HIV-1 Proviral DNA Loads (as Determined by Quantitative PCR) in Patients Subjected to Structured Treatment Interruption after Antiretroviral Therapy Failure

Komninakis, Shirley Vasconcelos; Santos, Domingos Ezenildo Matos dos; Santos, Carlos Alexandre dos; Oliveros, Marcia Perez Resende; Sanabani, Sabri Saeed; Diaz, Ricardo Sobhie

doi:10.1128/jcm.00393-12

Cited by 18 publications

(17 citation statements)

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“…One hundred sixteen patients were allocated to five treatment subgroups as follows: ( 1 ) patients treated with two nucleoside-analogue reverse-transcriptase inhibitors (NRTI) associated with the non-nucleoside analog reverse-transcriptase inhibitors (NNRTI) Efavirenz or Nevirapine as the first ART regimen; (2) patients treated with two NRTIs and a protease inhibitor boosted with ritonavir (PI-r) as the first ART regimen; (3) patients on salvage therapy with two NRTIs and a PI-r; (4) patients under salvage therapy containing two NRTIs, PI-r and the integrase inhibitor raltegravir; and (5) patients under antiretroviral virologic failure with the confirmed presence of HIV ART resistant strains. Peripheral blood samples were collected, and clinical data on the patients were analyzed, including CD4+ and CD8+ T-cell counts, the duration of treatment with undetectable viral loads and the number of ART schemes previously used by the patient.…”

Section: Methodsmentioning

confidence: 99%

Laboratory surrogate markers of residual HIV replication among distinct groups of individuals under antiretroviral therapy

Diaz

Giron

Tenore

et al. 2018

Preprint

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15 Background: Residual HIV-1 replication among individuals under antiretroviral therapy 16 (ART) relates to HIV micro-inflammation. 17 Objectives: To determine levels of residual HIV replication markers among distinct 18 subgroups of antiretroviral-treated individuals.19Methods: 116 patients were distributed into 5 treatment groups: first-line suppressive ART 20 with non-nucleoside reverse-transcriptase inhibitor (NNRTI) (n=26), first-line suppressive 21 ART with boosted protease inhibitors (PI-r) (n=25), salvage therapy using PI-r (n=27), 22 salvage therapy with PI-r and raltegravir (n=22) and virologic failure (n=16). Episomal and 23 total DNA quantitation was evaluated. ELISA was used for HIV antibody and LPS 24 quantitation. 25 Results: Episomal DNA was positive in 26% to 38% of individuals under suppressive ART, 26 being higher among individuals experiencing virologic failure (p=0.04). HIV proviral load 27 was higher among patients with detectable episomal DNA (p=0.01). Individuals receiving 28 initial PI-r treatment presented lower HIV antibodies (p=0.027) and LPS (p=0.029) than 29 individuals receiving NNRTI. There was a negative correlation between episomal DNA 30 quantitation and suppressive ART duration (p=0.04), CD4+ T-cell count (p=0.08), and CD8+ 31 T-cell count (p=0.07).32 Conclusions: Residual HIV replication has been inferred among individuals under 33 suppressive ART according to episomal DNA detection. Residual replication may decrease 34 with longer periods of suppressive ART and higher levels of CD4+ and CD8+ T cells. The 35 relationship between episomal DNA and total DNA suggests a replenishment of the proviral 36 reservoir with impacts on HIV persistence. Lower antibody and LPS levels among patients 37with initial PI-r ART suggest these regimens may more effectively suppress HIV with higher 38 capacity to decrease the HIV antigenic component. 39 Patients 61Patients were chosen between 2011 to 2013 in São Paulo Brazil according to their 62 current antiretroviral treatment (see Supplementary Table 1). Individuals were under ART 63 with undetectable plasma viral loads for at least one year, except for the virologic failure 64 4 group. This study was approved by the Ethics Committee in Research at the Federal 65 University of São Paulo (approval #0201/11), and informed consent was obtained from all 66 patients. 67One hundred sixteen patients were allocated to five treatment subgroups as follows: 68(1) patients treated with two nucleoside-analogue reverse-transcriptase inhibitors (NRTI) 69 associated with the non-nucleoside analog reverse-transcriptase inhibitors (NNRTI) Efavirenz 70 or Nevirapine as the first ART regimen; (2) patients treated with two NRTIs and a protease 71 inhibitor boosted with ritonavir (PI-r) as the first ART regimen; (3) patients on salvage 72 therapy with two NRTIs and a PI-r; (4) patients under salvage therapy containing two NRTIs, 73 PI-r and the integrase inhibitor raltegravir; and (5) patients under antiretroviral virologic 74 failure with the confirmed presence o...

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Section: Methodsmentioning

confidence: 99%

Laboratory surrogate markers of residual HIV replication among distinct groups of individuals under antiretroviral therapy

Diaz

Giron

Tenore

et al. 2018

Preprint

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“…UDS of V3. In order to estimate the viral input for the subsequent amplification, proviral DNA was quantified by quantitative PCR (qPCR) as described previously (68). In total, 11 baseline samples were subjected to ultradeep sequencing (UDS).…”

Section: Methodsmentioning

confidence: 99%

Pace of Coreceptor Tropism Switch in HIV-1-Infected Individuals after Recent Infection

Arif

Hunter

Léda

et al. 2017

J Virol

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HIV-1 entry into target cells influences several aspects of HIV-1 pathogenesis, including viral tropism, HIV-1 transmission and disease progression, and response to entry inhibitors. The evolution from CCR5- to CXCR4-using strains in a given human host is still unpredictable. Here we analyzed timing and predictors for coreceptor evolution among recently HIV-1-infected individuals. Proviral DNA was longitudinally evaluated in 66 individuals using Geno2pheno Demographics, viral load, CD4 and CD8 T cell counts, CCR5Δ32 polymorphisms, GB virus C (GBV-C) coinfection, and HLA profiles were also evaluated. Ultradeep sequencing was performed on initial samples from 11 selected individuals. A tropism switch from CCR5- to CXCR4-using strains was identified in 9/49 (18.4%) individuals. Only a low baseline false-positive rate (FPR) was found to be a significant tropism switch predictor. No minor CXCR4-using variants were identified in initial samples of 4 of 5 R5/non-R5 switchers. Logistic regression analysis showed that patients with an FPR of >40.6% at baseline presented a stable FPR over time whereas lower FPRs tend to progressively decay, leading to emergence of CXCR4-using strains, with a mean evolution time of 27.29 months (range, 8.90 to 64.62). An FPR threshold above 40.6% determined by logistic regression analysis may make it unnecessary to further determine tropism for prediction of disease progression related to emergence of X4 strains or use of CCR5 antagonists. The detection of variants with intermediate FPRs and progressive FPR decay over time not only strengthens the power of Geno2pheno in predicting HIV tropism but also indirectly confirms a continuous evolution from earlier R5 variants toward CXCR4-using strains. The introduction of CCR5 antagonists in the antiretroviral arsenal has sparked interest in coreceptors utilized by HIV-1. Despite concentrated efforts, viral and human host features predicting tropism switch are still poorly understood. Limited longitudinal data are available to assess the influence that these factors have on predicting tropism switch and disease progression. The present study describes longitudinal tropism evolution in a group of recently HIV-infected individuals to determine the prevalence and potential correlates of tropism switch. We demonstrated here that a low baseline FPR determined by the Geno2pheno algorithm can predict tropism evolution from CCR5 to CXCR4 coreceptor use.

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“…Another critical requirement for determining HIV DNA proviral load in clinical samples is the assessment of the number of human cells per sample before DNA extraction [ 85 ]. The number of cells determined by flow cytometry is used to normalise HIV DNA in a sample [ 86 ]. Normalisers are used to ensure that target quantities from an equivalent amount of samples are comparable in absolute quantification, [ 73 , 87 ].…”

Section: Quantitative Pcr Assays To Detect Total Hiv-1 Dnamentioning

confidence: 99%

Clinical Relevance of Total HIV DNA in Peripheral Blood Mononuclear Cell Compartments as a Biomarker of HIV-Associated Neurocognitive Disorders (HAND)

Ruhanya

Jacobs

Glashoff

et al. 2017

Viruses

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The pathogenesis of HIV-associated neurocognitive disorders is complex and multifactorial. It is hypothesized that the critical events initiating this condition occur outside the brain, particularly in the peripheral blood. Diagnoses of HIV-induced neurocognitive disorders largely rely on neuropsychometric assessments, which are not precise. Total HIV DNA in the peripheral blood mononuclear cells (PBMCs), quantified by PCR, correlate with disease progression, which is a promising biomarker to predict HAND. Numerous PCR assays for HIV DNA in cell compartments are prone to variation due to the lack of standardization and, therefore, their utility in predicting HAND produced different outcomes. This review evaluates the clinical relevance of total HIV DNA in circulating mononuclear cells using different published quantitative PCR (qPCR) protocols. The rationale is to shed light on the most appropriate assays and sample types used to accurately quantify HIV DNA load, which predicts severity of neurocognitive impairment. The role of monocytes as a vehicle for trafficking HIV into the CNS makes it the most suitable sample for determining a HAND associated reservoir. Studies have also shown significant associations between monocyte HIV DNA levels with markers of neurodamage. However, qPCR assays using PBMCs are cheaper and available commercially, thus could be beneficial in clinical settings. There is need, however, to standardise DNA extraction, normalisation and limit of detection.

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HIV-1 Proviral DNA Loads (as Determined by Quantitative PCR) in Patients Subjected to Structured Treatment Interruption after Antiretroviral Therapy Failure

Cited by 18 publications

References 10 publications

Laboratory surrogate markers of residual HIV replication among distinct groups of individuals under antiretroviral therapy

Laboratory surrogate markers of residual HIV replication among distinct groups of individuals under antiretroviral therapy

Pace of Coreceptor Tropism Switch in HIV-1-Infected Individuals after Recent Infection

Clinical Relevance of Total HIV DNA in Peripheral Blood Mononuclear Cell Compartments as a Biomarker of HIV-Associated Neurocognitive Disorders (HAND)

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