title: Phylogenetic insights into regional HIV transmission.
abstract: OBJECTIVE
  Despite prevention efforts, new HIV diagnoses continue in the southern United States, where the epidemic is characterized by significant racial/ethnic disparities. We integrated phylogenetic analyses with clinical data to reveal trends in local HIV transmission.
  
  
  METHODS
  Cross-sectional analysis of 1671 HIV-infected individuals each with one B-subtype pol sequence obtained during chronic (82%; UNC Center for AIDS Research Clinical Cohort) or acute/recent (18%; Duke/UNC Acute HIV Consortium) infection.
  
  
  METHODS
  Phylogenies were inferred using neighbor joining to select related sequences then confirmed with Bayesian methods. We characterized transmission clusters (clades n ≥ 3 sequences supported by posterior probabilities = 1) by factors including race/ethnicity and transmission risk. Factors associated with cluster membership were evaluated for newly diagnosed patients.
  
  
  RESULTS
  Overall, 72% were men, 59% black and 39% men who have sex with men (MSM). A total of 557 (33%) sequences grouped in either 108 pairs (n = 216) or 67 clusters (n = 341). Clusters ranged from three to 36 (median 4) members. Composition was delineated primarily by race, with 28% exclusively black, and to a lesser extent by risk group. Both MSM and heterosexuals formed discrete clusters, although substantial mixing was observed. In multivariable analysis, patients with age 30 years or less (P = 0.009), acute infection (P = 0.02), local residence (P = 0.002) and transmitted drug resistance (P = 0.02) were more likely to be cluster members, whereas Latinos were less likely (P < 0.001).
  
  
  CONCLUSIONS
  Integration of molecular, clinical and demographic data offers a unique view into the structure of local transmission networks. Clustering by black race, youth and transmitted drug resistance and inability to identify Latino clusters will inform prevention, testing and linkage to care strategies.
authors: Division of Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina 27599-7030, USA. adennis@med.unc.edu
authors: Ann M
authors: AM
authors: Dennis
authors: Stéphane
authors: S
authors: Hué
authors: Christopher B
authors: CB
authors: Hurt
authors: Sonia
authors: S
authors: Napravnik
authors: Joseph
authors: J
authors: Sebastian
authors: Deenan
authors: D
authors: Pillay
authors: Joseph J
authors: JJ
authors: Eron
mesh_terms: D000328:Adult; D001741:Black or African American / Q000706:statistics & numerical data*; D016000:Cluster Analysis; D003430:Cross-Sectional Studies; D005260:Female; D006679:HIV Seropositivity / Q000235:genetics* / Q000635:transmission; D015497:HIV-1 / Q000235:genetics*; D006630:Hispanic or Latino / Q000706:statistics & numerical data*; D018451:Homosexuality, Male / Q000706:statistics & numerical data; D006801:Humans; D008297:Male; D010802:Phylogeny; D012725:Sexual Behavior / Q000706:statistics & numerical data; D014481:United States / Q000453:epidemiology; D044465:White People / Q000706:statistics & numerical data*; D054302:pol Gene Products, Human Immunodeficiency Virus / Q000235:genetics*
chemical_list: D054302:pol Gene Products, Human Immunodeficiency Virus