Determination of HIV-1 coreceptor tropism using proviral DNA in women before and after viral suppression

Abstract

BackgroundAn HIV-1 tropism test is recommended prior to CCR5 antagonist administration to exclude patients harboring non-R5 virus from treatment with this class of antiretrovirals. HIV-1 tropism determination based on proviral DNA (pvDNA) may be useful in individuals with plasma viral RNA suppression. We developed a genotypic tropism assay for pvDNA and assessed its performance in a retrospective analysis of samples collected longitudinally.ResultsWe randomly selected paired plasma/PBMC samples from the Women’s Interagency HIV Study with plasma viral load ≥5,000 cp/mL at time 1 (T1), undetectable viral load maintained for ≥1 year and CD4+ >200 cells/μL at time 2 (T2). pvDNA was isolated from cryopreserved PBMCs. Sequences were analyzed in triplicate from 49/50 women, with tropism assigned using the geno2pheno (g2p) algorithm. The median time between T1 and T2 was 4.1 years. CXCR4-using virus was detected in 24% of the RNA samples and 33% of the pvDNA samples at T1, compared to 37% of the pvDNA samples at T2. Concordance between plasma RNA and pvDNA tropism was 88% at T1 and 80% at T2. The g2p scores for RNA (T1) vs DNA (T1, T2) were strongly correlated (Spearman rho: 0.85 (T1); 0.78 (T2)). In women with evidence of tropism switch at T2 (either R5 to non-R5 or non-R5 to R5), there was a correlation between change in tropism and time. Mean pvDNA viral load decreased by 0.4 log10 copies/106 cells between T1 and T2 (p < 0.0001), but this decrease was not significantly associated with tropism status.ConclusionsWe demonstrated that pvDNA tropism in women with HIV-1 suppression is concordant with prior RNA tropism results, even after a median time of >4 years. pvDNA tropism testing may be useful to determine eligibility of patients with viral suppression to switch to a CCR5-antagonist based regimen as well as for research purposes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12981-015-0055-x) contains supplementary material, which is available to authorized users.

HIV tropism switch in archived DNA of HIV-HCV subjects successfully treated with direct-acting antivirals for HCV infection

“…The small cohort size was composed of two groups of comparable numerosity and immuno-virological characteristics at BL and this is a strength of the study. The percentage of subjects with a X4 tropic virus infection at BL is high (42.9%) but comparable to that reported in previous studies in patients on successful ART 13 , 47 , 48 and possibly influenced by the immune activation state 49 .…”

Next generation sequencing reveals a high frequency of CXCR4 utilizing viruses in HIV-1 chronically infected drug experienced individuals in South Africa

“…The use of proviral DNA from PBMC for co-receptor determination (an approach that still has to be validated) may be a limitation of the current study. However, a number of studies, employing Sanger sequencing, have shown a strong correlation in co-receptor preference prediction between HIV variants obtained from plasma and PBMC [43][44][45][46].…”

Switch of predicted HIV-1 tropism in treated subjects and its association with disease progression

“…Co-receptor tropism was inferred with the geno2pheno algorithm setting the false positive rate (FPR) at 10% for plasma samples and 20% for PBMC samples, [ 1 ] based on previous studies [ 28 , 29 ] showing concordant results in the determination of co-receptor tropism for the same individual whether plasma RNA or proviral DNA was used. Co-receptor tropism for all PD patients was determined only on plasma RNA at either time-point; similarly in PU patients, co-receptor tropism was assessed only on proviral DNA at either time-point.…”