title: A public health model for the molecular surveillance of HIV transmission in San Diego, California.
abstract: BACKGROUND
  Current public health efforts often use molecular technologies to identify and contain communicable disease networks, but not for HIV. Here, we investigate how molecular epidemiology can be used to identify highly related HIV networks within a population and how voluntary contact tracing of sexual partners can be used to selectively target these networks.
  
  
  METHODS
  We evaluated the use of HIV-1 pol sequences obtained from participants of a community-recruited cohort (n = 268) and a primary infection research cohort (n = 369) to define highly related transmission clusters and the use of contact tracing to link other individuals (n = 36) within these clusters. The presence of transmitted drug resistance was interpreted from the pol sequences (Calibrated Population Resistance v3.0).
  
  
  RESULTS
  Phylogenetic clustering was conservatively defined when the genetic distance between any two pol sequences was less than 1%, which identified 34 distinct transmission clusters within the combined community-recruited and primary infection research cohorts containing 160 individuals. Although sequences from the epidemiologically linked partners represented approximately 5% of the total sequences, they clustered with 60% of the sequences that clustered from the combined cohorts (odds ratio 21.7; P < or = 0.01). Major resistance to at least one class of antiretroviral medication was found in 19% of clustering sequences.
  
  
  CONCLUSIONS
  Phylogenetic methods can be used to identify individuals who are within highly related transmission groups, and contact tracing of epidemiologically linked partners of recently infected individuals can be used to link into previously defined transmission groups. These methods could be used to implement selectively targeted prevention interventions.
authors.affiliation: University of California San Diego, La Jolla, CA 92093-0679, USA. davey@ucsd.edu
authors.forename: Davey M
authors.initials: DM
authors.lastname: Smith
authors.forename: Susanne J
authors.initials: SJ
authors.lastname: May
authors.forename: Samantha
authors.initials: S
authors.lastname: Tweeten
authors.forename: Lydia
authors.initials: L
authors.lastname: Drumright
authors.forename: Mary E
authors.initials: ME
authors.lastname: Pacold
authors.forename: Sergei L
authors.initials: SL
authors.lastname: Kosakovsky Pond
authors.forename: Rick L
authors.initials: RL
authors.lastname: Pesano
authors.forename: Yolanda S
authors.initials: YS
authors.lastname: Lie
authors.forename: Douglas D
authors.initials: DD
authors.lastname: Richman
authors.forename: Simon D W
authors.initials: SD
authors.lastname: Frost
authors.forename: Christopher H
authors.initials: CH
authors.lastname: Woelk
authors.forename: Susan J
authors.initials: SJ
authors.lastname: Little
mesh_terms: D000328:Adult; D002140:California / Q000453:epidemiology; D016358:Contact Tracing / Q000379:methods*; D024882:Drug Resistance, Viral; D004812:Epidemiologic Methods; D005260:Female; D015658:HIV Infections / Q000453:epidemiology / Q000635:transmission* / Q000821:virology; D015497:HIV-1 / Q000145:classification / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D008297:Male; D017146:Models, Organizational; D010802:Phylogeny; D012747:Sexual Partners; D054302:pol Gene Products, Human Immunodeficiency Virus / Q000235:genetics
chemical_list: D054302:pol Gene Products, Human Immunodeficiency Virus