title: Comparative analysis of measures of viral reservoirs in HIV-1 eradication studies.
abstract: HIV-1 reservoirs preclude virus eradication in patients receiving highly active antiretroviral therapy (HAART). The best characterized reservoir is a small, difficult-to-quantify pool of resting memory CD4(+) T cells carrying latent but replication-competent viral genomes. Because strategies targeting this latent reservoir are now being tested in clinical trials, well-validated high-throughput assays that quantify this reservoir are urgently needed. Here we compare eleven different approaches for quantitating persistent HIV-1 in 30 patients on HAART, using the original viral outgrowth assay for resting CD4(+) T cells carrying inducible, replication-competent viral genomes as a standard for comparison. PCR-based assays for cells containing HIV-1 DNA gave infected cell frequencies at least 2 logs higher than the viral outgrowth assay, even in subjects who started HAART during acute/early infection. This difference may reflect defective viral genomes. The ratio of infected cell frequencies determined by viral outgrowth and PCR-based assays varied dramatically between patients. Although strong correlations with the viral outgrowth assay could not be formally excluded for most assays, correlations achieved statistical significance only for integrated HIV-1 DNA in peripheral blood mononuclear cells and HIV-1 RNA/DNA ratio in rectal CD4(+) T cells. Residual viremia was below the limit of detection in many subjects and did not correlate with the viral outgrowth assays. The dramatic differences in infected cell frequencies and the lack of a precise correlation between culture and PCR-based assays raise the possibility that the successful clearance of latently infected cells may be masked by a larger and variable pool of cells with defective proviruses. These defective proviruses are detected by PCR but may not be affected by reactivation strategies and may not require eradication to accomplish an effective cure. A molecular understanding of the discrepancy between infected cell frequencies measured by viral outgrowth versus PCR assays is an urgent priority in HIV-1 cure research.
authors: Department of Diagnostics and Vaccinology, Swedish Institute for Communicable Diseases, Solna, Sweden.
authors: Susanne
authors: S
authors: Eriksson
authors: Erin H
authors: EH
authors: Graf
authors: Viktor
authors: V
authors: Dahl
authors: Matthew C
authors: MC
authors: Strain
authors: Steven A
authors: SA
authors: Yukl
authors: Elena S
authors: ES
authors: Lysenko
authors: Ronald J
authors: RJ
authors: Bosch
authors: Jun
authors: J
authors: Lai
authors: Stanley
authors: S
authors: Chioma
authors: Fatemeh
authors: F
authors: Emad
authors: Mohamed
authors: M
authors: Abdel-Mohsen
authors: Rebecca
authors: R
authors: Hoh
authors: Frederick
authors: F
authors: Hecht
authors: Peter
authors: P
authors: Hunt
authors: Ma
authors: M
authors: Somsouk
authors: Joseph
authors: J
authors: Wong
authors: Rowena
authors: R
authors: Johnston
authors: Robert F
authors: RF
authors: Siliciano
authors: Douglas D
authors: DD
authors: Richman
authors: Una
authors: U
authors: O'Doherty
authors: Sarah
authors: S
authors: Palmer
authors: Steven G
authors: SG
authors: Deeks
authors: Janet D
authors: JD
authors: Siliciano
mesh_terms: D000328:Adult; D000368:Aged; D023241:Antiretroviral Therapy, Highly Active; D015496:CD4-Positive T-Lymphocytes / Q000187:drug effects; D004279:DNA, Viral / Q000032:analysis* / Q000187:drug effects / Q000235:genetics; D004197:Disease Reservoirs / Q000821:virology*; D005260:Female; D006678:HIV / Q000235:genetics / Q000254:growth & development / Q000302:isolation & purification*; D015658:HIV Infections / Q000188:drug therapy / Q000235:genetics / Q000821:virology*; D006801:Humans; D007963:Leukocytes, Mononuclear / Q000187:drug effects / Q000821:virology; D008137:Longitudinal Studies; D008297:Male; D008875:Middle Aged; D016133:Polymerase Chain Reaction; D011533:Proviruses / Q000235:genetics / Q000254:growth & development / Q000302:isolation & purification*; D012367:RNA, Viral / Q000032:analysis* / Q000187:drug effects / Q000235:genetics; D019562:Viral Load / Q000187:drug effects*; D016662:Virus Integration / Q000187:drug effects
chemical_list: D004279:DNA, Viral; D012367:RNA, Viral