027-021-00355-6.

Type-specific persistence, clearance and incidence of high-risk HPV among screen-positive Rwandan women living with HIV