title: Evidence for limited genetic compartmentalization of HIV-1 between lung and blood.
abstract: BACKGROUND
  HIV-1 is frequently detected in the lungs of infected individuals and is likely important in the development of pulmonary opportunistic infections. The unique environment of the lung, rich in alveolar macrophages and with specialized local immune responses, may contribute to differential evolution or selection of HIV-1.
  
  
  RESULTS
  We characterized HIV-1 in the lung in relation to contemporaneous viral populations in the blood. The C2-V5 region of HIV-1 env was sequenced from paired lung (induced sputum or bronchoalveolar lavage) and blood (plasma RNA and proviral DNA from sorted or unsorted PBMC) from 18 subjects. Compartmentalization between tissue pairs was assessed using 5 established tree or distance-based methods, including permutation tests to determine statistical significance. We found statistical evidence of compartmentalization between lung and blood in 10/18 subjects, although lung and blood sequences were intermingled on phylogenetic trees in all subjects. The subject showing the greatest compartmentalization contained many nearly identical sequences in BAL sample, suggesting clonal expansion may contribute to reduced viral diversity in the lung in some cases. However, HIV-1 sequences in lung were not more homogeneous overall, nor were we able to find a lung-specific genotype associated with macrophage tropism in V3. In all four subjects in whom predicted X4 genotypes were found in blood, predicted X4 genotypes were also found in lung.
  
  
  CONCLUSIONS
  Our results support a picture of continuous migration of HIV-1 between circulating blood and lung tissue, with perhaps a very limited degree of localized evolution or clonal replication.
authors.affiliation: Department of Microbiology, University of Washington, Seattle, WA, USA.
authors.forename: Laura
authors.initials: L
authors.lastname: Heath
authors.forename: Alan
authors.initials: A
authors.lastname: Fox
authors.forename: Jan
authors.initials: J
authors.lastname: McClure
authors.forename: Kurt
authors.initials: K
authors.lastname: Diem
authors.forename: Angélique B
authors.initials: AB
authors.lastname: van 't Wout
authors.forename: Hong
authors.initials: H
authors.lastname: Zhao
authors.forename: David R
authors.initials: DR
authors.lastname: Park
authors.forename: Jeffrey T
authors.initials: JT
authors.lastname: Schouten
authors.forename: Homer L
authors.initials: HL
authors.lastname: Twigg
authors.forename: Lawrence
authors.initials: L
authors.lastname: Corey
authors.forename: James I
authors.initials: JI
authors.lastname: Mullins
authors.forename: John E
authors.initials: JE
authors.lastname: Mittler
mesh_terms: D018893:Bronchoalveolar Lavage; D014644:Genetic Variation; D005838:Genotype; D006031:Glycosylation; D015658:HIV Infections / Q000097:blood* / Q000378:metabolism*; D015497:HIV-1 / Q000378:metabolism*; D006801:Humans; D007963:Leukocytes, Mononuclear / Q000821:virology; D008168:Lung / Q000378:metabolism / Q000821:virology*; D015233:Models, Statistical; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012313:RNA / Q000378:metabolism; D017422:Sequence Analysis, DNA; D013601:T-Lymphocytes / Q000821:virology
chemical_list: D012313:RNA