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.
Public Health Relevance Statement: 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, including an increased number of patients receiving protease-inhibitor (PI)-based ART following failure of first-line regimens. High rates of virologic failure observed in patients on PI-based ART in resource-limited countries, together with the high drug cost of a genotype-blind approach to therapeutic decision-making, necessitate an affordable HIV genotyping option for these patients in these settings. This SBIR project aims to develop 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.
Project Terms: adulthood; Adult Human; 21+ years old; Adult; Biologic Assays; Bioassay; Assay; Biological Assay; Life Sciences; Bioscience; Biologic Sciences; Biological Sciences; youngster; childrens'; children; Children (0-21); Child Youth; 0-11 years old; Child; Molecular Cloning; Infectious Disorder; Infectious Diseases; Infectious Disease Pathway; Communicable Diseases; Decision Making; resistant to Drug; resistance to Drug; drug resistant; Drug resistance; drug/agent; Pharmaceutic Preparations; Medication; Drugs; Pharmaceutical Preparations; Exhibits; Feasibility Studies; Lyophilization; Freeze Dryings; Freeze Drying; Future; Patient Care Delivery; Patient Care; Genotype; Virus-HIV; Lymphadenopathy-Associated Virus; LAV-HTLV-III; Human T-Lymphotropic Virus Type III; Human T-Cell Lymphotropic Virus Type III; Human T-Cell Leukemia Virus Type III; Human Immunodeficiency Viruses; HTLV-III; Acquired Immunodeficiency Syndrome Virus; Acquired Immune Deficiency Syndrome Virus; AIDS Virus; HIV; human T lymphotropic virus III; human T cell leukemia virus III; Human immunodeficiency virus 1; Human Immunodeficiency Virus Type 1; HIV1; HIV-I; HIV-1; In Vitro; Institutes; Laboratories; Mutation; genome mutation; Genetic defect; Genetic Change; Genetic Alteration; Patients; Genetic Polymorphism; polymorphism; Production; Protease Inhibitor; Proteinase Inhibitors; Protease Antagonists; Peptide Peptidohydrolase Inhibitors; Peptide Hydrolase Inhibitors; Peptidase Inhibitors; Endopeptidase Inhibitors; Antiproteases; Quality Control; Reagent; research and development; R&D; R & D; Development and Research; Resources; Research Resources; RNA; Ribonucleic Acid; RNA Gene Products; Non-Polyadenylated RNA; Sensitivity and Specificity; Specificity; Vertebral column; backbone; Spine; Spinal Column; Target Populations; Technology; Testing; Time; virology; Measures; Drug Costs; Cost Savings; therapy failure; Treatment Failure; Point Mutation; Guidelines; base; method development; improved; Site; Clinical; Phase; Variation; Variant; Ensure; Failure; Therapeutic; Diagnostic; programs; Viral Load result; Viral Load; Viral Burden; System; Country; Viral; Performance; thermostability; thermolability; Anti-Retroviral Agents; antiretroviral; anti-retroviral; Antiretroviral Agents; novel; Positioning Attribute; Position; Sampling; Genomics; prevent; preventing; non-nucleoside reverse transcriptase inhibitors; nonnucleoside reverse transcriptase inhibitors; non-nucleoside RT inhibitors; NNRTI; Adherence; Data; Detection; Dideoxy Chain Termination DNA Sequencing; Sanger Sequencing; Reproducibility; Small Business Innovation Research; SBIR; Small Business Innovation Research Grant; Validation; Preparation; developmental; Development; cost; designing; design; resistant to HIV drug; resistance to antiHIV; resistance to anti-HIV; resistance to HIV drug; drug resistant HIV; HIV drug resistant; Drug resistance in HIV; AntiHIV resistant; AntiHIV resistance; Anti-HIV resistant; Anti-HIV resistance; HIV drug resistance; cost effective; cost-effective; blind; Drug-sensitive; innovation; innovative; innovate; Resistance; resistant; drug testing; drug detection; prototype; resistance mutation; Regimen; clinical decision-making; HIV resistance; HIV resistant; low and middle-income countries; LMIC; patient stratification; stratified patient; Formulation
