- Josefsson, Lina;
- von Stockenstrom, Susanne;
- Faria, Nuno R;
- Sinclair, Elizabeth;
- Bacchetti, Peter;
- Killian, Maudi;
- Epling, Lorrie;
- Tan, Alice;
- Ho, Terence;
- Lemey, Philippe;
- Shao, Wei;
- Hunt, Peter W;
- Somsouk, Ma;
- Wylie, Will;
- Douek, Daniel C;
- Loeb, Lisa;
- Custer, Jeff;
- Hoh, Rebecca;
- Poole, Lauren;
- Deeks, Steven G;
- Hecht, Frederick;
- Palmer, Sarah
The source and dynamics of persistent HIV-1 during long-term combinational antiretroviral therapy (cART) are critical to understanding the barriers to curing HIV-1 infection. To address this issue, we isolated and genetically characterized HIV-1 DNA from naïve and memory T cells from peripheral blood and gut-associated lymphoid tissue (GALT) from eight patients after 4-12 y of suppressive cART. Our detailed analysis of these eight patients indicates that persistent HIV-1 in peripheral blood and GALT is found primarily in memory CD4(+) T cells [CD45RO(+)/CD27((+/-))]. The HIV-1 infection frequency of CD4(+) T cells from peripheral blood and GALT was higher in patients who initiated treatment during chronic compared with acute/early infection, indicating that early initiation of therapy results in lower HIV-1 reservoir size in blood and gut. Phylogenetic analysis revealed an HIV-1 genetic change between RNA sequences isolated before initiation of cART and intracellular HIV-1 sequences from the T-cell subsets after 4-12 y of suppressive cART in four of the eight patients. However, evolutionary rate analyses estimated no greater than three nucleotide substitutions per gene region analyzed during all of the 4-12 y of suppressive therapy. We also identified a clearly replication-incompetent viral sequence in multiple memory T cells in one patient, strongly supporting asynchronous cell replication of a cell containing integrated HIV-1 DNA as the source. This study indicates that persistence of a remarkably stable population of infected memory cells will be the primary barrier to a cure, and, with little evidence of viral replication, this population could be maintained by homeostatic cell proliferation or other processes.