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Abstract Background The association between subclinical CMV replication and HIV persistence has not been investigated in cis-gender women with HIV. Methods Fifty virologically suppressed female participants with HIV were prospectively enrolled and provided oral, vaginal, urine samples and peripheral blood mononuclear cells (PBMCs) at one cross-sectional time-point. Cytomegalovirus (CMV) DNA was quantified in each specimen by real-time PCR. Cellular HIV DNA and HIV RNA transcripts (unspliced and multiply spliced [ms] encoding tat-rev) were quantified by droplet digital (dd)PCR. Historical data from 49 male individuals with HIV and CMV were used as controls. Results Levels of cellular HIV DNA and unspliced HIV RNA were not different between sexes, but female participants had less detectable msHIV RNA and CMV DNA compared to males (both P<0.01). Unlike previously described for males, the presence of CMV DNA was not associated with increased HIV DNA in females. Among female participants, pre-menopausal status was independently associated with lower HIV DNA compared to post-menopause, after adjusting for nadir CD4 count (P<0.01). Conclusions Female participants with HIV have reduced cellular HIV RNA and less subclinical CMV DNA compared to males, but overall similar HIV DNA levels in our study. Post-menopausal status was independently associated with higher HIV DNA levels among female participants.

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