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.
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.
Int J Infect Dis. 2021 Mar;104:306-314. doi: 10.1016/j.ijid.2021.01.015. Epub 2021 Jan 12.
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).
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).
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.
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.
人类免疫缺陷病毒（HIV）准种多样性对 HIV 的根除构成了巨大障碍。本研究旨在研究抗逆转录病毒治疗（ART）期间病毒发病机制的内在 HIV 准种多样性和进化模式。
2004 年，45 名 HIV-1 感染患者入组了一项随访队列，随访时间超过 84 个月，接受了基于拉米夫定的一线 ART 方案。每 6 个月采集一次血样，以测量病毒载量和 CD4 细胞计数。采用超深度测序和系统发育分析来描述控制治疗失败（TF，n=20）或病毒学抑制（VS，n=25）患者血浆 RNA 和细胞 DNA 中 HIV-1 准种多样性的动力学。
分析宿主内单核苷酸变异（iSNV）的分布及其突变等位基因频率表明，ART 前后约有 65%的准种同时存在于血浆 HIV RNA 和细胞 DNA 中。iSNV 的数量和频率更能代表宿主内 HIV 多样性，并且通过测量系统发育关联来推断系统发育比更具有普遍性。此外，耐药相关突变（DRAMs）积累到高水平，使 TF 患者的 DRAM 与总突变比显著增加。线性回归分析显示，与 VS 患者相比，TF 患者的新出现突变以每天每千碱基 0.02 个突变的速度更快地积累。
基于 iSNV 分析，结果表明了接受 ART 的患者体内 HIV 准种多样性的动态，为 HIV 的持续存在和 DRAMs 的发展提供了新的见解。
