title: Integrated and Total HIV-1 DNA Predict Ex Vivo Viral Outgrowth.
abstract: The persistence of a reservoir of latently infected CD4 T cells remains one of the major obstacles to cure HIV. Numerous strategies are being explored to eliminate this reservoir. To translate these efforts into clinical trials, there is a strong need for validated biomarkers that can monitor the reservoir over time in vivo. A comprehensive study was designed to evaluate and compare potential HIV-1 reservoir biomarkers. A cohort of 25 patients, treated with suppressive antiretroviral therapy was sampled at three time points, with median of 2.5 years (IQR: 2.4-2.6) between time point 1 and 2; and median of 31 days (IQR: 28-36) between time point 2 and 3. Patients were median of 6 years (IQR: 3-12) on ART, and plasma viral load (<50 copies/ml) was suppressed for median of 4 years (IQR: 2-8). Total HIV-1 DNA, unspliced (us) and multiply spliced HIV-1 RNA, and 2LTR circles were quantified by digital PCR in peripheral blood, at 3 time points. At the second time point, a viral outgrowth assay (VOA) was performed, and integrated HIV-1 DNA and relative mRNA expression levels of HIV-1 restriction factors were quantified. No significant change was found for long- and short-term dynamics of all HIV-1 markers tested in peripheral blood. Integrated HIV-1 DNA was associated with total HIV-1 DNA (p<0.001, R² = 0.85), us HIV-1 RNA (p = 0.029, R² = 0.40), and VOA (p = 0.041, R2 = 0.44). Replication-competent virus was detected in 80% of patients by the VOA and it correlated with total HIV-1 DNA (p = 0.039, R² = 0.54). The mean quantification difference between Alu-PCR and VOA was 2.88 log10, and 2.23 log10 between total HIV-1 DNA and VOA. The levels of usHIV-1 RNA were inversely correlated with mRNA levels of several HIV-1 restriction factors (TRIM5α, SAMHD1, MX2, SLFN11, pSIP1). Our study reveals important correlations between the viral outgrowth and total and integrated HIV-1 DNA measures, suggesting that the total pool of HIV-1 DNA may predict the size of the replication-competent virus in ART suppressed patients.
authors.affiliation: HIV Translational Research Unit (HTRU), Department of Internal Medicine, Ghent University and Ghent University Hospital, Ghent, Belgium.|Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America.
authors.forename: Maja
authors.initials: M
authors.lastname: Kiselinova
authors.affiliation: HIV Translational Research Unit (HTRU), Department of Internal Medicine, Ghent University and Ghent University Hospital, Ghent, Belgium.
authors.forename: Ward
authors.initials: W
authors.lastname: De Spiegelaere
authors.affiliation: Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America.|Infectious Disease Division, Massachusetts General Hospital, Boston, Massachusetts, United States of America.
authors.forename: Maria Jose
authors.initials: MJ
authors.lastname: Buzon
authors.affiliation: HIV Translational Research Unit (HTRU), Department of Internal Medicine, Ghent University and Ghent University Hospital, Ghent, Belgium.
authors.forename: Eva
authors.initials: E
authors.lastname: Malatinkova
authors.affiliation: Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, United States of America.|Infectious Disease Division, Massachusetts General Hospital, Boston, Massachusetts, United States of America.|Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts, United States of America.
authors.forename: Mathias
authors.initials: M
authors.lastname: Lichterfeld
authors.affiliation: HIV Translational Research Unit (HTRU), Department of Internal Medicine, Ghent University and Ghent University Hospital, Ghent, Belgium.
authors.forename: Linos
authors.initials: L
authors.lastname: Vandekerckhove
mesh_terms: D000328:Adult; D015331:Cohort Studies; D004279:DNA, Viral / Q000032:analysis / Q000302:isolation & purification; D004197:Disease Reservoirs / Q000821:virology; D005260:Female; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000235:genetics / Q000254:growth & development*; D006801:Humans; D016014:Linear Models; D008297:Male; D008875:Middle Aged; D012367:RNA, Viral / Q000032:analysis / Q000302:isolation & purification; D019562:Viral Load; D016662:Virus Integration
chemical_list: D004279:DNA, Viral; D012367:RNA, Viral