A cost-effective conventional endpoint PCR assay for HLA-B*13:01 genotyping to guide personalized dapsone therapy in leprosy in low-resource settings

Abstract

Background Dapsone is a drug used to treat leprosy. Dapsone causes a highly morbid and potentially fatal severe drug hypersensitivity reaction (DHS) in 1–3% of leprosy cases. The allele HLA-B*13:01 is a known genetic risk factor for DHS. However, resource-intensive genotyping methods preclude its testing in resource-limited settings. This study aimed to develop an endpoint PCR assay to detect the presence of HLA-B*13:01.Research design and methods DNA was extracted from blood samples of leprosy patients at Anandaban Hospital, Nepal (2022–24). A duplex endpoint PCR was optimized and validated against a previously validated commercial qPCR method and NGS (next‑generation sequencing).Results In 113 samples, duplex PCR showed 100% (95% CI: 79.4–100%) sensitivity and 100% specificity (95% CI: 96.2–100%) compared to the validated qPCR method. The same accuracy was confirmed in 58 NGS-typed samples (concordance 98.3%, 95% CI: 90.7–99.9%). The assay reliably differentiated HLA-B*13:01 from closely related allele. Analytical sensitivity reached a lower detection limit of 100 genome equivalents (0.67 ng DNA/reaction).Conclusion The developed duplex endpoint PCR offers a simple and affordable method for detecting HLA-B*13:01, suitable in low-resource settings. Its use may significantly reduce the risk of DHS by guiding safer drug choices prior to MDT initiation.