title: Local phylogenetic analysis identifies distinct trends in transmitted HIV drug resistance: implications for public health interventions.
abstract: BACKGROUND
  HIV transmitted drug resistance (TDR) surveillance is usually conducted by sampling from a large population. However, overall TDR prevalence results may be inaccurate for many individual clinical setting. We analyzed HIV genotypes at a tertiary care setting in Ottawa, Ontario in order to evaluate local TDR patterns among sub-populations.
  
  
  METHODS
  Genotyping reports were digitized from ART naïve patients followed at the Immunodeficiency Clinic at the Ottawa Hospital, between 2008 and 2010. Quality controlled, digitized sequence data were assessed for TDR using the Stanford HIV Database. Patient characteristics were analyzed according to TDR patterns. Finally, a phylogenetic tree was constructed to elucidate the observed pattern of HIV TDR.
  
  
  RESULTS
  Among the 155 clinic patients there was no statistically significantly difference in demographics as compared to the Ontario provincial HIV population. The clinic prevalence of TDR was 12.3%; however, in contrast to the data from Ontario, TDR patterns were inverted with a 21% prevalence among MSM and 5.5% among IDU. Furthermore, nearly 80% of the observed TDR was a D67N/K219Q pattern with 87% of these infections arising from a distinct phylogenetic cluster.
  
  
  CONCLUSIONS
  Local patterns of TDR were distinct to what had been observed provincially. Phylogenetic analysis uncovered a cluster of related infections among MSM that appeared more likely to be recent infections. Results support a paradigm of routine local TDR surveillance to identify the sub-populations under care. Furthermore, the routine application of phylogenetic analysis in the TDR surveillance context provides insights into how best to target prevention strategies; and how to correctly measure outcomes.
authors.affiliation: National HIV & Retrovirology Laboratories, Public Health Agency of Canada, Ottawa, Canada. james.brooks@phac-aspc.gc.ca.
authors.forename: James I
authors.initials: JI
authors.lastname: Brooks
authors.forename: Harrison
authors.initials: H
authors.lastname: Niznick
authors.forename: Marianna
authors.initials: M
authors.lastname: Ofner
authors.forename: Harriet
authors.initials: H
authors.lastname: Merks
authors.forename: Jonathan B
authors.initials: JB
authors.lastname: Angel
mesh_terms: D000328:Adult; D019380:Anti-HIV Agents / Q000494:pharmacology; D024882:Drug Resistance, Viral; D005260:Female; D005838:Genotype; D015658:HIV Infections / Q000453:epidemiology / Q000821:virology*; D015497:HIV-1 / Q000145:classification / Q000187:drug effects / Q000235:genetics*; D006801:Humans; D008297:Male; D008875:Middle Aged; D017720:Molecular Epidemiology; D008969:Molecular Sequence Data; D009864:Ontario / Q000453:epidemiology; D010802:Phylogeny; D015995:Prevalence; D011634:Public Health; D055815:Young Adult
chemical_list: D019380:Anti-HIV Agents