Abstract
Genetic recombination contributes to the diversity of human immunodeficiency virus (HIV-1). Productive HIV-1 recombination is, however, dependent on both the number of HIV-1 genomes per infected cell and the genetic relationship between these viral genomes. A detailed analysis of the number of proviruses and their genetic relationship in infected cells isolated from peripheral blood and tissue compartments is therefore important for understanding HIV-1 recombination, genetic diversity and the dynamics of HIV-1 infection. To address these issues, we used a previously developed single-cell sequencing technique to quantify and genetically characterize individual HIV-1 DNA molecules from single cells in lymph node tissue and peripheral blood. Analysis of memory and naïve CD4+ T cells from paired lymph node and peripheral blood samples from five untreated chronically infected patients revealed that the majority of these HIV-1-infected cells (>90%) contain only one copy of HIV-1 DNA, implying a limited potential for productive recombination in virus produced by these cells in these two compartments. Phylogenetic analysis revealed genetic similarity of HIV-1 DNA in memory and naïve CD4+ T-cells from lymph node, peripheral blood and HIV-1 RNA from plasma, implying exchange of virus and/or infected cells between these compartments in untreated chronic infection.
Highlights
The genetic diversity of human immunodeficiency virus (HIV-1) allows the virus to develop resistance to antiviral therapy and escape immune pressure
To investigate the numbers of cells co-infected by different HIV-1 variants in peripheral blood, we developed the single-cell sequencing (SCS) assay, which allows for the analysis of HIV-1 DNA molecules at a single cell level
One of the main factors contributing to HIV-1 diversity is recombination between two genetically different viral RNA genomes that enter a cell in the same virion
Summary
The genetic diversity of human immunodeficiency virus (HIV-1) allows the virus to develop resistance to antiviral therapy and escape immune pressure. HIV-1 recombination, which generates new viral variants through a process of genetic exchange, is initiated when a cell is infected by genetically distinct HIV-1 variants and two RNAs transcribed from the different proviruses are co-packaged into a virion. To investigate the numbers of cells co-infected by different HIV-1 variants in peripheral blood, we developed the single-cell sequencing (SCS) assay, which allows for the analysis of HIV-1 DNA molecules at a single cell level. Using this assay, we found that the majority of CD4+ T-cells (.90%) from the peripheral blood of untreated HIV-1-infected patients contain a single HIV-1 DNA molecule [6].
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