Quantifying the turnover of transcriptional subclasses of HIV-1-infected cells.

Christian L. Althaus,Alan S. Perelson,Beda Joos,Huldrych F. Günthard

doi:10.1371/journal.pcbi.1003871

Abstract

HIV-1-infected cells in peripheral blood can be grouped into different transcriptional subclasses. Quantifying the turnover of these cellular subclasses can provide important insights into the viral life cycle and the generation and maintenance of latently infected cells. We used previously published data from five patients chronically infected with HIV-1 that initiated combination antiretroviral therapy (cART). Patient-matched PCR for unspliced and multiply spliced viral RNAs combined with limiting dilution analysis provided measurements of transcriptional profiles at the single cell level. Furthermore, measurement of intracellular transcripts and extracellular virion-enclosed HIV-1 RNA allowed us to distinguish productive from non-productive cells. We developed a mathematical model describing the dynamics of plasma virus and the transcriptional subclasses of HIV-1-infected cells. Fitting the model to the data allowed us to better understand the phenotype of different transcriptional subclasses and their contribution to the overall turnover of HIV-1 before and during cART. The average number of virus-producing cells in peripheral blood is small during chronic infection. We find that a substantial fraction of cells can become defectively infected. Assuming that the infection is homogenous throughout the body, we estimate an average in vivo viral burst size on the order of 104 virions per cell. Our study provides novel quantitative insights into the turnover and development of different subclasses of HIV-1-infected cells, and indicates that cells containing solely unspliced viral RNA are a good marker for viral latency. The model illustrates how the pool of latently infected cells becomes rapidly established during the first months of acute infection and continues to increase slowly during the first years of chronic infection. Having a detailed understanding of this process will be useful for the evaluation of viral eradication strategies that aim to deplete the latent reservoir of HIV-1.

Highlights

higher transcriptional activity (High) levels of cell-associated HIV-1 RNA can be observed in peripheral blood of patients with undetectable plasma viremia during combination antiretroviral therapy [1,2,3,4]
Gaining a quantitative understanding of the development and turnover of different HIV-1-infected subpopulations of cells is crucial to improve the outcome of patients on combination antiretroviral therapy
We developed a mathematical model that describes the dynamics of different transcriptionally active subclasses of HIV-1-infected cells and the viral load in peripheral blood

Summary

Introduction

High levels of cell-associated HIV-1 RNA can be observed in peripheral blood of patients with undetectable plasma viremia during combination antiretroviral therapy (cART) [1,2,3,4]. Sensitive assays for HIV-1 plasma RNA in patients on cART usually provide bulk measurements of viral activity and cannot distinguish between different infected subpopulations [11]. The study by Fischer et al [12] combined highly sensitive PCR assays for unspliced (UsRNA) and multiply spliced (MsRNA-tatrev and MsRNA-nef) HIV-1 RNA species with limiting dilution endpoint analysis of peripheral blood mononuclear cells (PBMCs). The study identified four distinct viral transcriptional classes: two overlapping cell classes of high viral transcriptional activity, representative of a virus producing phenotype; and two cell classes that express HIV1 RNA at low and intermediate levels that match definitions of viral latency [12,13]

Methods

Results

Discussion

Conclusion