HIV reservoir characterization symposium 19 September 2016, Ghent, Belgium

The HIV Cure Research Center (HCRC) in Ghent organised the first HIV Reservoir Characterization Symposium, and brought together virologists, molecular biologists, immunologists and clinicians to discuss the most recent developments in HIV reservoir characterisation with a view to achieving an HIV cure. The one-day symposium covered new developments in the field of HIV reservoir and HIV cure research, with the latest news on the European HIV cure trials. This report summarises the major themes discussed during the symposium

Protein expression from unintegrated HIV-1 DNA introduces bias in primary in vitro post-integration latency models

To understand the persistence of latently HIV-1 infected cells in virally suppressed infected patients, a number of in vitro models of HIV latency have been developed. In an attempt to mimic the in vivo situation as closely as possible, several models use primary cells and replication-competent viruses in combination with antiretroviral compounds to prevent ongoing replication. Latency is subsequently measured by HIV RNA and/or protein production after cellular activation. To discriminate between pre- and post-integration latency, integrase inhibitors are routinely used, preventing novel integrations upon cellular activation. Here, we show that this choice of antiretrovirals may still cause a bias of pre-integration latency in these models, as unintegrated HIV DNA can form and directly contribute to the levels of HIV RNA and protein production. We further show that the addition of reverse transcriptase inhibitors effectively suppresses the levels of episomal HIV DNA (as measured by 2-LTR circles) and decreases the levels of HIV transcription. Consequently, we show that latency levels described in models that only use integrase inhibitors may be overestimated. The inclusion of additional control conditions, such as 2-LTR quantification and the addition of reverse transcriptase inhibitors, is crucial to fully elucidate the actual levels of post-integration latency

Underestimated effect of intragenic HIV-1 DNA methylation on viral transcription in infected individuals

Background: The HIV-1 proviral genome harbors multiple CpG islands (CpGIs), both in the promoter and intragenic regions. DNA methylation in the promoter region has been shown to be heavily involved in HIV-1 latency regulation in cultured cells. However, its exact role in proviral transcriptional regulation in infected individuals is poorly understood or characterized. Moreover, methylation at intragenic CpGIs has never been studied in depth. Results: A large, well-characterized HIV-1 patient cohort (n = 72), consisting of 17 long-term non-progressors and 8 recent seroconverters (SRCV) without combination antiretroviral therapy (cART), 15 early cART-treated, and 32 late cART-treated patients, was analyzed using a next-generation bisulfite sequencing DNA methylation method. In general, we observed low level of promoter methylation and higher levels of intragenic methylation. Additionally, SRCV showed increased promoter methylation and decreased intragenic methylation compared with the other patient groups. This data indicates that increased intragenic methylation could be involved in proviral transcriptional regulation. Conclusions: Contrasting in vitro studies, our results indicate that intragenic hypermethylation of HIV-1 proviral DNA is an underestimated factor in viral control in HIV-1-infected individuals, showing the importance of analyzing the complete proviral genome in future DNA methylation studies

Highlights from the 24th conference on retroviruses and opportunistic infections, 13-16 February 2017, Seattle, Washington, USA

From the 13th to 16th February 2017, researchers from around the world convened for the 24th annual Conference on Retroviruses and Opportunistic Infections (CROI) at the Washington State Convention Center in Seattle, Washington. The conference was organised by the International Antiviral Society-USA (IAS-USA) in partnership with the CROI Foundation. The conference included over 1000 oral and poster presentations of peer-reviewed original research as well as lectures and symposia featuring insights from leading basic, translational and clinical researchers. Highlighted here are key data presented at the conference

Early treated HIV-1 positive individuals demonstrate similar restriction factor expression profile as long-term non-progressors

Background: A wide range of host restriction factors (RF) become upregulated upon HIV-1 infection to suppress viral infectivity and may aid viremic control in vivo. This cross-sectional study evaluated HIV-1 RFs and dependency factors in HIV infected individuals with progressive or non-progressive infection, as well as in early and late treated cohorts that exhibit different viro-immunological profiles due to differences in timing of treatment-initiation. Methods: The expression profile of IFIT1, MX1, APOBEC3G, SAMHD1, BST2 (encoding TETHERIN), TRIM5, MX2, SLFN11, PAF1, PSIP1 (encoding LEDGF/p75), and NLRX1 was measured by qPCR in 104 HIV-1 positive individuals: seroconverters (SRCV; n =19), long term non-progressors (LTNP; n =17), viremic progressors (VP; n =12), patients treated during seroconversion (Early treated; n =24) or chronic infection (Late treated; n =32), and non-infected controls. Findings: Expression levels of early treated HIV-1 positive individuals were significantly upregulated in comparison to late treated patients (IFIT1: p=0.0003; MX1: p=0.008; APOBEC3G: p=0.002; SAMHD1: p=0.0008; SLFN11: p<0.0001; BST2: p<0.0001). Similarly, SLFN11, BST2, and SAMHD1 were highly expressed in LTNPs at comparable levels as in early treated HIV-1 positive individuals. Furthermore, SLFN11 and SAMHD1 expression negatively correlated with total and integrated HIV-1 DNA levels. Interpretation: Early treatment initiation maintains initial RF elevation even after a decade of ART. Elevated expression of SLFN11, BST2, and SAMHD1 in LTNP and early treated subjects implies that these RFs may be associated with spontaneous virological control

Comparison of methods for in-house screening of HLA*B57:01 to prevent abacavir hypersensitivity in HIV-1 care

Abacavir is a nucleoside reverse transcriptase inhibitor used as part of combination antiretroviral therapy in HIV-1-infected patients. Because this drug can cause a hypersensitivity reaction that is correlated with the presence of the HLA-B*57:01 allotype, screening for the presence of HLA-B*57:01 is recommended before abacavir initiation. Different genetic assays have been developed for HLA-B*57:01 screening, each with specific sensitivity, turnaround time and assay costs. Here, a new real-time PCR (qPCR) based analysis is described and compared to sequence specific primer PCR with capillary electrophoresis (SSP PCR CE) on 149 patient-derived samples, using sequence specific oligonucleotide hybridization combined with high resolution SSP PCR as gold standard. In addition to these PCR based methods, a complementary approach was developed using flow cytometry with an HLA-B17 specific monoclonal antibody as a pre-screening assay to diminish the number of samples for genetic testing. All three assays had a maximum sensitivity of >99. However, differences in specificity were recorded, i.e. 84.3%, 97.2% and >99% for flow cytometry, qPCR and SSP PCR CE respectively. Our data indicate that the most specific and sensitive of the compared methods is the SSP PCR CE. Flow cytometry pre-screening can substantially decrease the number of genetic tests for HLA-B*57:01 typing in a clinical setting

Droplet digital PCR, the new tool in HIV reservoir quantification?

Background: Digital PCR is a relatively old concept for absolute quantification of DNA using PCR, but recent technological developments allowed its wide use. The current state of art technique for performing digital PCR is based on microdroplet technology. Direct absolute quantification relieves the necessity of standard curves and increases assay accuracy. In addition, the end point PCR set-up allows higher assay flexibility and decreases quantitative bias due to variations in PCR efficiency. In the present work, these theoretical advantages were assessed on the QX100 droplet digital PCR (Bio-rad) on various virological markers to assess the possible use of ddPCR in HIV research. Methods: First, ddPCR was compared to a highly sensitive method of real-time PCR based quantification of cellular associated spliced and unspliced HIV RNA. Second, different methods of DNA extractions in combination with ddPCR were compared for quantification of total and episomal HIV DNA. Hereby, the maximal amount of restriction digested DNA was assessed in the ddPCR. Third, a touchdown procedure was optimized for an HIV specific primer probe set with a low melting temperature using touchdown ddPCR. Results: The comparsion of the nested real-time quantitative PCR to ddPCR indicated that ddPCR is at least equally sensitive to qPCR but also that false positive negative control samples may interfere with quantification at the level of single copies. Episomal 2LTR quantification was compared on ddPCR between total DNA extracted DNA and plasmid purified DNA, revealing a higher accuracy of 2LTR measurements in the total DNA extracts. Assessment of total DNA load in digital PCR reactions revealed a higher tolerance for inhibition compared to qPCR, but a strong influence of the concentration of restriction digestion mix on ddPCR efficiency. Finally, a touchdown procedure revealed that digital PCR can combine a higher flexibility in assay design while retaining accurate quantitative power compared to qPCR Conclusions: We transferred 4 assays used in HIV reservoir research to the ddPCR platform. Although ddPCR has some major advantages for low level quantification in HIV reservoir research, some technical hurdles, including the occurrence of false negative control samples need still be addressed to ameliorate the current technology