Examination of real-time PCR for HIV-1 RNA and DNA quantitation in patients infected with HIV-1 BF intersubtype recombinant variants

Development of a sensitive, quantitative assay with broad subtype specificity for detection of total HIV-1 nucleic acids in plasma and PBMC

An LTR-based quantitative PCR (qPCR) assay was modified and optimized for the quantification of total HIV-1 nucleic acids in plasma and PBMC. TaqMan qPCR primers and probes were designed against the NCBI/LANL HIV-1 compendium database by analyzing sequences used in assays for sensitive cross-clade detection of HIV-1 as reported in the literature and elucidating regions of improved cross-subtype specificity. Inosine and mixed nucleotide bases were included at polymorphic sites. Real-time RT-qPCR and qPCR were performed on plasma viral RNA and cellular lysates. A step-up amplification approach to allow binding of primers across polymorphic regions showed improved sensitivity compared to universal cycling. Unlike a lead competing laboratory-developed assay, all major HIV-1 subtypes, and a wide range of recombinants from a 127-member diversity panel were detected and accurately quantified in spiked plasmas. Semi-nested PCR increased detection sensitivity even further. The assay was able to detect down to 88 copies/mL of HIV-1 in plasma with 95% efficiency or the equivalent of a single infected cell. The PCR assay will be valuable in studies that monitor very low viral levels including residual or break through HIV-1 in patients receiving antiretroviral therapy, in HIV-1 cure, and in other research studies.

Cytotoxic CD8+ T Cells Expressing CXCR5 Are Detectable in HIV-1 Elite Controllers After Prolonged In Vitro Peptide Stimulation

Antiretroviral therapy (ART) is not curative as HIV-1 persists in long-lived viral reservoirs. Consequently, patients are dependent on life-long drug adherence with possible side effects. To overcome these limitations strategies of a functional cure aim at ART free viral remission. In this study, we sought to identify detailed subsets of anti-viral CD8⁺ T cell immunity linked to natural long-term control of HIV-1 infection. Here, we analyzed HIV controllers and ART suppressed progressors for in vitro viral suppressive capacity (VSC) at baseline and after peptide stimulation. Functional properties and phenotypes of CD8⁺ T cells were assessed by IFN-γ ELISPOT and 18 color flow cytometry. HIV controllers showed significantly increased suppression at baseline as well as after peptide stimulation. IFN-γ secretion and the proliferation marker Ki67 positively correlated with VSC. Moreover, the detailed phenotype of three distinct multifunctional memory CD8⁺ T cell subsets were specific traits of HIV controllers of which two correlated convincingly with VSC. Our results underline the importance of multifunctional CD8⁺ T cell responses during natural control. Especially the role of CXCR5 expressing cytotoxic subsets emphasizes potential surveillance in sites of reservoir persistence and demand further study.

Rapid viral rebound after analytical treatment interruption in patients with very small HIV reservoir and minimal on-going viral transcription

INTRODUCTION

Viral remission after analytical treatment interruption (ATI), termed post-treatment control, has been described in a small proportion of HIV-positive patients. This phenomenon has been separately associated to both low levels of HIV-1 proviral DNA as well as cell-associated RNA. We investigated whether the combination of both parameters could help predict delayed viral rebound after treatment interruption (TI).

METHODS

We conducted an open single-arm ATI study in four Belgian HIV reference centres from January 2016 to July 2018. Eligible participants were adults who had fewer than 50 HIV-1 RNA copies/mL for more than two years, more than 500 CD4 cells/µL for more than three months, and were in general good health. Consenting participants who had fewer than 66 copies total HIV-1 DNA (t-DNA) and fewer than 10 copies cell-associated HIV-1 unspliced RNA (US-RNA) per million peripheral blood mononuclear cells (PBMCs), interrupted therapy and were monitored closely. Antiretroviral therapy (ART) was resumed after two consecutive viral loads exceeding 1000 copies or one exceeding 10,000 copies/mL. The primary outcome was the proportion of participants with fewer than 50 HIV-1 RNA copies/mL 48 weeks after TI. Secondary outcomes were time to viral rebound, the frequency of serious adverse events (AEs) and evolution of t-DNA and US-RNA after TI.

RESULTS

All 16 consenting participants who interrupted therapy experienced rapid viral rebound two to eight weeks after TI. No serious AEs were observed. Levels of t-DNA and US-RNA increased after TI but returned to pre-ATI levels after treatment restart. None of the studied demographic, clinical and biological parameters were predictive of time of viral rebound.

CONCLUSIONS

The combination of low levels of t-DNA and US-RNA in PBMCs, corresponding respectively to a small and transcriptionally silent viral reservoir, is not predictive of viral remission after TI in patients on ART.

In-depth validation of total HIV-1 DNA assays for quantification of various HIV-1 subtypes

HIV-1 DNA quantification serves as an important reservoir biomarker in HIV cure trials. However, the high genetic diversity of HIV-1 represented by different subtypes may bring inaccuracy in quantifying HIV-1 DNA and a sensitive and validated assay covering diverse HIV-1 subtypes is lacking. Therefore, we cross-validated total HIV-1 DNA assays described in literature using a three-step comparative analysis. First, a bioinformatics tool was developed in-house to perform an in silico evaluation of 67 HIV-1 DNA assays. Secondly, these selected assays were in vitro validated using a panel of different HIV-1 subtypes and, finally, ex vivo assessed on selected patient samples with different HIV-1 subtypes. Our results show that quantification of HIV-1 DNA substantially differs between assays and we advise five best performing HIV-1 DNA assays for ddPCR and qPCR (Schvachsa_2007, Viard_2004, Heeregrave_2009, Van_der_Sluis_2013, Yu_2008 and Yun_2002). This in-depth analysis of published HIV-1 DNA assays indicates that not all assays guarantee an optimal measurement of HIV-1 DNA, especially when looking across subtypes. Using an in-depth cross-validation, we were able to validate HIV-1 DNA assays that are suitable for quantification of HIV-1 DNA in a wide variety of HIV-1 infected patients.

Predictors of virological failure in HIV-1-infected patients switching to dolutegravir maintenance monotherapy

Objectives

The Dolutegravir Monotherapy for HIV (DOMONO; NCT02401828) study showed that maintenance monotherapy with dolutegravir (DTG) is associated with virological failure (VF) and leads to DTG resistance and as a result should not be used. However, data on clinical and virological factors associated with VF during DTG monotherapy are lacking. We identified factors associated with VF during DTG monotherapy.

Methods

A randomized trial was carried out in which patients on combination antiretroviral therapy (cART) with an HIV‐1 RNA zenith < 100 000 copies/mL and a CD4 T‐cell nadir ≥ 200 cells/μL, who had never experienced VF, switched to DTG monotherapy. Clinical and virological factors were compared between patients with and without VF, using univariate analyses.

Results

Eight of the 95 patients developed VF during DTG monotherapy. A total of 78 participants had reached week 48 when the study was discontinued. The median CD4 T‐cell nadir was lower in patients with VF than in patients without VF [260 (interquartile range (IQR) 223–320) versus 380 (IQR 290–520) cells/μL, respectively; P = 0.011]. Patients with VF had a longer time between HIV diagnosis and cART initiation than those without VF [median 49 (IQR 27–64) versus 15 (IQR 1–38) months, respectively; P = 0.015]. The median total peripheral blood mononuclear cell (PBMC) HIV DNA copy number was higher in patients with VF than in those without VF [417 (range 85–4151) versus 147 (range 16–4132) copies/10⁶PBMCs, respectively; P = 0.022].

Conclusions

A lower CD4 nadir, a longer time between HIV diagnosis and cART initiation, and a higher HIV DNA copy number at the time of DTG monotherapy initiation were associated with VF. While there clearly is no future role for DTG monotherapy, ongoing and future studies on the efficacy of maintenance dual therapy (e.g. DTG lamivudine) may have to take these variables into account in their study design and analysis.

Hypermulticolor Detector for Quantum-Antibody Based Concurrent Detection of Intracellular Markers for HIV Diagnosis

Antiretroviral treatment can reduce the death rate of human immunodeficiency virus (HIV) infection, and its effectiveness is maximized at the early stage of HIV infection. The present protocol demonstrates an early stage high-content HIV diagnosis based on multicolor concurrent monitoring of CD4, CD8, and CD3 coreceptors and F-actin cytoskeleton using quantum dot (Qdot)-antibody conjugates at the single cell level. Artificial HIV infection of peripheral blood mononuclear cells (PBMCs) can be achieved by treating PBMCs with gp120. Using the present methodology, we can determine the CD4-CD8 ratios of normal PBMCs and artificial HIV-infected PBMCs. In addition, this protocol enables monitoring of structural changes of actin filament alignments in PBMCs bound to gp120 proteins using the multicolor single cell imaging system. Overall, this approach presents a new model for accurate early stage HIV diagnosis. Simultaneously the approach provides information on actin cytoskeleton and subtypes of PBMCs as well as their CD4-CD8 ratios.

Evaluation of dried blood spot diagnosis using HIV1-DNA and HIV1-RNA Biocentric assays in infants in Abidjan, Côte d'Ivoire. The Pedi-Test DBS ANRS 12183 Study

This study evaluates HIV infant diagnosis on DBS using Biocentric HIV1-DNA and HIV1-RNA assays, in field conditions in Côte d'Ivoire. Paediatric screening was offered to children≤3 years in clinical sites in Côte d'Ivoire in 2008. For each HIV-infected child, two non-infected children were included and blood samples were collected. HIV-DNA results obtained on EDTA blood samples with Biocentric assay were the reference for HIV infant diagnosis. Plasma and DBS viral loads were measured using HIV-RNA Biocentric assay. DBS samples were also tested for HIV-DNA detection using both Biocentric and Amplicor Roche assays. Sensitivity, specificity and concordance between tests were calculated. Overall samples from 138 HIV-exposed children, 46 infected, 92 non-infected were included. All tests were 100% sensitive and specific including 100% concordance with the two HIV-DNA assays. The median level of HIV-DNA on EDTA samples was 3.15 log10 copies/10(6) PBMCs; the median level of HIV RNA in plasma and DBS were respectively 5.82 and 5.17 log10 copies/ml (Pearson's correlation R2=0.92, p<0.0001). The threshold for detectable HIV-RNA on DBS was 3.3 log10. Although there are differences between viral load measured on DBS and plasma, the two Biocentric assays present very good performances for HIV infant diagnosis on DBS while cheap and feasible.

Lopinavir/Ritonavir versus Lamivudine peri-exposure prophylaxis to prevent HIV-1 transmission by breastfeeding: the PROMISE-PEP trial Protocol ANRS 12174

BACKGROUND

Postnatal transmission of HIV-1 through breast milk remains an unsolved challenge in many resource-poor settings where replacement feeding is not a safe alternative. WHO now recommends breastfeeding of infants born to HIV-infected mothers until 12 months of age, with either maternal highly active antiretroviral therapy (HAART) or peri-exposure prophylaxis (PEP) in infants using nevirapine. As PEP, lamivudine showed a similar efficacy and safety as nevirapine, but with an expected lower rate of resistant HIV strains emerging in infants who fail PEP, and lower restrictions for future HIV treatment. Lopinavir/ritonavir (LPV/r) is an attractive PEP candidate with presumably higher efficacy against HIV than nevirapine or lamivudine, and a higher genetic barrier to resistance selection. It showed an acceptable safety profile for the treatment of very young HIV-infected infants. The ANRS 12174 study aims to compare the risk of HIV-1 transmission during and safety of prolonged infant PEP with LPV/r (40/10 mg twice daily if 2-4 kg and 80/20 mg twice daily if >4 kg) versus Lamivudine (7,5 mg twice daily if 2-4 kg, 25 mg twice daily if 4-8 kg and 50 mg twice daily if >8 kg) from day 7 until one week after cessation of BF (maximum 50 weeks of prophylaxis) to prevent postnatal HIV-1 acquisition between 7 days and 50 weeks of age.

METHODS

The ANRS 12174 study is a multinational, randomised controlled clinical trial conducted on 1,500 mother-infant pairs in Burkina Faso, South Africa, Uganda and Zambia. We will recommend exclusive breastfeeding (EBF) until 26th week of life and cessation of breastfeeding at a maximum of 49 weeks in both trial arms.HIV-uninfected infants at day 7 (± 2 days) born to HIV-1 infected mothers not eligible for HAART who choose to breastfeed their infants.The primary endpoint is the acquisition of HIV-1 (as assessed by HIV-1 DNA PCR) between day 7 and 50 weeks of age. Secondary endpoints are safety (including resistance, adverse events and growth) until 50 weeks and HIV-1-free survival until 50 weeks.

DISCUSSION

This study will provide a new evidence-based intervention to support HIV-1-infected women not eligible for HAART to safely breastfeed their babies.

Alpha interferon administration during structured interruptions of combination antiretroviral therapy in patients with chronic HIV-1 infection: INTERVAC ANRS 105 trial

Interferon-α administration during structured treatment interruptions (STIs) was studied in a phase III trial. We randomized 168 chronically infected HIV undetectable under combined antiretroviral therapy patients to have three STIs with or without α-interferon. The number of patients who had to resume treatment during post-STI follow-up was not significantly different between the two arms. Patients with a low CD4 nadir and a high baseline HIV-DNA had a higher risk of treatment resumption in the interferon arm.

Comparison of early CD4 T-cell count in HIV-1 seroconverters in Côte d'Ivoire and France: the ANRS PRIMO-CI and SEROCO cohorts

OBJECTIVE

We compared CD4+ decline among untreated HIV-1-infected seroconverters living in Côte d'Ivoire (CI) and in France.

METHODS

HIV-1-infected adults were enrolled in the ANRS1220 PRIMO-CI (CI, 1997-2006) and ANRSCO2 SEROCO (France, 1988-1995) cohorts. CD4+ count and percentage declines were estimated from enrollment until 24 months of seroconversion by linear random-effect models adjusted for time since seroconversion, age, gender, cell-associated HIV DNA, HIV RNA, and country.

RESULTS

Overall 521 seroconverters (CI 148, 62% men; France 373, 77% men) were enrolled after a median of 7.6 months since seroconversion. Median follow-up duration was 12.7 months. Median age was 28 years. Median baseline CD4+ count was 472 and 560 cells per cubic millimeter, respectively. Median baseline HIV RNA was 4.4 and 4.0 log10 copies per milliliter and median HIV DNA was 3.0 and 2.8 log10 copies per 10(6) peripheral blood mononuclear cells, respectively. In adjusted models, CD4+ count and percentage at baseline were lower in CI than in France (P < 0.01), and the difference did not vary during follow-up (P = 0.55). Low HIV RNA and low HIV DNA at baseline were associated with higher CD4+ count at baseline.

CONCLUSIONS

CD4+ count and percentage were lower in CI than in France. These differences were already observed during early infection and remained similar after adjustment.

Assessment of the low-cost Cavidi ExaVir Load assay for monitoring HIV viral load in pediatric and adult patients

BACKGROUND

Viral load (VL) is a critical marker for monitoring HIV disease progression and response to antiretroviral therapy. In resource-constrained settings, there is a need for a simple and inexpensive assay to monitor infected adults and children.

METHODS

We compared versions 2 and 3 of the ExaVir Load assay, Cavidi AB (HIV RT) with the Roche, COBAS Amplicor HIV-1 Monitor assay (HIV RNA) for quantifying HIV VL.

RESULTS

The HIV RT version 2 assay showed good sensitivity with detection in 94% of samples with HIV RNA >1000 copies per milliliter. Adult samples were tested using HIV RT version 2 (n = 35) and version 3 (n = 23) assays with plasma volumes of 1 mL (recommended), 0.5 mL and 0.25 mL in comparison with HIV RNA. The HIV RT and HIV RNA assay results were comparable when tested using different volumes. Comparison of results from pediatric samples (n = 27), tested using 1 mL and a smaller volume by HIV RT version 2 were not significantly different.

CONCLUSIONS

The HIV RT assay was comparable to the HIV RNA assay with sensitivity approaching that of HIV RNA. Smaller volumes than the recommended 1 mL can be used, improving utility of this assay for pediatric monitoring.

Improvement of an ultrasensitive human immunodeficiency virus type 1 real-time reverse transcriptase-polymerase chain reaction targeting the long terminal repeat region

BACKGROUND

Human immunodeficiency virus Type 1 (HIV-1) assays applying nucleic acid testing (NAT) rely on HIV-1 sequence-specific primers and probes. Their hybridization can be limited or abolished by genetic polymorphisms occurring in the target sequence.

STUDY DESIGN AND METHODS

Blood donations are routinely tested for HIV-1/2 antibodies and for HIV-1 RNA in our blood transfusion unit. Recently, HIV-1 RNA was undetectable with an established in-house real-time long terminal repeat (LTR) reverse transcriptase-polymerase chain reaction (RT-PCR) in two cases, whereas serologic assays were positive. The reason for this discrepancy was elucidated by sequencing of the NAT target region in the respective single donations. An improved primer was designed and tested on HIV-1 reference panels and blood donations to ensure reliable detection of HIV-1 RNA.

RESULTS

Direct sequencing of the target region, isolated from samples of two unrelated HIV-positive blood donors, revealed one and four mismatches in the hybridization domain of the forward primer, respectively. Both viruses belong to HIV-1 Subtype B. LTR RT-PCR with an additional forward primer was suitable for all strains of HIV-1 tested with high sensitivity.

CONCLUSIONS

Surveillance of HIV-1 genetic diversity is essentially required to continually evaluate its impact on performance of diagnostic and patient monitoring assays.

In-house HIV-1 RNA real-time RT-PCR assays: principle, available tests and usefulness in developing countries

The principle of currently available licensed HIV-1 RNA assays is based on real-time technologies that continuously monitor the fluorescence emitted by the amplification products. Besides these assays, in-house quantitative (q) real-time reverse transcription (RT)-PCR (RT-qPCR) tests have been developed and evaluated particularly in developing countries, for two main reasons. First, affordable and generalized access to HIV-1 RNA viral load is urgently needed in the context of expected universal access to prevention and antiretroviral treatment programs in these settings. Second, since many non-B subtypes, circulating recombinant forms and unique recombinant forms circulate in these areas, in-house HIV-1 RNA RT-qPCR assays are ideal academic tools to thoroughly evaluate the impact of HIV-1 genetic diversity on the accuracy of HIV-1 RNA quantification, as compared with licensed techniques. To date, at least 15 distinct in-house assays have been designed. They differ by their chemistry and the HIV-1 target sequence (located in gag, Pol-IN or LTR gene). Analytical performances of the tests that have been extensively evaluated appear at least as good as (or even better than) those of approved assays, with regard to HIV-1 strain diversity. Their clinical usefulness has been clearly demonstrated for early diagnosis of pediatric HIV-1 infection and monitoring of highly active antiretroviral therapy efficacy. The LTR-based HIV-1 RNA RT-qPCR assay has been evaluated by several groups under the auspices of the Agence Nationale de Recherches sur le SIDA et les hépatites virales B et C. It exists now as a complete standardized commercial test.

HIV-DNA in rectal cells is well correlated with HIV-DNA in blood in different groups of patients, including long-term non-progressors

Most of the body's lymphoid tissue is in gut and constitutes an immense HIV reservoir. We quantified HIV-DNA in rectum and compared it with blood levels for 27 HIV-infected adults from different groups. We observed a large range of rectal and blood HIV-DNA levels. They were positively correlated (r = 0.841, P<0.0001). Long-term nonprogressors and patients in 'remission' after antiretroviral treatment interruption had the lowest blood and mucosal HIV-DNA levels.