title: Transmission network parameters estimated from HIV sequences for a nationwide epidemic.
abstract: BACKGROUND
  Many studies of sexual behavior have shown that individuals vary greatly in their number of sexual partners over time, but it has proved difficult to obtain parameter estimates relating to the dynamics of human immunodeficiency virus (HIV) transmission except in small-scale contact tracing studies. Recent developments in molecular phylodynamics have provided new routes to obtain these parameter estimates, and current clinical practice provides suitable data for entire infected populations.
  
  
  METHODS
  A phylodynamic analysis was performed on partial pol gene sequences obtained for routine clinical care from 14,560 individuals, representing approximately 60% of the HIV-positive men who have sex with men (MSM) under care in the United Kingdom.
  
  
  RESULTS
  Among individuals linked to others in the data set, 29% are linked to only 1 individual, 41% are linked to 2-10 individuals, and 29% are linked to ≥10 individuals. The right-skewed degree distribution can be approximated by a power law, but the data are best fitted by a Waring distribution for all time depths. For time depths of 5-7 years, the distribution parameter ρ lies within the range that indicates infinite variance.
  
  
  CONCLUSIONS
  The transmission network among UK MSM is characterized by preferential association such that a randomly distributed intervention would not be expected to stop the epidemic.
authors.affiliation: Institute of Evolutionary Biology, University of Edinburgh, London, United Kingdom. a.leighbrown@ed.ac.uk
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Leigh Brown
authors.forename: Samantha J
authors.initials: SJ
authors.lastname: Lycett
authors.forename: Lucy
authors.initials: L
authors.lastname: Weinert
authors.forename: Gareth J
authors.initials: GJ
authors.lastname: Hughes
authors.forename: Esther
authors.initials: E
authors.lastname: Fearnhill
authors.forename: David T
authors.initials: DT
authors.lastname: Dunn
mesh_terms: D016000:Cluster Analysis; D016358:Contact Tracing; D058872:Epidemics; D015658:HIV Infections / Q000453:epidemiology* / Q000635:transmission*; D015497:HIV-1 / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D008297:Male; D017720:Molecular Epidemiology; D008969:Molecular Sequence Data; D058889:Molecular Typing; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D006113:United Kingdom / Q000453:epidemiology