PANDAA for rapid genotyping of HIV-1 infected patients failing protease inhibitor ART in resource-limited settings

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The 2015 WHO guidelines recommend anti-retroviral therapy (ART) for all HIV-infected people, and massive efforts to expand ART access will result in >30M adults and >1.7M children on ART by 2020, at a cost of almost US$53B. Consequently, the number of patients prescribed alternative, protease-inhibitor (PI)-based ART following failure of first-line regimens will also increase. Studies of patients on PI-based ART in resource-limited countries have shown high rates of virologic failure at 12 and 24 months on treatment, and patients maintained on failing PI-based regimens accumulate drug resistance mutations (DRMs) that hamper current and future treatment options. Resource constraints often limit the ability to collect genotype information, and genotype-blind drug switching has been shown to be cost-ineffective when compared to stratifying patients based on resistance genotype. Thus, there is an urgent unmet need for an affordable HIV genotyping option for patients failing PI- based ART. Focused genotyping could significantly enhance patient care by: 1) optimizing the NRTI backbone in patients failing a PI-based regimen with only NRTI resistance; or 2) preventing ART switches in patients failing without resistance until adherence issues are rectified. Aldatu’s Pan-Degenerate Amplification and Adaptation (PANDAA™) technology is a novel point mutation assay that enables inexpensive and high-throughput focused genotypic resistance testing, and such an approach could be cost-saving for national ART programs. PANDAA compensates for high intra- and inter-patient HIV genomic variability by removing secondary polymorphisms, minimizing their impact on qPCR sensitivity/specificity, and enabling qPCR for HIV genotyping for the first time. Feasibility studies have demonstrated that PANDAA: 1) detects NNRTI and NRTI-resistant HIV variants with >99% sensitivity; 2) is HIV subtype-independent; and 3) can be multiplexed to simultaneously quantify resistance at multiple genomic positions. Aldatu has pioneered the commercial development of PANDAA and established a reagent formulation that allows for the production of PANDAA-based diagnostics in a thermostable, sample- ready format. In this Phase II project, Aldatu will apply the PANDAA technology to the development of PANDAA PIDR+, a rapid, low-cost, thermostable test for detection of drug resistance in patients failing a PI-based ART regimen, which can radically improve clinical decision-making in low- and middle-income countries. Through the aims proposed here, we will 1) experimentally validate the design of PANDAA reagents to quantify mutations associated with protease inhibitor resistance comprising 10% of the viral quasispecies; 2) establish an extensive, collaborative proficiency panel of drug resistant and drug sensitive HIV-1 isolates for PANDAA PIDR+ validation; 3) assess PANDAA PIDR+ using established performance criteria for HIV drug resistance genotyping and produce PANDAA PIDR+ under GMP conditions; and 4) verify that end-user, multi-site implementation of PANDAA PIDR+ is highly reproducible. The first of its kind, a validated, GMP-produced PANDAA PIDR+ test kit from Aldatu will be poised to capture a significant share of this rapidly growing diagnostic market opportunity.