Abstract
BackgroundHIV-1 coreceptor tropism testing is used to evaluate eligibility for CCR5 antagonist therapy. However, HIV-1 RNA-based tests are not suitable for virologically suppressed patients, therefore the use of proviral DNA tropism testing has been investigated. We describe a novel proviral DNA-based genotypic tropism assay and compare its performance to that of a sensitive HIV-1 RNA-based genotypic test.MethodsTropism was determined using HIV-1 plasma RNA and proviral DNA from 42 paired samples from patients with plasma viral loads ≥1000 HIV-1 RNA copies/mL. Proviral DNA sample types included whole blood, separated peripheral blood mononuclear cells resuspended in phosphate-buffered saline and peripheral blood mononuclear cells resuspended in spun plasma. The HIV-1 envelope V3 region was PCR-amplified, sequenced in triplicate, and analyzed for tropism with the geno2pheno algorithm using a 10% false-positive rate (FPR).ResultsAmplicons were obtained from proviral DNA and plasma RNA in 41/42 samples. Tropism predictions were highly concordant (93%–98%) between proviral DNA and plasma RNA, regardless of the proviral DNA isolation method. Non-R5 proviral DNA results were obtained for 100% of patients with detectable non-R5 plasma HIV-1 RNA results. Geno2pheno FPRs for proviral DNA and plasma RNA were highly correlated (Spearman rho = 0.86).ConclusionsOur findings demonstrate that proviral DNA tropism determinations from whole blood or peripheral blood mononuclear cells were highly concordant with plasma HIV-1 RNA tropism determinations. This assay may be useful for screening virologically suppressed patients for CCR5-antagonist eligibility and for research purposes.
Highlights
Human immunodeficiency virus type 1 (HIV-1) requires contact with two receptors to gain entry to host cells and initiate infection: CD4 is the primary receptor and the chemokine receptors CCR5 and CXCR4 serve as secondary or co-receptors [1]
Plasma viral RNA represents currently replicating HIV-1, while proviral DNA (pvDNA) is intracellular viral DNA that represents a population of archived virus [7,8,9,10]. pvDNA can be extracted from the blood of HIV-1 patients with undetectable RNA viral loads in plasma [10,11]
We evaluated concordance of tropism predictions using pvDNA and plasma viral RNA obtained from paired specimens
Summary
Human immunodeficiency virus type 1 (HIV-1) requires contact with two receptors to gain entry to host cells and initiate infection: CD4 is the primary receptor and the chemokine receptors CCR5 and CXCR4 serve as secondary or co-receptors [1]. Genotypic and phenotypic tropism assays of plasma HIV-1 are available as clinical tests and are recommended in US and European guidelines [7,8,9]. PvDNA can be extracted from the blood of HIV-1 patients with undetectable RNA viral loads in plasma [10,11]. This permits tropism testing to extend to virologically suppressed patients on effective antiretroviral regimens, who may be candidates for CCR5 antagonist therapy because of the need for regimen switches or simplification. HIV-1 RNA-based tests are not suitable for virologically suppressed patients, the use of proviral DNA tropism testing has been investigated. We describe a novel proviral DNA-based genotypic tropism assay and compare its performance to that of a sensitive HIV-1 RNA-based genotypic test
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