title: Paired quantitative and qualitative assessment of the replication-competent HIV-1 reservoir and comparison with integrated proviral DNA.
abstract: HIV-1-infected individuals harbor a latent reservoir of infected CD4+T cells that is not eradicated by antiretroviral therapy (ART). This reservoir presents the greatest barrier to an HIV-1 cure and has remained difficult to characterize, in part, because the vast majority of integrated sequences are defective and incapable of reactivation. To characterize the replication-competent reservoir, we have combined two techniques, quantitative viral outgrowth and qualitative sequence analysis of clonal outgrowth viruses. Leukapheresis samples from four fully ART-suppressed, chronically infected individuals were assayed at two time points separated by a 4- to 6-mo interval. Overall, 54% of the viruses emerging from the latent reservoir showed gp160 env sequences that were identical to at least one other virus. Moreover, 43% of the env sequences from viruses emerging from the reservoir were part of identical groups at the two time points. Groups of identical expanded sequences made up 54% of proviral DNA, and, as might be expected, the sequences of replication-competent viruses in the active reservoir showed limited overlap with integrated proviral DNA, most of which is known to represent defective viruses. Finally, there was an inverse correlation between proviral DNA clone size and the probability of reactivation, suggesting that replication-competent viruses are less likely to be found among highly expanded provirus-containing cell clones.
authors.affiliation: Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065.
authors.forename: Julio C C
authors.initials: JC
authors.lastname: Lorenzi
authors.affiliation: Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065.
authors.forename: Yehuda Z
authors.initials: YZ
authors.lastname: Cohen
authors.affiliation: Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065.
authors.forename: Lillian B
authors.initials: LB
authors.lastname: Cohn
authors.affiliation: Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104.|Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104.
authors.forename: Edward F
authors.initials: EF
authors.lastname: Kreider
authors.affiliation: Department of Chemical Engineering, Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139.|Department of Physics, Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139.|Department of Chemistry, Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139.|Department of Biological Engineering, Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139.|Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139.
authors.forename: John P
authors.identifier: 0000-0003-1467-421X
authors.initials: JP
authors.lastname: Barton
authors.affiliation: Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104.|Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104.
authors.forename: Gerald H
authors.identifier: 0000-0003-0434-7733
authors.initials: GH
authors.lastname: Learn
authors.affiliation: Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065.
authors.forename: Thiago
authors.initials: T
authors.lastname: Oliveira
authors.affiliation: Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215.
authors.forename: Christy L
authors.initials: CL
authors.lastname: Lavine
authors.affiliation: Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065.
authors.forename: Joshua A
authors.initials: JA
authors.lastname: Horwitz
authors.affiliation: Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065.
authors.forename: Allison
authors.initials: A
authors.lastname: Settler
authors.affiliation: Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065.
authors.forename: Mila
authors.initials: M
authors.lastname: Jankovic
authors.affiliation: Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215.
authors.forename: Michael S
authors.initials: MS
authors.lastname: Seaman
authors.affiliation: Department of Chemical Engineering, Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139.|Department of Physics, Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139.|Department of Chemistry, Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139.|Department of Biological Engineering, Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139.|Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139.
authors.forename: Arup K
authors.initials: AK
authors.lastname: Chakraborty
authors.affiliation: Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104.|Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104.
authors.forename: Beatrice H
authors.initials: BH
authors.lastname: Hahn
authors.affiliation: Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065.
authors.forename: Marina
authors.initials: M
authors.lastname: Caskey
authors.affiliation: Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065; nussen@rockefeller.edu.|Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065.
authors.forename: Michel C
authors.initials: MC
authors.lastname: Nussenzweig
keywords: HIV; culture; method; replication-competent; reservoir