Single Cell Analysis of Lymph Node Tissue from HIV-1 Infected Patients Reveals that the Majority of CD4+ T-cells Contain One HIV-1 DNA Molecule

• DOI: 10.1371/journal.ppat.1003432
• Publication Date: 2013-07-16T19:47:55Z
• Authors: Lina Josefsson; Sarah Palmer; Nuno R. Faria; Philippe Lemey; Joseph Casazza; David Ambrozak; Mary Kearney; Wei Shao; Shyamasundaran Ko...; Michael Sneller; John Mellors; John M. Coffin; Frank Maldarelli
• Keywords: Adult; CD4-Positive T-Lymphocytes; Male; 0301 basic medicine; QH301-705.5; HIV Infections; Genome, Viral; RC581-607; 3. Good health; 03 medical and health sciences; Chronic Disease; DNA, Viral; HIV-1; Humans; Lymph Nodes; Immunologic diseases. Allergy; Biology (General); Phylogeny; Research Article

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.