External quality assessment of HIV-1 DNA quantification assays used in the clinical setting in Italy

Digital PCR in Virology: Current Applications and Future Perspectives

Digital PCR (dPCR) has been used in the field of virology since its inception. Technological innovations in microfluidics more than a decade ago caused a sharp increase in its use. There is an emerging consensus that dPCR now outperforms quantitative PCR (qPCR) in the basic parameters such as precision, sensitivity, accuracy, repeatability and resistance to inhibitors. These strengths have led to several current applications in quantification, mutation detection and environmental DNA and RNA samples. In high throughput scenarios, such as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, the cost and throughput still significantly hampered the adaption of dPCR. There is much unexplored potential within the multiplexing capabilities of dPCR. This will allow simultaneous multi-target quantification and can also partially alleviate the throughput and cost drawback. In this review, we discuss the strengths and weaknesses of dPCR with a focus on virology applications and we discuss future applications. Finally, we discuss recent evolutions of the technology in the form of real-time dPCR and digital high-resolution melting.

Validation of digital droplet PCR assays for cell-associated HIV-1 DNA, HIV-1 2-LTR circle, and HIV-1 unspliced RNA for clinical studies in HIV-1 cure research

BACKGROUND

Cell-associated HIV-1 DNA, HIV-1 2-LTR circle, and HIV-1 unspliced RNA (usRNA) are important virological parameters for monitoring HIV-1 persistence and activation of latent HIV-1. Assays fully validated by CLIA and/or GCLP standards are needed for future clinical trials that seek to evaluate treatments directed towards HIV-1 cure.

OBJECTIVES

To determine performance characteristics of sensitive, moderate-throughput, digital droplet PCR (ddPCR) assays for cell-associated HIV-1 DNA, HIV-1 2-LTR circle, and HIV-1 usRNA that can detect a broad range of HIV-1 M-group subtypes.

STUDY DESIGN

To evaluate linearity, limit of detection, precision, and accuracy of each assay, contrived specimens were analyzed in a background of uninfected PBMC. Detection breadth was evaluated by in silico analysis of primer and probes sets and analysis of material harvested from PBMC infected in vitro with various HIV-1 subtypes. A cohort of clinical specimens from viremic and virologically suppressed individuals was analyzed to demonstrate applicability to clinical research.

RESULTS

The empirically determined limit of detection of these assays was 29, 7, and 60 copies per million PBMC for HIV-1 DNA, HIV-1 2-LTR circle, and HIV-1 usRNA, respectively. The assays detect a broad range of HIV-1 M-group subtypes. Finally, analysis of clinical specimens demonstrate that these assays can detect low levels of cell-associated HIV-1 DNA, HIV-1 usRNA, and HIV-1 2-LTR circle and correlate with clinical histories and viral loads of untreated and antiretroviral treated individuals.

CONCLUSIONS

We report the clinical validation of three HIV reservoir assays with broad HIV-1 coverage for future cure studies.

Sensitive HIV-1 DNA Pol Next-Generation Sequencing for the Characterisation of Archived Antiretroviral Drug Resistance

Modern HIV-1 treatment effectively suppresses viral amplification in people living with HIV. However, the persistence of HIV-1 DNA as proviruses integrated into the human genome remains the main barrier to achieving a cure. Next-generation sequencing (NGS) offers increased sensitivity for characterising archived drug resistance mutations (DRMs) in HIV-1 DNA for improved treatment options. In this study, we present an ultra-sensitive targeted PCR assay coupled with NGS and a robust pipeline to characterise HIV-1 DNA DRMs from buffy coat samples. Our evaluation supports the use of this assay for Pan-HIV-1 analyses with reliable detection of DRMs across the HIV-1 Pol region. We propose this assay as a new valuable tool for monitoring archived HIV-1 drug resistance in virologically suppressed individuals, especially in clinical trials investigating novel therapeutic approaches.

Evaluation of HIV-DNA and residual viremia levels through week 96 in HIV-infected individuals who continue a two-drug or switch to a three-drug integrase strand transfer inhibitor based regimen

OBJECTIVES

To investigate HIV-DNA and residual viremia (RV) levels over 96 weeks (W96) in virologically suppressed HIV-1 infected individuals enrolled in the Be-OnE Study. Individuals were randomized to continue a two-drug regimen with dolutegravir (DTG) plus one RTI or to switch to elvitegravir/cobicistat/emtricitabine/tenofovir-alafenamide (E/C/F/TAF).

STUDY DESIGN

Total HIV-DNA and RV were evaluated at baseline, W48 and W96 with ddPCR technique. Potential relationships between viro-immunological parameters and between/within arms were also assessed.

RESULTS

Median (IQR) HIV-DNA was 2247 (767;4268), 1587 (556;3543) and 1076 (512;2345) copies/10⁶ CD4+T-cells at baseline, W48 and at W96, respectively, while RV was 3 (1;5), 4 (1;9) and 2 (2;4) copies/mL, without significant differences between arms. A significant reduction in HIV-DNA and in RV from baseline to W96 was observed in the E/C/F/TAF-arm (HIV-DNA: -285 [-2257;-45], p=0.010; RV: (-1 [-3;0], p=0.007). In the DTG+1RTI-arm, HIV-DNA and RV levels remained stable (HIV-DNA: -549 [-2269;+307], p=0.182; RV: (-1 [-3;+1], p=0.280). For both HIV-DNA and RV, no significant changes were found overtime between the arms. A positive correlation was found between baseline HIV-DNA and HIV-DNA at W96 (E/C/F/TAF: rs=0.726, p=0.0004; DTG+1RTI: rs=0.589, p=0.010). In general, no significant correlations were found between HIV-DNA, RV and immunological parameters overtime.

CONCLUSIONS

In virologically suppressed individuals, a small reduction in the HIV-DNA and HIV-RNA levels was found from baseline to W96 in individuals who switched to the E/C/F/TAF arm compared to those who remained under DTG+1RTI. However, no significant differences were found in the changes of HIV-DNA and HIV-RNA between the two arms over time.