title: CRF01_AE dominates the HIV-1 epidemic in Indonesia.
abstract: BACKGROUND
  The HIV epidemic in Indonesia remains concentrated in vulnerable populations, namely injecting drug users (IDUs), commercial sex workers (CSWs) and men who have sex with men (MSM). We aimed to determine the HIV-1 subtypes present in Indonesia and to establish the extent of the viral overlap between individuals with different risk factors.
  
  
  METHODS
  Venous blood samples were collected from HIV-positive individuals primarily from sexually transmissible infection clinics and drug rehabilitation centres in Bali and Jakarta, and applied to filter paper. A polymerase chain reaction-based assay designed to amplify a 330-bp region of the HIV-1 envelope was used to determine HIV-1 subtype result and to perform phylogenetic analysis.
  
  
  RESULTS
  Of the 175 individuals recruited to the study, a subtype result was obtained for 108 (62%). Four subtypes were found to exist in the population, CRF01_AE (n=96, 88.9%), B (n=10, 9.3%), C (n=1, 0.9%) and G (n=1, 0.9%). Of these 108 individuals, 65 (60%) were IDUs, and the remaining 40% were CSWs, MSM, transgender individuals, people with multiple sexual partners or those with no obvious risk factor. CRF01_AE was found to be more common among IDUs with 100% of individuals infected with this subtype. Subtype B was more common among MSM and CSWs (P=<0.001). Phylogenetic analysis revealed a lack of viral segregation between risk groups.
  
  
  CONCLUSIONS
  In Indonesia, CRF01_AE continues to dominate the HIV epidemic, although HIV subtype B is responsible for a significant number of sexually acquired infections.
authors.affiliation: Udayana University, Jalan P.B, Sudirman, Denpasar, Bali, Indonesia.
authors.forename: Tuti Parwati
authors.initials: TP
authors.lastname: Merati
authors.forename: Claire E
authors.initials: CE
authors.lastname: Ryan
authors.forename: Tim
authors.initials: T
authors.lastname: Spelmen
authors.forename: Dewa N
authors.initials: DN
authors.lastname: Wirawan
authors.forename: I Made
authors.initials: IM
authors.lastname: Bakta
authors.forename: Brad
authors.initials: B
authors.lastname: Otto
authors.forename: Robert B
authors.initials: RB
authors.lastname: Oelrichs
authors.forename: Suzanne M
authors.initials: SM
authors.lastname: Crowe
mesh_terms: D003431:Cross-Cultural Comparison; D003430:Cross-Sectional Studies; D058872:Epidemics / Q000706:statistics & numerical data*; D005260:Female; D015658:HIV Infections / Q000635:transmission* / Q000821:virology*; D015528:HIV Seroprevalence; D015497:HIV-1 / Q000145:classification / Q000235:genetics*; D018451:Homosexuality, Male / Q000706:statistics & numerical data; D006801:Humans; D007214:Indonesia; D008297:Male; D017720:Molecular Epidemiology; D011995:Recombination, Genetic / Q000235:genetics*; D012307:Risk Factors; D017422:Sequence Analysis, DNA; D011477:Sex Work / Q000706:statistics & numerical data; D015819:Substance Abuse, Intravenous / Q000150:complications / Q000453:epidemiology; D063106:Transgender Persons / Q000706:statistics & numerical data; D047568:Unsafe Sex / Q000706:statistics & numerical data