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
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
a State Key Laboratory of Bioactive Molecules and Druggability Assessment, Center of Clinical Laboratory, The First Affiliated Hospital, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China;
b Department of Infectious Diseases, Institute of HIV/AIDS, The First Hospital of Changsha, Changsha, 410005, China;
c Department of Infectious Disease, Guiyang Public Health Treatment Center, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550001, China;
d Department of Antiviral Therapy, The First People's Hospital of Yuexi County, Liangshan, Sichuan, 615000, China;
e Department of Infectious Diseases, Guangxi AIDS Clinical Treatment Center, The Fourth People's Hospital of Nanning, Nanning, 530023, China;
f Department of Infectious Diseases, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, China;
g Department of Infectious Diseases, Henan Infectious Disease Hospital, Zhengzhou, 450015, China;
h Department of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, 400036, China;
i Jiangxi Chest Hospital, Nanchang, 330000, China;
j The Third People's Hospital of Shenzhen, Shenzhen, 518112, China;
k Department of Laboratory Medicine, Xinjiang Uygur Autonomous Region Infectious Disease Hospital, Urumqi, 830000, China;
l Guangzhou SupBio Bio-Technologies and Science Co., Ltd., Guangzhou, 510530, China;
m Dongguan Institute of Microscale and Precision Medical Measurement Co., Ltd., Dongguan, 523808, China;
n Department of Infectious Diseases, The Third People's Hospital of Kunming, Kunming, 650500, China;
o Department of Infectious Disease, The Ninth People's Hospital of Dongguan, Dongguan, Guangdong, 523076, China;
p Department of Infectious Disease, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, China;
q National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
Funds:
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).
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.