title: Well-mixed plasma and tissue viral populations in RT-SHIV-infected macaques implies a lack of viral replication in the tissues during antiretroviral therapy.
abstract: BACKGROUND
  Determining the anatomic compartments that contribute to plasma HIV-1 is critical to understanding the sources of residual viremia during combination antiretroviral therapy (ART). We analyzed viral DNA and RNA populations in the plasma and tissues from macaques infected with SIV containing HIV-1 RT (RT-SHIV) to identify possible sources of persistent viremia and to investigate the effect of ART on viral replication in tissues. Tissues were collected at necropsy from four pigtailed macaques infected for 30 weeks with a diverse population of RT-SHIV. Two animals (6760 and 8232) were untreated and two animals (8030 and 8272) were treated with efavirenz, tenofovir, and emtricitabine for 20 weeks.
  
  
  RESULTS
  A total of 1800 single-genome RT-SHIV pol and env DNA and RNA sequences were analyzed from the plasma, PBMCs, axillary and mesenteric lymph nodes, spleen, thymus, small intestine, bone marrow, lung, and brain. Analyses of intracellular DNA and RNA populations revealed that the majority of proviruses in tissues from untreated animal 8232 were not expressed, whereas a greater proportion of proviruses in tissues were expressed from 6760. Few intracellular RNA sequences were detected in treated animals and most contained inactivating mutations, such as frame shifts or large deletions. Phylogenetics showed that RT-SHIV DNA populations in tissues were not different from virus in contemporary plasma samples in the treated or untreated animals, demonstrating a lack of anatomic compartmentalization and suggesting that plasma viremia is derived from multiple tissue sources. No sequence divergence was detected in the plasma or between tissues in the treated animals after 20 weeks of ART indicating a lack of ongoing replication in tissues during treatment.
  
  
  CONCLUSIONS
  Virus populations in plasma and tissues did not differ significantly in either treated or untreated macaques, suggesting frequent exchange of virus or infected cells between tissues and plasma, consistent with non-compartmentalized and widely disseminated infection. There was no genetic evidence of ongoing replication in tissues during suppressive ART.
authors.affiliation: HIV Dynamics and Replicaton Program, National Cancer Institute at Frederick, 1050 Boyles Street, Building 535, Room 109, Frederick, MD, 21702-1201, USA. kearneym@mail.nih.gov.
authors.forename: Mary F
authors.initials: MF
authors.lastname: Kearney
authors.affiliation: HIV Dynamics and Replicaton Program, National Cancer Institute at Frederick, 1050 Boyles Street, Building 535, Room 109, Frederick, MD, 21702-1201, USA. elizabeth.anderson@nih.gov.
authors.forename: Elizabeth M
authors.initials: EM
authors.lastname: Anderson
authors.affiliation: HIV Dynamics and Replicaton Program, National Cancer Institute at Frederick, 1050 Boyles Street, Building 535, Room 109, Frederick, MD, 21702-1201, USA. charles.coomer506@topper.wku.edu.
authors.forename: Charles
authors.initials: C
authors.lastname: Coomer
authors.affiliation: HIV Dynamics and Replicaton Program, National Cancer Institute at Frederick, 1050 Boyles Street, Building 535, Room 109, Frederick, MD, 21702-1201, USA. lsmith18@nd.edu.
authors.forename: Luke
authors.initials: L
authors.lastname: Smith
authors.affiliation: Advanced Biomedical Computing Center, SAIC, Frederick, USA. shaow@mail.nih.gov.
authors.forename: Wei
authors.initials: W
authors.lastname: Shao
authors.affiliation: HIV Dynamics and Replicaton Program, National Cancer Institute at Frederick, 1050 Boyles Street, Building 535, Room 109, Frederick, MD, 21702-1201, USA. nicholas.johnson@nih.gov.
authors.forename: Nicholas
authors.initials: N
authors.lastname: Johnson
authors.affiliation: Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA. cjk14@pitt.edu.
authors.forename: Christopher
authors.initials: C
authors.lastname: Kline
authors.affiliation: HIV Dynamics and Replicaton Program, National Cancer Institute at Frederick, 1050 Boyles Street, Building 535, Room 109, Frederick, MD, 21702-1201, USA. jspindler@mail.nih.gov.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Spindler
authors.affiliation: Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA. jwm1@pitt.edu.
authors.forename: John W
authors.initials: JW
authors.lastname: Mellors
authors.affiliation: Department of Molecular Biology and Microbiology, Tufts University, Boston, MA, USA. john.coffin@tufts.edu.
authors.forename: John M
authors.initials: JM
authors.lastname: Coffin
authors.affiliation: Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA. zaa4@pitt.edu.
authors.forename: Zandrea
authors.initials: Z
authors.lastname: Ambrose
mesh_terms: D000818:Animals; D019380:Anti-HIV Agents / Q000008:administration & dosage / Q000627:therapeutic use*; D023241:Antiretroviral Therapy, Highly Active; D001853:Bone Marrow / Q000821:virology; D001921:Brain / Q000821:virology; D004279:DNA, Viral / Q000097:blood; D004195:Disease Models, Animal; D024882:Drug Resistance, Viral; D015658:HIV Infections / Q000188:drug therapy / Q000821:virology; D008168:Lung / Q000821:virology; D008198:Lymph Nodes / Q000821:virology; D008253:Macaca mulatta; D010802:Phylogeny; D012367:RNA, Viral / Q000097:blood; D016097:Simian Acquired Immunodeficiency Syndrome / Q000188:drug therapy* / Q000821:virology*; D015302:Simian Immunodeficiency Virus / Q000235:genetics / Q000502:physiology*; D013154:Spleen / Q000821:virology; D013950:Thymus Gland / Q000821:virology; D019562:Viral Load / Q000187:drug effects; D014766:Viremia / Q000188:drug therapy / Q000821:virology; D014779:Virus Replication / Q000187:drug effects*
chemical_list: D019380:Anti-HIV Agents; D004279:DNA, Viral; D012367:RNA, Viral