Laurent Debaisieux

Standardisation of primers and an algorithm for HIV-1 diagnostic PCR evaluated in patients harbouring strains of diverse geographical origin

Eight Belgian AIDS Reference Laboratories established a multicentre quality control to evaluate the performance of their diagnostic human immunodeficiency virus type 1 (HIV-1) DNA polymerase chain reaction (PCR). A set of Belgian and African HIV-1 seropositive and seronegative patient samples, collected in Belgium, and the British Medical Research Council (MRC) HIV-1 PCR reference reagent kit, containing plasmid HIV-1 DNA at several dilutions in human carrier DNA with appropriate negative controls, were tested by the laboratories. No false positive results were reported. All laboratories were able to detect one to two copies of HIV-1 DNA. Among the 17 Belgian and African HIV-1 seropositives, some laboratories reported up to four indeterminate results, mainly due to failure of the SK38-39, SK68-69 (Ou et al. (1988) Science 239, 295-297) and/or gag881-882 (Simmonds et al. (1990) J. Virol. 64, 864-872) primers and a poorly performing algorithm. Only the H1POL4235-4538 nested pol primer set, developed by one of the laboratories, correctly identified all the tested HIV-1 positive and negative samples. Consequently, the laboratories decided to evaluate these pol primers as a reference primer set and to standardise the testing algorithm. All laboratories achieved a sensitivity and specificity of 100% on testing 10 additional Belgian and African patient samples, when adapting a standardised algorithm based on three HIV-1 primer sets, one of which is the H1POL4235-4538 primer set.

HIV-1 low-level viraemia assessed with 3 commercial real-time PCR assays show high variability.

BackgroundCurrent real-time PCR-based HIV-1 viral load (VL) assays allow the detection of residual viraemia in antiretroviral-treated patients. The clinical outcome of HIV1 patients experiencing low-level replication (<50 cop/mL) in comparison with fully suppressed patients is currently debated. We analysed variability of 3 VL assays <50 cop/mL, and evaluated the reproducibility of viral blips <100 cop/mL.MethodsThree commercial VL assays were tested: Versant HIV-1 RNA 1.0 kPCR (Siemens), Abbott Realtime HIV-1, and Cobas Ampliprep/Cobas Taqman HIV-1 v2.0 (Roche). Ten replicates of a reference sample at 4 low target dilutions were tested to evaluate assay variability. Prospective collection of 181 clinical samples with detectable VL <50 cop/mL was used to evaluate intra-and inter-assay variability by triplicate testing. Samples from 26 patients experiencing a viral blip were retested.ResultsAll assays showed substantial variability at low VL level: the coefficient of variation at 100, 50, 25 and 12 cop/mL ranged respectively from 32 to 44%, 35 to 68%, 41 to 83% and 33 to 77%. In the intra-assay evaluation of repeatability, 52.5 to 57.5% of detectable VL <50 cop/mL tested in triplicate showed at least one fully undetected result. Variability was similar in the inter-assay arm. The VL blips could only be reproduced in 19% of cases.ConclusionsThe most recent versions of widespread commercial VL assays showed substantial variability at low levels and residual viraemia could not be consistently reproduced. Patient outcome studies comparing residual VL to full suppression are therefore biased when using commercial assays.

Correction of Underquantification of Human Immunodeficiency Virus Type 1 Load with the Second Version of the Roche Cobas AmpliPrep/Cobas TaqMan Assay

ABSTRACT Initial evaluations of the Cobas AmpliPrep/Cobas TaqMan human immunodeficiency virus type 1 (HIV-1) test (CAP/CTM) demonstrated good performance but, afterwards, reports about underquantification were published. We investigated whether the problem was solved with a second version of this assay, the Cobas AmpliPrep/Cobas TaqMan HIV-1 test, version 2.0 (CAP/CTM v2.0). The remaining plasma of 375 consecutive HIV-1 positive samples with a viral load of ≥4,000 copies/ml was collected in three laboratories. The samples were diluted and retested with our routine method Cobas AmpliPrep/Cobas Amplicor HIV-1 monitor test v1.5 in ultrasensitive mode (CAP/CA PHS), as well as with the CAP/CTM and CAP/CTM v2.0 tests. An absolute difference between the results of two methods of ≥0.71 log10 copies/ml was defined as moderately discrepant, and an absolute difference of ≥0.93 log10 copies/ml was defined as severely discrepant. In addition, criteria for considering the new methods equivalent to the routine method were formulated. (i) For CAP/CTM compared to CAP/CA PHS, 36 (9.5%) and 20 (5.3%) samples were, respectively, considered moderately and severely underquantified by CAP/CTM. The mean difference between CAP/CTM and CAP/CA PHS was −0.32 log10 copies/ml. Eight of nineteen of the severely underquantified samples were from patients infected with HIV-1 subtype B strain. (ii) For CAP/CTM v2.0 compared to CAP/CA PHS, no sample was moderately or severely underquantified by CAP/CTM v2.0. A mean difference of 0.08 log10 copies/ml was found with CAP/CTM v2.0 compared to CAP/CA PHS. The underquantification problem of the CAP/CTM kit was clearly demonstrated. The criteria for the equivalence of CAP/CTM v2.0 to the routine test CAP/CA PHS were fulfilled.

Development and evaluation of single sperm washing for risk reduction in artificial reproductive technology (ART) for extreme oligospermic HIV positive patients

The serodiscordant couples, where the male is HIV-positive, are treated in fertility clinics, using the sperm washing technique by gradient centrifugation. This protocol cannot be carried out in oligo-azoospermic patients, where spermatozoa retrieval from the epididymis and testis must be performed. We developed a single sperm washing technique, where the spermatozoa, after the retrieval, are washed with the aid of a micromanipulator, to obtain virus decontamination and then used for the intracytoplasmic sperm injection (ICSI). The experiment was performed by using sperm samples containing three different viral loads. After one hour of incubation, spermatozoa were taken one by one from the HIV loaded drop and washed in four different microdrops. Before each passage into the next washing drop, the pipette was emptied in a first waste drop and then loaded with new washing medium from a second separate loading drop. After transferring of 10 spermatozoa in these four successive drops, the washing medium and the virus-loaded drops were tested for the HIV RNA presence by the nested RT-PCR technique. The presence of the virus was detected in the waste drop of all three viral loads. The four washing microdrops were each time negative for the presence of HIV-1 RNA, tested by the nested RT-PCR technique. The results show that by rinsing the spermatozoa four times, we are able to diminish the viral load to an undetectable level. Our data demonstrate that single sperm washing can be performed in the cases of extreme male sterility in HIV-positive men. From now on the couples, where the male is oligoazoospermic and HIV positive, could be included in our ICSI program, respecting the usual viral safety level of the ART techniques for the embryo.

Cultured Kaposi's sarcoma tumor cells exhibit a chemokine receptor repertoire that does not allow infection by HIV-1

BackgroundHIV-1 is known to play a critical role in the pathogenesis of AIDS-associated Kaposis sarcoma (KS). However, it remains controversial whether KS cells are target cells for HIV infection. The aim of this study was to investigate the expression of chemokine receptors in KS cell cultures and to determine whether these cells can be infected by HIV-1.Material and MethodsKS-derived cells and KS-Y1 cells were investigated using RT-PCR for the expression of CD4, CCR3, CCR5, CCR8 and CXCR4 mRNA. HIV infectivity of these cells was determined by p24 antigen and HIV-1 RNA production, as well as by HIV-1 DNA integration.Results and DiscussionWith the exception of CCR8 which is expressed by KS-derived spindle cell cultures but not by KS-Y1 cells, unstimulated KS cells express no significant levels of CD4, CCR3, CCR5 or CXCR4 mRNA. HIV infectivity assays showed that KS cells were unpermissive to HTLVIIIB and JRFL strains. Although the expression of CXCR4 mRNA could be upregulated by interleukin-1β, stimulation of KS cells by this cytokine did not allow infection by HIV-1.ConclusionsThis shows that KS cells exhibit a chemokine receptor repertoire that does not allow infection by HIV-1. Other cell types making up KS lesions, such as inflammatory cells, are likely to represent the source of HIV-1 products cooperating to promote KS development and progression.

Phylogenetic analysis of the Belgian HIV-1 epidemic reveals that local transmission is almost exclusively driven by men having sex with men despite presence of large African migrant communities

To improve insight in the drivers of local HIV-1 transmission in Belgium, phylogenetic, demographic, epidemiological and laboratory data from patients newly diagnosed between 2013 and 2015 were combined and analyzed. Characteristics of clustered patients, paired patients and patients on isolated branches in the phylogenetic tree were compared. The results revealed an overall high level of clustering despite the short time frame of sampling, with 47.6% of all patients having at least one close genetic counterpart and 36.6% belonging to a cluster of 3 or more individuals. Compared to patients on isolated branches, patients in clusters more frequently reported being infected in Belgium (95.1% vs. 47.6%; p < 0.001), were more frequently men having sex with men (MSM) (77.9% vs. 42.8%; p < 0.001), of Belgian origin (68.2% vs. 32.9%; p < 0.001), male gender (92.6% vs. 65.8%; p < 0.001), infected with subtype B or F (87.8% vs. 43.4%; p < 0.001) and diagnosed early after infection (55.4% vs. 29.0%; p < 0.001). Strikingly, Sub-Saharan Africans (SSA), overall representing 27.1% of the population were significantly less frequently found in clusters than on individual branches (6.0% vs. 41.8%; p < 0.001). Of the SSA that participated in clustered transmission, 66.7% were MSM and this contrasts sharply with the overall 12.0% of SSA reporting MSM. Transmission clusters with SSA were more frequently non-B clusters than transmission clusters without SSA (44.4% versus 18.2%). MSM-driven clusters with patients of mixed origin may account, at least in part, for the increasing spread of non-B subtypes to the native MSM population, a cross-over that has been particularly successful for subtype F and CRF02_AG. The main conclusions from this study are that clustered transmission in Belgium remains almost exclusively MSM-driven with very limited contribution of SSA. There were no indications for local ongoing clustered transmission of HIV-1 among SSA.

A21 HIV-1 sub-subtype F1 outbreak among MSM in Belgium

Current antiretroviral therapies for HIV-1 are not curative because a small number of CD4þT-cells remain infected with a latent, replication-competent provirus that contributes to viral rebound after the cessation of therapy. Several approaches to purge persistent HIV-1 reservoirs are in the beginning phases of clinical trials. To ensure future curative therapies target replication-competent HIV-1 proviruses for eradication, a thorough understanding of the distribution of replication-competent HIV1 within T-cell subsets and how activation and proliferation of these cells contribute to the maintenance of the replicationcompetent HIV-1 reservoir is required. This study will employ a full-length single-proviral sequencing assay based on Next Generation Sequencing (NGS) techniques to sequence the entire HIV-1 genome of proviruses isolated from CD4þT-cell subsets (central, transitional, and effector) sorted from peripheral blood and lymphoid tissue after 5–15 years of suppressive therapy from two groups of participants (1) three participants who initiated therapy during acute/early infection and (2) three participants who initiated therapy during chronic infection. Replication-competent proviruses will be identified by the absence of deletions and APOBEC3G induced hypermutation. The infection rates of replication-competent proviruses located in specific cell populations between participants will be compared along with the frequencies of replication-competent proviruses between different T-cell populations and within tissuederived cells from these participants. This important study will allow us to determine whether specific cellular compartments harbour replication-competent HIV-1 and will provide valuable information for future curative HIV-1 clinical trials.

Screening for Chlamydia trachomatis and Neisseria gonorrhoeae infections in MSM: Diagnostic accuracy of NAAT on pooled urine, anorectal and pharyngeal specimens

Abstract Neisseria gonorrhoeae and Chlamydia trachomatis screening was performed in a cohort of 100 men who have sex with men. A nucleic acid amplification test on a pooled sample of first-pass urine, pharyngeal, and anorectal specimens was compared with results on nonpooled samples. Despite an excellent agreement (Cohen &kgr;, 0.932), pooling specimens reduced test sensitivity to 89.5%.