ArticleVirology journal2024
Development of a highly sensitive and specific intact proviral DNA assay for HIV-1 subtype B and C.
Article in Virology journal, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers, 1 of them a synthesis that pooled it.
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Who cites it
19 citing papers in PubMed, 1 synthesis or guideline pooled it, 22 citations in OpenAlex.
- Reservoir differences across HIV-1 subtypes: a systematic review to guide cure research.Frontiers in immunology · 2026Pooled it
- In vivo effect of anti-PD-1 on HIV-specific CD8+T-cells in men with HIV.Nature communications · 2026Article
- Implications of HIV persistence and pathogenesis in microglia.Current opinion in HIV and AIDS · 2026Review
- Quantification and localization of integrated HIV-1 in memory and naïve CD4+ T cells from adolescents and young adults with perinatally-acquired HIV-1.PLoS pathogens · 2026Article
- Dynamics of Intact and Defective Human Immunodeficiency Virus Type 1 (HIV-1) Proviruses During Decades of Suppressive Antiretroviral Treatment in Young Adults With Perinatal HIV.The Journal of infectious diseases · 2026Article
- Q4ddPCR: a flexible, 4-target assay for high-resolution HIV reservoir profiling.Nature communications · 2026Article
- Tools to Quantify and Characterize the Persistent Reservoir in People with HIV-1: Focus on Non-B Subtypes.Viruses · 2026Review
- Persistent cell-associated HIV-1 RNA in virally suppressed individuals on INSTI-based ART.Journal of virus eradication · 2025Article
- Within-Subtype HIV-1 Polymorphisms and Their Impacts on Intact Proviral DNA Assay (IPDA) for Viral Reservoir Quantification.Viruses · 2025Article
- Advancements in single-cell techniques for examining the HIV reservoir: pathways to a cure.mBio · 2025Review
- Selective decline of intact HIV reservoirs during the first decade of ART followed by stabilization in memory T cell subsets.AIDS (London, England) · 2025Article
- Intact HIV DNA decays in children with and without complete viral load suppression.PLoS pathogens · 2025Article
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- Article
- Meeting Summary for Keystone Symposia on HIV Cure: Antiretroviral Therapy (ART)-Free Control of HIV Infection in Durban, South Africa, 2025.Pathogens & immunity · 2025Article
- Differences in HIV-1 reservoir size, landscape characteristics and decay dynamics in acute and chronic treated HIV-1 Clade C infection.medRxiv : the preprint server for health sciences · 2024Article
- HIV-1 subtype A1, D, and recombinant proviral genome landscapes during long-term suppressive therapy.Nature communications · 2024Article
- Dynamics of Low-Level Viremia and Immune Activation after Switching to a Darunavir-Based Regimen.Viruses · 2024Observational
- Defective proviruses significantly impact viral transcription and immune activation in men and women with HIV-1 subtype C in rural South Africa.Frontiers in immunology · 2024Article
Corrections and comments
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Authors and funding
12 authors at 7 institutions in 6 countries.
Funding
Abstract
introductionHIV reservoir quantification is essential for evaluation of HIV curative strategies and may provide valuable insights about reservoir dynamics during antiretroviral therapy. The Intact Proviral DNA Assay (IPDA) provides the unique opportunity to quantify the intact and defective reservoir. The current IPDA is optimized for HIV-1 subtype B, the dominant subtype in resource-rich settings. However, subtype C is dominant in Sub-Saharan Africa, jointly accounting for around 60% of the pandemic. We developed an assay capable of quantifying intact and defective proviral HIV-1 DNA of subtype B and C.
methodsPrimer and probe sequences were strategically positioned at conserved regions in psi and env and adapted to subtype B&C. In silico analysis of 752 subtype B and 697 subtype C near-full length genome sequences (nFGS) was performed to predict the specificity and sensitivity. Gblocks were used to determine the limit of blank (LoB), limit of detection (LoD), and different annealing temperatures were tested to address impact of sequence variability.
resultsThe in silico analysis showed that the HIV-1 B&C IPDA correctly identified 100% of the intact subtype B, and 86% of the subtype C sequences. In contrast, the original IPDA identified 86% and 12% of these subtype B and C sequences as intact. Furthermore, the HIV-1 B&C IPDA correctly identified hypermutated (87% and 88%) and other defective sequences (73% and 66%) for subtype B and C with comparable specificity as the original IPDA for subtype B (59% and 63%). Subtype B cis-acting sequences were more frequently identified as intact by the HIV-1 B&C IPDA compared to the original IPDA (39% and 2%). The LoB for intact proviral DNA copies was 0, and the LoD for intact proviral DNA copies was 6 (> 95% certainty) at 60 °C. Quantification of 2-6 copies can be performed with > 80% certainty. Lowering the annealing temperature to 55 °C slightly lowered the specificity but prevented exclusion of samples with single mutations in the primer/probe region.
conclusionsWe developed a robust and sensitive assay for the quantification of intact and defective HIV-1 subtype B and C proviral DNA, making this a suitable tool to monitor the impact of (large-scale) curative interventions.
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