Evaluating Clonal Expansion of HIV-Infected Cells: Optimization of PCR Strategies to Predict Clonality
نویسندگان
چکیده
In HIV-infected individuals receiving suppressive antiretroviral therapy, the virus persists indefinitely in a reservoir of latently infected cells. The proliferation of these cells may contribute to the stability of the reservoir and thus to the lifelong persistence of HIV-1 in infected individuals. Because the HIV-1 replication process is highly error-prone, the detection of identical viral genomes in distinct host cells provides evidence for the clonal expansion of infected cells. We evaluated alignments of unique, near-full-length HIV-1 sequences to determine the relationship between clonality in a short region and clonality in the full genome. Although it is common to amplify and sequence short, subgenomic regions of the viral genome for phylogenetic analysis, we show that sequence identity of these amplicons does not guarantee clonality across the full viral genome. We show that although longer amplicons capture more diversity, no subgenomic region can recapitulate the diversity of full viral genomes. Consequently, some identical subgenomic amplicons should be expected even from the analysis of completely unique viral genomes, and the presence of identical amplicons alone is not proof of clonally expanded HIV-1. We present a method for evaluating evidence of clonal expansion in the context of these findings.
منابع مشابه
HIV-infected cells are frequently clonally expanded after prolonged antiretroviral therapy: implications for HIV persistence
HIV infection is controlled but not eradicated by combination antiretroviral therapy (cART), and persistence during therapy represents a substantial barrier to strategies to eradicate infection. The nature of persistence is uncertain, and a number of mechanisms have been proposed to explain HIV persistence in vivo, including low-level HIV replication, sanctuary sites for HIV-infected cells, and...
متن کاملClonal predominance of cytomegalovirus-specific CD8+ cytotoxic T lymphocytes in bone marrow recipients.
After lymphocyte-depleted BMT, CD8+ T cells have been expanded to or above normal levels in 45% of the recipients within 3 months. The mechanisms underlying proliferation of donor-derived CD8+ T cells after BMT are still unclear. We investigated whether these CD8+ T cells proliferate in response to specific antigens by determination of TCR clonality and whether these cells exert specific cytoto...
متن کاملIntegration Site and Clonal Expansion in Human Chronic Retroviral Infection and Gene Therapy
Retroviral vectors have been successfully used therapeutically to restore expression of genes in a range of single-gene diseases, including several primary immunodeficiency disorders. Although clinical trials have shown remarkable results, there have also been a number of severe adverse events involving malignant outgrowth of a transformed clonal population. This clonal expansion is influenced ...
متن کاملmolein the clonal expansion of lymphocytes and the prolonged survival of CD4-positive cells in vivo. Surviving T-lympho
Clonal proliferation of human T-lymphotropic virus type I (HTLV-I) infected cells has been detected by Southern blot analysis and inverse PCR in patients with adult 1-cell leukemia, patients with HTLV-I-associated diseases, and even in asymptomatic carriers. Combining inverse PCR with long PCR, we amplified the genomic DNA regions flanking the integration sites ofthe HTLV-I provirus to detect c...
متن کاملThe role of HIV integration in viral persistence: no more whistling past the proviral graveyard.
A substantial research effort has been directed to identifying strategies to eradicate or control HIV infection without a requirement for combination antiretroviral therapy (cART). A number of obstacles prevent HIV eradication, including low-level viral persistence during cART, long-term persistence of HIV-infected cells, and latent infection of resting CD4+ T cells. Mechanisms of persistence r...
متن کامل