title: The impact of clinical, demographic and risk factors on rates of HIV transmission: a population-based phylogenetic analysis in British Columbia, Canada.
abstract: BACKGROUND
  The diversification of human immunodeficiency virus (HIV) is shaped by its transmission history. We therefore used a population based province wide HIV drug resistance database in British Columbia (BC), Canada, to evaluate the impact of clinical, demographic, and behavioral factors on rates of HIV transmission.
  
  
  METHODS
  We reconstructed molecular phylogenies from 27,296 anonymized bulk HIV pol sequences representing 7747 individuals in BC-about half the estimated HIV prevalence in BC. Infections were grouped into clusters based on phylogenetic distances, as a proxy for variation in transmission rates. Rates of cluster expansion were reconstructed from estimated dates of HIV seroconversion.
  
  
  RESULTS
  Our criteria grouped 4431 individuals into 744 clusters largely separated with respect to risk factors, including large established clusters predominated by injection drug users and more-recently emerging clusters comprising men who have sex with men. The mean log10 viral load of an individual's phylogenetic neighborhood (composed of 5 other individuals with shortest phylogenetic distances) increased their odds of appearing in a cluster by >2-fold per log10 viruses per milliliter.
  
  
  CONCLUSIONS
  Hotspots of ongoing HIV transmission can be characterized in near real time by the secondary analysis of HIV resistance genotypes, providing an important potential resource for targeting public health initiatives for HIV prevention.
authors.affiliation: BC Centre for Excellence in HIV/AIDS Department of Medicine, University of British Columbia, Vancouver.
authors.forename: Art F Y
authors.initials: AF
authors.lastname: Poon
authors.affiliation: BC Centre for Excellence in HIV/AIDS.
authors.forename: Jeffrey B
authors.initials: JB
authors.lastname: Joy
authors.affiliation: BC Centre for Excellence in HIV/AIDS.
authors.forename: Conan K
authors.initials: CK
authors.lastname: Woods
authors.affiliation: BC Centre for Excellence in HIV/AIDS.
authors.forename: Susan
authors.initials: S
authors.lastname: Shurgold
authors.affiliation: BC Centre for Excellence in HIV/AIDS.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Colley
authors.affiliation: BC Centre for Excellence in HIV/AIDS.
authors.forename: Chanson J
authors.initials: CJ
authors.lastname: Brumme
authors.affiliation: BC Centre for Excellence in HIV/AIDS Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada.
authors.forename: Robert S
authors.initials: RS
authors.lastname: Hogg
authors.affiliation: BC Centre for Excellence in HIV/AIDS Department of Medicine, University of British Columbia, Vancouver.
authors.forename: Julio S G
authors.initials: JS
authors.lastname: Montaner
authors.affiliation: BC Centre for Excellence in HIV/AIDS Department of Medicine, University of British Columbia, Vancouver.
authors.forename: P Richard
authors.initials: PR
authors.lastname: Harrigan
mesh_terms: D000328:Adult; D019380:Anti-HIV Agents / Q000494:pharmacology / Q000627:therapeutic use; D001955:British Columbia; D016000:Cluster Analysis; D024882:Drug Resistance, Viral; D005260:Female; D014644:Genetic Variation; D006678:HIV / Q000235:genetics*; D015658:HIV Infections / Q000188:drug therapy / Q000453:epidemiology / Q000635:transmission*; D006801:Humans; D008297:Male; D008875:Middle Aged; D010802:Phylogeny; D012307:Risk Factors
chemical_list: D019380:Anti-HIV Agents
keywords: human immunodeficiency virus (HIV); injection drug use; men who have sex with men (MSM); molecular epidemiology; phylogenetic clustering; transmission network