HIV-1 evolutionary dynamics under non-suppressive antiretroviral therapy
HIV-1 evolutionary dynamics under non-suppressive antiretroviral therapy
复制标题
非抑制性抗逆转录病毒治疗下的 HIV-1 进化动态
DOI：
10.1101/2021.04.09.21254592
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发表时间：
2021
期刊：
影响因子：
--
通讯作者：
Kemp S
中科院分区：
文献类型：
--
作者：
Kemp S
Viral population dynamics in long term viraemic antiretroviral therapy (ART) treated individuals have not been well characterised. Prolonged virologic failure on 2nd-line protease inhibitor (PI) based ART without emergence of major protease mutations is well recognised, providing an opportunity to study within-host evolution.Using next-generation Illumina short read sequencing and in silico haplotype reconstruction we analysed whole genome sequences from longitudinal plasma samples of eight chronically infected HIV-1 individuals failing 2nd-line regimens from the ANRS 12249 TasP trial, in the absence of high frequency major PI resistance mutations. Plasma drug levels were measured by HPLC. Three participants were selective for in-depth variant and haplotype analyses, each with five or more timepoints spanning at least 16 months. Recombination and linkage disequilibrium between haplotypes and genes was also explored.During PI failure synonymous mutations were around twice as frequent as non-synonymous mutations across participants. Prior to or during exposure to PI, we observed several polymorphic amino acids ingag(e.g. T81A, T375N) which are have also been previously associated with exposure to protease inhibitor exposure. Although overall SNP frequency at abundance above 2% appeared stable across time in each individual, divergence from the consensus baseline sequence did increase over time. Non-synonymous changes were enriched in known polymorphic regions such asenvwhereas synonymous changes were more often observed to fluctuate in the conservedpolgene. Phylogenetic analyses of whole genome viral haplotypes demonstrated two common features: Firstly, evidence for selective sweeps following therapy switches or large changes in plasma drug concentrations, with hitchhiking of synonymous and non-synonymous mutations. Secondly, competition between multiple viral haplotypes that intermingled phylogenetically alongside soft selective sweeps. The diversity of viral populations was maintained between successive timepoints with ongoing viremia, particularly inenv. Changes in haplotype dominance were often distinct from the dynamics of drug resistance mutations inreverse transcriptase(RT), indicating the presence of softer selective sweeps and/or recombination.Large fluctuations in variant frequencies with diversification occur during apparently ‘stable’ viremia on non-suppressive ART. Reconstructed haplotypes provided further evidence for sweeps during periods of partial adherence, and competition between haplotypes during periods of low drug exposure. Drug resistance mutations in RT can be used as markers of viral populations in the reservoir and we found evidence for loss of linkage disequilibrium for drug resistance mutations, indicative of recombination. These data imply that even years of exposure to PIs, within the context of large stable populations displaying ongoing selective competition, may not precipitate emergence of major PI resistance mutations, indicating significant fitness costs for such mutations. Ongoing viral diversification within reservoirs may compromise the goal of sustained viral suppression.
