title: Identification of HIV-1 genitourinary tract compartmentalization by analyzing the env gene sequences in urine.
abstract: OBJECTIVE
  HIV-1 persists indefinitely in memory CD4 T cells and other long-lived cellular reservoirs despite antiretroviral therapy. Our group had previously demonstrated that HIV-1 can establish a productive infection in renal epithelial cells and that the kidney represents a separate compartment for HIV-1 replication. Here, to better understand the viruses in this unique site, we genetically characterized and compared the viruses in blood and urine specimens from 24 HIV-1 infected patients with detectable viremia.
  
  
  METHODS
  Blood and urine samples were obtained from 35 HIV-1 positive patients. Single-genome amplification was performed on HIV-1 env RNA and DNA isolated from urine supernatants and urine-derived cell pellets, respectively, as well as from plasma and peripheral blood mononuclear cell from the same individuals. Neighbor-joining trees were constructed under the Kimura 2-parameter model.
  
  
  RESULTS
  We amplified and sequenced the full-length HIV-1 envelope (env) gene from 12 of the 24 individuals, indicating that 50% of the viremic HIV-1-positive patients had viral RNA in their urine. Phylogenetic analysis of the env sequences from four individuals with more than 15 urine-derived env sequences showed that the majority of the sequences from urine formed distinct cluster(s) independent of those peripheral blood mononuclear cell and plasma-derived sequences, consistent with viral compartmentalization in the urine.
  
  
  CONCLUSIONS
  Our results suggest the presence of a distinct HIV compartment in the genitourinary tract.
authors.affiliation: aDuke University Medical Center, Durham, North Carolina, USA bIstituto Superiore di Sanità, Rome, Italy.
authors.forename: Maria
authors.initials: M
authors.lastname: Blasi
authors.forename: J Harris
authors.initials: JH
authors.lastname: Carpenter
authors.forename: Bala
authors.initials: B
authors.lastname: Balakumaran
authors.forename: Andrea
authors.initials: A
authors.lastname: Cara
authors.forename: Feng
authors.initials: F
authors.lastname: Gao
authors.forename: Mary E
authors.initials: ME
authors.lastname: Klotman
mesh_terms: D001769:Blood / Q000821:virology; D004279:DNA, Viral / Q000652:urine; D005260:Female; D015686:Gene Products, env / Q000235:genetics*; D014644:Genetic Variation; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D006801:Humans; D007963:Leukocytes, Mononuclear / Q000821:virology; D008297:Male; D016133:Polymerase Chain Reaction; D012367:RNA, Viral / Q000652:urine; D017422:Sequence Analysis, DNA; D014552:Urinary Tract Infections / Q000821:virology*; D014556:Urine / Q000821:virology*
chemical_list: D004279:DNA, Viral; D015686:Gene Products, env; D012367:RNA, Viral