title: Large number of rebounding/founder HIV variants emerge from multifocal infection in lymphatic tissues after treatment interruption.
abstract: Antiretroviral therapy (ART) suppresses HIV replication in most individuals but cannot eradicate latently infected cells established before ART was initiated. Thus, infection rebounds when treatment is interrupted by reactivation of virus production from this reservoir. Currently, one or a few latently infected resting memory CD4 T cells are thought be the principal source of recrudescent infection, but this estimate is based on peripheral blood rather than lymphoid tissues (LTs), the principal sites of virus production and persistence before initiating ART. We, therefore, examined lymph node (LN) and gut-associated lymphoid tissue (GALT) biopsies from fully suppressed subjects, interrupted therapy, monitored plasma viral load (pVL), and repeated biopsies on 12 individuals as soon as pVL became detectable. Isolated HIV RNA-positive (vRNA+) cells were detected by in situ hybridization in LTs obtained before interruption in several patients. After interruption, multiple foci of vRNA+ cells were detected in 6 of 12 individuals as soon as pVL was measureable and in some subjects, in more than one anatomic site. Minimal estimates of the number of rebounding/founder (R/F) variants were determined by single-gene amplification and sequencing of viral RNA or DNA from peripheral blood mononuclear cells and plasma obtained at or just before viral recrudescence. Sequence analysis revealed a large number of R/F viruses representing recrudescent viremia from multiple sources. Together, these findings are consistent with the origins of recrudescent infection by reactivation from many latently infected cells at multiple sites. The inferred large pool of cells and sites to rekindle recrudescent infection highlights the challenges in eradicating HIV.
authors.affiliation: Department of Medicine, University of Minnesota, Minneapolis, MN 55455;
authors.forename: Meghan K
authors.initials: MK
authors.lastname: Rothenberger
authors.affiliation: AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702;
authors.forename: Brandon F
authors.initials: BF
authors.lastname: Keele
authors.affiliation: Department of Microbiology, University of Minnesota, Minneapolis, MN 55455;
authors.forename: Stephen W
authors.initials: SW
authors.lastname: Wietgrefe
authors.affiliation: College of Pharmacy, University of Nebraska Medical Center, Omaha, NE 68198;
authors.forename: Courtney V
authors.initials: CV
authors.lastname: Fletcher
authors.affiliation: Department of Surgery, University of Minnesota, Minneapolis, MN 55455;
authors.forename: Gregory J
authors.initials: GJ
authors.lastname: Beilman
authors.affiliation: Department of Surgery, University of Minnesota, Minneapolis, MN 55455;
authors.forename: Jeffrey G
authors.initials: JG
authors.lastname: Chipman
authors.affiliation: Department of Medicine, University of Minnesota, Minneapolis, MN 55455;
authors.forename: Alexander
authors.initials: A
authors.lastname: Khoruts
authors.affiliation: AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702;
authors.forename: Jacob D
authors.initials: JD
authors.lastname: Estes
authors.affiliation: Department of Medicine, University of Minnesota, Minneapolis, MN 55455;
authors.forename: Jodi
authors.initials: J
authors.lastname: Anderson
authors.affiliation: Department of Medicine, University of Minnesota, Minneapolis, MN 55455;
authors.forename: Samuel P
authors.initials: SP
authors.lastname: Callisto
authors.affiliation: Department of Medicine, University of Minnesota, Minneapolis, MN 55455;
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Schmidt
authors.affiliation: Department of Medicine, University of Minnesota, Minneapolis, MN 55455;
authors.forename: Ann
authors.initials: A
authors.lastname: Thorkelson
authors.affiliation: School of Public Health, Division of Biostatistics, University of Minnesota, Minneapolis, MN 55455;
authors.forename: Cavan
authors.initials: C
authors.lastname: Reilly
authors.affiliation: Department of Microbiology, University of Minnesota, Minneapolis, MN 55455;
authors.forename: Katherine
authors.initials: K
authors.lastname: Perkey
authors.affiliation: Department of Medicine, University of Minnesota, Minneapolis, MN 55455;
authors.forename: Thomas G
authors.initials: TG
authors.lastname: Reimann
authors.affiliation: Department of Medicine, University of Texas Medical Branch, Galveston, TX 77555;
authors.forename: Netanya S
authors.initials: NS
authors.lastname: Utay
authors.affiliation: NIH Vaccine Research Center, National Institutes of Health, Bethesda, MD 20814; and.
authors.forename: Krystelle
authors.initials: K
authors.lastname: Nganou Makamdop
authors.affiliation: Department of Medicine, University of Miami Miller Medical School, Miami, FL 33136.
authors.forename: Mario
authors.initials: M
authors.lastname: Stevenson
authors.affiliation: NIH Vaccine Research Center, National Institutes of Health, Bethesda, MD 20814; and.
authors.forename: Daniel C
authors.initials: DC
authors.lastname: Douek
authors.affiliation: Department of Microbiology, University of Minnesota, Minneapolis, MN 55455;
authors.forename: Ashley T
authors.initials: AT
authors.lastname: Haase
authors.affiliation: Department of Medicine, University of Minnesota, Minneapolis, MN 55455; schacker@umn.edu.
authors.forename: Timothy W
authors.initials: TW
authors.lastname: Schacker
mesh_terms: D000328:Adult; D019380:Anti-HIV Agents / Q000008:administration & dosage / Q000627:therapeutic use*; D018791:CD4 Lymphocyte Count; D004334:Drug Administration Schedule; D006678:HIV / Q000235:genetics / Q000502:physiology*; D015658:HIV Infections / Q000188:drug therapy* / Q000821:virology; D006801:Humans; D017403:In Situ Hybridization; D008221:Lymphoid Tissue / Q000821:virology*; D008875:Middle Aged; D008969:Molecular Sequence Data; D010802:Phylogeny; D012367:RNA, Viral / Q000097:blood; D019562:Viral Load
chemical_list: D019380:Anti-HIV Agents; D012367:RNA, Viral
keywords: HIV/AIDS; founder population; treatment interruption; viral recrudescence