Undetectable unintegrated HIV-DNA in persons with HIV: frequency and determinants

Despite suppressive antiretroviral therapy (ART), HIV-1 persists in infected cells as integrated proviral DNA and as more labile unintegrated DNA forms (uDNA). The presence of uDNA has been proposed as a surrogate marker of recent infection events occurring below the detection limits of plasma HIV-1 RNA assays. The aim of this study was to evaluate the performance of an assay for the quantification of uDNA in peripheral whole blood of people with HIV (PWH), with the intent of identifying individuals with no evidence of recent infection events, defined as undetectable uDNA, and to characterize associated clinical and immunological factors.

Total and unintegrated HIV-1 DNA were quantified by real-time PCR in whole blood samples from 87 chronically treated PWH. Samples were derived from a real-world, retrospective cohort and reflected the antiretroviral regimens actually received by patients over time. Clinical, virological, and immunological parameters were analyzed in relation to uDNA detectability.

Overall, uDNA was quantifiable in 11/87 (13%) samples, detectable below the assay quantification limit in 52/87 (60%), and undetectable (target not detected) in 24/87 (28%). Undetectable uDNA was associated with higher CD4⁺ T-cell nadir, higher current CD4⁺ T-cell counts, and lower total HIV-1 DNA levels. In multivariable analysis, CD4⁺ T-cell nadir was the only factor independently associated with uDNA undetectability (p = 0.001). Antiretroviral regimen characteristics were not independently associated with uDNA detectability.

A substantial proportion of chronically treated PWH exhibited undetectable uDNA in peripheral blood. The uDNA measurement provides complementary information to plasma HIV-1 RNA and CD4⁺ T-cell counts and may help identify individuals with no evidence of recent infection events and higher immunological fitness. These findings support the potential utility of uDNA quantification as a biomarker of HIV-1 reservoir dynamics in real-world clinical settings.