title: Molecular epidemiology reveals long-term changes in HIV type 1 subtype B transmission in Switzerland.
abstract: BACKGROUND
  Sequence data from resistance testing offer unique opportunities to characterize the structure of human immunodeficiency virus (HIV) infection epidemics.
  
  
  METHODS
  We analyzed a representative set of HIV type 1 (HIV-1) subtype B pol sequences from 5700 patients enrolled in the Swiss HIV Cohort Study. We pooled these sequences with the same number of sequences from foreign epidemics, inferred a phylogeny, and identified Swiss transmission clusters as clades having a minimal size of 10 and containing >or=80% Swiss sequences.
  
  
  RESULTS
  More than one-half of Swiss patients were included within 60 transmission clusters. Most transmission clusters were significantly dominated by specific transmission routes, which were used to identify the following patient groups: men having sex with men (MSM) (38 transmission clusters; average cluster size, 29 patients) or patients acquiring HIV through heterosexual contact (HETs) and injection drug users (IDUs) (12 transmission clusters; average cluster size, 144 patients). Interestingly, there were no transmission clusters dominated by sequences from HETs only. Although 44% of all HETs who were infected between 1983 and 1986 clustered with injection drug users, this percentage decreased to 18% for 2003-2006 (P<.001), indicating a diminishing role of injection drug users in transmission among HETs over time.
  
  
  CONCLUSIONS
  Our analysis suggests (1) the absence of a self-sustaining epidemic of HIV-1 subtype B in HETs in Switzerland and (2) a temporally decreasing clustering of HIV infections in HETs and IDUs.
authors.affiliation: Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland. roger.kouyos@env.ethz.ch
authors.forename: Roger D
authors.initials: RD
authors.lastname: Kouyos
authors.forename: Viktor
authors.initials: V
authors.lastname: von Wyl
authors.forename: Sabine
authors.initials: S
authors.lastname: Yerly
authors.forename: Jürg
authors.initials: J
authors.lastname: Böni
authors.forename: Patrick
authors.initials: P
authors.lastname: Taffé
authors.forename: Cyril
authors.initials: C
authors.lastname: Shah
authors.forename: Philippe
authors.initials: P
authors.lastname: Bürgisser
authors.forename: Thomas
authors.initials: T
authors.lastname: Klimkait
authors.forename: Rainer
authors.initials: R
authors.lastname: Weber
authors.forename: Bernard
authors.initials: B
authors.lastname: Hirschel
authors.forename: Matthias
authors.initials: M
authors.lastname: Cavassini
authors.forename: Hansjakob
authors.initials: H
authors.lastname: Furrer
authors.forename: Manuel
authors.initials: M
authors.lastname: Battegay
authors.forename: Pietro L
authors.initials: PL
authors.lastname: Vernazza
authors.forename: Enos
authors.initials: E
authors.lastname: Bernasconi
authors.forename: Martin
authors.initials: M
authors.lastname: Rickenbach
authors.forename: Bruno
authors.initials: B
authors.lastname: Ledergerber
authors.forename: Sebastian
authors.initials: S
authors.lastname: Bonhoeffer
authors.forename: Huldrych F
authors.initials: HF
authors.lastname: Günthard
mesh_terms: D015658:HIV Infections / Q000453:epidemiology / Q000635:transmission* / Q000821:virology*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics*; D020010:Heterosexuality; D018451:Homosexuality, Male; D006801:Humans; D008297:Male; D017720:Molecular Epidemiology; D010802:Phylogeny; D012307:Risk Factors; D015819:Substance Abuse, Intravenous; D013557:Switzerland / Q000453:epidemiology; D013997:Time Factors