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Caihong Wu, Limin Zhang, Zhong Chen, Wencui Ma, Yanhua Fu, Ke Yang, Mei Liu, Yanjun Li, Xiaohong Chen, Mingjie Hou, Min Liu, Aihua Deng, Qingxia Zhao, Lukun Zhang, Quan Wang, Jun Peng, Yongli Li, Keji Deng, Jingsong Bai, Hai Long, Yaokai Chen, Hui Wang, Yun He, Jin Li, Jiahui Guo, Bianchuan Cao, Yizhi Cui, Min Wang, Tuofu Zhu, Jun Yao, Tong Wang. Large-scale evaluation of HIV-1 DNA drug resistance testing as a robust tool for clinical decision-making: A nationwide study in China[J]. Journal of Pharmaceutical Analysis. doi: 10.1016/j.jpha.2025.101513
Citation: Caihong Wu, Limin Zhang, Zhong Chen, Wencui Ma, Yanhua Fu, Ke Yang, Mei Liu, Yanjun Li, Xiaohong Chen, Mingjie Hou, Min Liu, Aihua Deng, Qingxia Zhao, Lukun Zhang, Quan Wang, Jun Peng, Yongli Li, Keji Deng, Jingsong Bai, Hai Long, Yaokai Chen, Hui Wang, Yun He, Jin Li, Jiahui Guo, Bianchuan Cao, Yizhi Cui, Min Wang, Tuofu Zhu, Jun Yao, Tong Wang. Large-scale evaluation of HIV-1 DNA drug resistance testing as a robust tool for clinical decision-making: A nationwide study in China[J]. Journal of Pharmaceutical Analysis. doi: 10.1016/j.jpha.2025.101513

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

doi: 10.1016/j.jpha.2025.101513
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This study was supported by the National Key Research and Development Program of China (Grant No.: 2022YFC2305003), Science and Technology Project in Guangzhou, China (Grant No.: 202102070001), Guangdong Basic and Applied Basic Research Foundation, China (Grant No.: 2025A1515012532, 2023A1515011874, and 2025A1515010405), the Major Scientific Research Project of National Key Clinical Specialty (2023) from Hunan Provincial Health Commission, China (Grant No.: Z2023111), the Fundamental Research Funds for Guangdong Province Key Laboratory of Bioengineering Medicine, China, Key Medical Discipline Construction Project of Hunan Province, China, and the Innovation and Entrepreneurship Leading Team Project of Guangzhou, China (Grant No.: 201809010009).

  • Received Date: Oct. 19, 2025
  • Rev Recd Date: Dec. 08, 2025
  • Available Online: Dec. 11, 2025
  • 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 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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