Yuanyuan Zhang1, Qianqian Yin2, Ming Ni3, Tingting Liu4, Chen Wang5, Chuan Song4, Lingjie Liao5, Hui Xing5, Shibo Jiang6, Yiming Shao5, Chen Chen7, Liying Ma8. 1. State Key Laboratory of Infectious Disease Prevention and Control, National Centre for AIDS/STD Control and Prevention, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, Chinese Centre for Disease Control and Prevention, Beijing, China; Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China. 2. State Key Laboratory of Infectious Disease Prevention and Control, National Centre for AIDS/STD Control and Prevention, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, Chinese Centre for Disease Control and Prevention, Beijing, China; State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Centre for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China. 3. Beijing Institute of Radiation Medicine, Beijing, China. 4. Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China. 5. State Key Laboratory of Infectious Disease Prevention and Control, National Centre for AIDS/STD Control and Prevention, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, Chinese Centre for Disease Control and Prevention, Beijing, China. 6. Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai, China. 7. Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China. Electronic address: chenchen1@ccmu.edu.cn. 8. State Key Laboratory of Infectious Disease Prevention and Control, National Centre for AIDS/STD Control and Prevention, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, Chinese Centre for Disease Control and Prevention, Beijing, China. Electronic address: mal@chinaaids.cn.
Abstract
OBJECTIVES: Human immunodeficiency virus (HIV) quasispecies diversity presents a large barrier to the eradication of HIV. The aim of this study was to investigate intrahost HIV quasispecies diversity and evolutionary patterns underpinning the mechanisms of viral pathogenesis during antiretroviral therapy (ART). METHODS: Forty-five participants with HIV-1 infection were enrolled in a follow-up cohort for >84 months in 2004, and received a lamivudine-based first-line ART regimen. Blood samples were collected every 6 months to measure viral load and CD4+ cell count. Ultra-deep sequencing and phylogenetic analysis were used to characterize the dynamics governing quasispecies diversity of HIV-1 circulating between plasma RNA and cellular DNA of participants with treatment failure (TF, n = 20) or virologic suppression (VS, n = 25). RESULTS: Analysis of the distribution of intrahost single-nucleotide variations (iSNVs) and their mutated allele frequencies revealed that approximately 65% of the quasispecies co-occurred in plasma HIV RNA and cellular DNA either before or after ART. The number and frequency of iSNVs are more representative of intrahost HIV diversity, and have better generalizability than phylogenetic inference by measurement of phylogenetic associations. Furthermore, drug-resistance-associated mutations (DRAMs) accumulated to high levels, dramatically increasing the DRAM-to-total-mutation ratio for TF patients. Linear regression analysis revealed that emergent mutations accumulated faster in TF patients compared with VS patients, at a rate of 0.02 mutations/day/kb. CONCLUSIONS: Based on iSNV analysis, the results demonstrate the dynamics of intrahost HIV quasispecies diversity in patients on ART, and provide a novel insight into the persistence of HIV and development of DRAMs.
OBJECTIVES: Human immunodeficiency virus (HIV) quasispecies diversity presents a large barrier to the eradication of HIV. The aim of this study was to investigate intrahost HIV quasispecies diversity and evolutionary patterns underpinning the mechanisms of viral pathogenesis during antiretroviral therapy (ART). METHODS: Forty-five participants with HIV-1 infection were enrolled in a follow-up cohort for >84 months in 2004, and received a lamivudine-based first-line ART regimen. Blood samples were collected every 6 months to measure viral load and CD4+ cell count. Ultra-deep sequencing and phylogenetic analysis were used to characterize the dynamics governing quasispecies diversity of HIV-1 circulating between plasma RNA and cellular DNA of participants with treatment failure (TF, n = 20) or virologic suppression (VS, n = 25). RESULTS: Analysis of the distribution of intrahost single-nucleotide variations (iSNVs) and their mutated allele frequencies revealed that approximately 65% of the quasispecies co-occurred in plasma HIV RNA and cellular DNA either before or after ART. The number and frequency of iSNVs are more representative of intrahost HIV diversity, and have better generalizability than phylogenetic inference by measurement of phylogenetic associations. Furthermore, drug-resistance-associated mutations (DRAMs) accumulated to high levels, dramatically increasing the DRAM-to-total-mutation ratio for TF patients. Linear regression analysis revealed that emergent mutations accumulated faster in TF patients compared with VS patients, at a rate of 0.02 mutations/day/kb. CONCLUSIONS: Based on iSNV analysis, the results demonstrate the dynamics of intrahost HIV quasispecies diversity in patients on ART, and provide a novel insight into the persistence of HIV and development of DRAMs.