XIX International AIDS Conference


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THAA0105 - Oral Abstract

Characterization of persistent HIV-1 in a broad spectrum of CD4+ T cells isolated from peripheral blood and gut associated lymphoid tissue from patients on long-term suppressive therapy

Presented by Lina Josefsson (Sweden).

L. Josefsson1,2, S. Eriksson2, E. Sinclair3, T. Ho3, M. Killian3, L. Epling3, A. Tan3, P. Lemey4, N.R. Faria4, W. Shao5, P. Hunt3, M. Somsouk3, D. Douek6, P. Bacchetti7, L. Loeb3, J. Custer3, L. Poole3, S. Deeks3, F.M. Hecht3, S. Palmer1,2

1Karolinska Institutet, Department of Microbiology, Tumor and Cellbiology, Solna, Sweden, 2The Swedish Institute for Communicable Disease Control, Department of Diagnostics and Vaccinology, Solna, Sweden, 3University of California - San Francisco, Department of Medicine, San Francisco, United States, 4KU Leuven, Rega Institute, Leuven, Belgium, 5National Institiute of Cancer, Advanced Biomedical Computing Center, SAIC, Frederick, United States, 6National Institute of Allergy and Infectious Diseases, National Institutes of Health, Immunology Laboratory, Vaccine Research Center, Bethesda, United States, 7University of California - San Francisco, Department of Epidemiology and Biostatistics, San Francisco, United States

Background: The role of ongoing virus replication in HIV persistence during long-term antiretroviral therapy is unknown. Since residual replication should result in detectable evolution, we investigated the degree of sequence evolution in blood-derived and rectal tissue-derived CD4+ T cells.
Methods: Using single-genome and single-proviral sequencing techniques, we obtained 20-50 single viral genomes from pre-therapy plasma samples from 5 subjects who initiated therapy during acute infection and 3 subjects who initiated therapy during chronic infection. Pre-therapy plasma viral sequences were compared to single proviral HIV-1 genomes derived from HIV-1-infected T-cells (naïve, memory, central- and effector-memory) from peripheral blood (PB) and gut-associated lymphoid tissue (GALT) samples collected after 4-12 years of suppressive therapy. Maximum likelihood phylogenetic trees were constructed using the general time reversible model incorporating rate variation among sites. Evolutionary divergence was explored using root-to-tip analysis (Path-O-Gen).
Results: The geometric mean infection frequency of memory and naïve CD4+ T-cells in the PB was 13- and 24-fold higher respectively in subjects treated during chronic compared to acute infection. This was also true for effector memory CD4+ T-cells from the GALT (6-fold higher). Phylogenetic analysis revealed clear evidence against any substantial evolution between the pre-therapy plasma-derived HIV RNA sequences and on-therapy intracellular HIV DNA sequences. Numerous intracellular HIV sequences identified after long-term therapy contained replication-incompetent virus. One patient had a predominant intracellular clone in both memory and effector memory T-cells containing a 380bp deletion after >9 years of therapy.
Conclusions: Early initiation of effective therapy results in substantially lower reservoir size in blood and gut. The lack of HIV-1 genetic evolution in the HIV-1 infected CD4+ T-cell populations after years of therapy argues against virus replication as a major cause of persistence in these cell populations. The role of replication in other tissues and cell types however remains to be defined.

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