ArticleCommunications biology2021
PANDAA intentionally violates conventional qPCR design to enable durable, mismatch-agnostic detection of highly polymorphic pathogens.
Article in Communications biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Oligonucleotide Ligation Assay (OLA)-Simple: Field Implementation, Usability, and Performance of a near Point-of-Care HIV Drug Resistance Assay in Kenya.Laboratories · 2026Article
- High throughput AS LNA qPCR method for the detection of a specific mutation in poliovirus vaccine strains.Vaccine · 2024Article
- Advancing HIV Drug Resistance Technologies and Strategies: Insights from South Africa's Experience and Future Directions for Resource-Limited Settings.Diagnostics (Basel, Switzerland) · 2023Review
- Need assessment for HIV drug resistance testing and landscape of current and future technologies in low- and middle-income countries.PLOS global public health · 2023Review
- Point-of-Care Tests for HIV Drug Resistance Monitoring: Advances and Potentials.Pathogens (Basel, Switzerland) · 2022Article
- Differential Laboratory Diagnosis of Acute Fever in Guinea: Preparedness for the Threat of Hemorrhagic Fevers.International journal of environmental research and public health · 2021Article
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Authors and funding
3 authors.
Funding
Abstract
Sensitive and reproducible diagnostics are fundamental to containing the spread of existing and emerging pathogens. Despite the reliance of clinical virology on qPCR, technical challenges persist that compromise their reliability for sustainable epidemic containment as sequence instability in probe-binding regions produces false-negative results. We systematically violated canonical qPCR design principles to develop a Pan-Degenerate Amplification and Adaptation (PANDAA), a point mutation assay that mitigates the impact of sequence variation on probe-based qPCR performance. Using HIV-1 as a model system, we optimized and validated PANDAA to detect HIV drug resistance mutations (DRMs). Ultra-degenerate primers with 3' termini overlapping the probe-binding site adapt the target through site-directed mutagenesis during qPCR to replace DRM-proximal sequence variation. PANDAA-quantified DRMs present at frequency ≥5% (2 h from nucleic acid to result) with a sensitivity and specificity of 96.9% and 97.5%, respectively. PANDAA is an innovative advancement with applicability to any pathogen where target-proximal genetic variability hinders diagnostic development.
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Registered trials
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