Large-scale evaluation of HIV-1 DNA drug resistance testing as a robust tool for clinical decision-making: A nationwide study in China

Human immunodeficiency virus type 1 (HIV-1) drug resistance remains a major challenge in HIV/AIDS management, particularly in individuals with low-level viremia (LLV) where RNA-based drug resistance testing (DRT) often fails. Although HIV-1 DNA DRT represents a promising alternative, its clinical utility has been constrained by insufficient evidence. This nationwide study in China enrolled 9,428 people living with HIV (PLWH), analyzing 10,903 samples spanning a wide viral load (VL) spectrum. To improve RNA detection, an optimized primer design combined with an extracellular particle (EP)-HIV co-isolation technique was developed. We then evaluated the reproducibility of drug resistance mutation (DRM) profiles between paired RNA and DNA DRTs using Sanger sequencing (SS), with single-molecule sequencing employed to establish a dominant sequence threshold. Our findings demonstrated that primer optimization and EP-co-isolation significantly enhanced RNA amplification success. DRMs were prevalent across all VL strata. The combined concordance and degeneracy rates (C/D rates) (where multiple DNA DRMs included all RNA-derived DRMs) between RNA and DNA DRTs ranged from 90.4% to 100% in different gene regions, with higher discordance rates observed in the nucleoside reverse transcriptase inhibitor (NRTI) and non-NRTI (NNRTI) regions. Based on Stanford penalty scores across 25 antiretroviral drugs, the degeneracy group showed a 98.3% ± 1.7% interpretation agreement. Even within the discordance group, mean agreement remained high (89.5% ± 5.0%), with only four NNRTIs exhibiting agreement below 85%. The dominant sequence proportion threshold for HIV-1 DNA was determined to be 24.6%. This study provides strong evidence supporting the integration of HIV-1 DNA DRT into clinical practice for reliable drug resistance surveillance and treatment monitoring.

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Journal
Journal of Pharmaceutical Analysis
Published
2025-12-09
DOI
https://doi.org/10.1016/j.jpha.2025.101513
Primary Topic
HIV/AIDS drug development and treatment
Type
article
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article

Large-scale evaluation of HIV-1 DNA drug resistance testing as a robust tool for clinical decision-making: A nationwide study in China

Zhong Chen, Mingjie Hou, Caihong Wu, Jiahui Guo et al.
Journal of Pharmaceutical Analysis
HIV/AIDS drug development and treatment
article

Large-scale evaluation of HIV-1 DNA drug resistance testing as a robust tool for clinical decision-making: A nationwide study in China

Zhong Chen, Mingjie Hou, Caihong Wu, Jiahui Guo, Mei Liu, Yaokai Chen, Xiaohong Chen, Lukun Zhang, Aihua Deng, Yongli Li, Hui Wang, Keji Deng, Yizhi Cui, Bianchuan Cao, Hai Long, Yanhua Fu, Min Wang, Yanjun Li, Jun Yao, Quan Wang, Tong Wang, Li Jin, Min Liu, Yun He, Ke Yang, Jun Peng, Tuofu Zhu, W.D. Ma, Limin Zhang, Qingxia Zhao, Jingsong Bai
article en

Abstract

Human immunodeficiency virus type 1 (HIV-1) drug resistance remains a major challenge in HIV/AIDS management, particularly in individuals with low-level viremia (LLV) where RNA-based drug resistance testing (DRT) often fails. Although HIV-1 DNA DRT represents a promising alternative, its clinical utility has been constrained by insufficient evidence. This nationwide study in China enrolled 9,428 people living with HIV (PLWH), analyzing 10,903 samples spanning a wide viral load (VL) spectrum. To improve RNA detection, an optimized primer design combined with an extracellular particle (EP)-HIV co-isolation technique was developed. We then evaluated the reproducibility of drug resistance mutation (DRM) profiles between paired RNA and DNA DRTs using Sanger sequencing (SS), with single-molecule sequencing employed to establish a dominant sequence threshold. Our findings demonstrated that primer optimization and EP-co-isolation significantly enhanced RNA amplification success. DRMs were prevalent across all VL strata. The combined concordance and degeneracy rates (C/D rates) (where multiple DNA DRMs included all RNA-derived DRMs) between RNA and DNA DRTs ranged from 90.4% to 100% in different gene regions, with higher discordance rates observed in the nucleoside reverse transcriptase inhibitor (NRTI) and non-NRTI (NNRTI) regions. Based on Stanford penalty scores across 25 antiretroviral drugs, the degeneracy group showed a 98.3% ± 1.7% interpretation agreement. Even within the discordance group, mean agreement remained high (89.5% ± 5.0%), with only four NNRTIs exhibiting agreement below 85%. The dominant sequence proportion threshold for HIV-1 DNA was determined to be 24.6%. This study provides strong evidence supporting the integration of HIV-1 DNA DRT into clinical practice for reliable drug resistance surveillance and treatment monitoring.

Journal of Pharmaceutical AnalysisVol. 16(1)
Guiyang Medical University (CN), Harbin Medical University (CN), Affiliated Hospital of Southwest Medical University (CN), The Fourth People's Hospital (CN), Kunming Third People's Hospital (CN), Affiliated Hospital of Guizhou Medical University (CN), The First Hospital of Changsha (CN), Jiangxi Chest Hospital (CN), People's Hospital of Xinjiang Uygur Autonomous Region (CN), Fourth Affiliated Hospital of Harbin Medical University (CN), Dongguan People’s Hospital (CN), Luxshare ICT (China) (CN), Xinjiang Uygur Autonomous Region Uygur Medicine Hospital (CN), The Second Nanning People's Hospital (CN), The Sixth People's Hospital of Zhengzhou (CN), Chongqing Public Health Medical Center (CN), Xiangshan County First People's Hospital (CN), First Affiliated Hospital of Jinan University (CN), Guangzhou Zoo (CN), Shenzhen Third People’s Hospital (CN)
Openalex Percentile: Top 54%
HIV/AIDS drug development and treatment
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