Latent HIV Reservoirs Characterization
This report is part of a series of focused summaries from the “5th International Workshop on HIV Persistence, Reservoirs & Eradication Strategies” held in St Maarten, December 6-9, 2011. This article recaps the presentation given by Doctor Sarah Palmer from the Karolinska Institute, Stockholm, Sweden.
Identifying where HIV persists in HIV-infected patients on suppressive ART is an important step towards HIV eradication.
The study of viral reservoirs has largely been focused on components of peripheral blood, but recent findings suggest that tissue sites harbor the vast majority of infected cells. Consequently, there remains uncertainty regarding the source of persistent HIV in patients on suppressive ART.
The purpose of this study is to identify the type of cells producing persistent virus and whether replication is ongoing.
The authors have enrolled 8 patients: 5 patients that started ART in early infection and 3 that started therapy in chronic infection. They wanted to investigate the issue of ongoing viral replication by phylogenetically comparing viral genomes isolated before initiation of therapy.
The second question they wanted to answer was which cells contribute to the viral reservoir during treatment and which cells are the source of persistent viremia. To investigate this they have phylogenetically compared viral genomes from the persistent viremia to viral genomes isolated from different cell types.
In practice, the genetic variation and average pair-wise difference of pretherapy sequences were compared to single proviral HIV-1 genomes derived from a broad spectrum of HIV-infected cells (including naive and memory CD4+ T-cells, myeloid cells, and hematopoietic progenitor cells (HPCs)) from peripheral blood, GALT, and BMT samples of the 8 patients collected after 4-10 years of suppressive therapy.
Unlike what was previously reported by other labs, neither early nor late progenitors were infected in the bone marrow tissue of patients on long-term suppressive therapy treated during acute or late infection, indicating that progenitor cells in bone marrow are not a source of persistent HIV.
The genetic similarity between the HIV populations in CD4+ cells from bone marrow and peripheral blood implied an ongoing exchange of infected cells between these compartments (figure 1).
Globally, the striking lack of genetic evolution in the HIV populations after years of therapy strongly indicated very little viral replication in the majority of cells from different tissue sources during suppressive therapy.
In all 8 patients, regardless whether therapy was initiated during acute or chronic infection, phylogenetic analyses and measurements of intra-patient diversity revealed no change in viral diversity or population structure between pre-therapy plasma-derived RNA sequences and intracellular DNA sequences from T cells located in the peripheral blood and GALT despite 3-12 years of suppressive ART.
Numerous intracellular HIV sequences identified after long-term therapy contained replication-incompetent virus. This finding of multiple T cells with identical replication incompetent virus after long-term therapy is strong evidence that this persistent virus was due to expansion of cells with integrated pro-viral DNA rather than active viral replication. This means that the measurements of HIV DNA will in some part be measuring viral genomes that are functionally dead, and that these HIV DNA "fossils" may even expand if they are located in CD4 cell clones that are expanding.
Key words: HIV ongoing replication, HIV persistence diversity, defective HIV, proviral HIV DNA