title: Transmitted drug resistance and phylogenetic relationships among acute and early HIV-1-infected individuals in New York City.
abstract: BACKGROUND
  Transmitted drug resistance (TDR) is critical to managing HIV-1-infected individuals and being a public health concern. We report on TDR prevalence and include analyses of phylogenetic clustering of HIV-1 in a predominantly men who have sex with men cohort diagnosed during acute/recent HIV-1 infection in New York City.
  
  
  METHODS
  Genotypic resistance testing was conducted on plasma samples of 600 individuals with acute/recent HIV-1 infection (1995-2010). Sequences were used for resistance and phylogenetic analyses. Demographic and clinical data were abstracted from medical records. TDR was defined according to International AIDS Society-USA and Stanford HIV database guidelines. Phylogenetic and other analyses were conducted using PAUP*4.0 and SAS, respectively.
  
  
  RESULTS
  The mean duration since HIV-1 infection was 66.5 days. TDR prevalence was 14.3% and stably ranged between 10.8% and 21.6% (P(trend) = 0.42). Nucleoside reverse transcriptase inhibitors resistance declined from 15.5% to 2.7% over the study period (P(trend) = 0.005). M41L (3.7%), T215Y (4.0%), and K103N/S (4.7%) were the most common mutations. K103N/S prevalence increased from 1.9% to 8.0% between 1995 and 2010 (P(trend) = 0.04). Using a rigorous definition of clustering, 19.3% (112 of 581) of subtype B viral sequences cosegregated into transmission clusters and clusters increased over time. There were fewer and smaller transmission clusters than had been reported in a similar cohort in Montreal but similar to reports from elsewhere.
  
  
  CONCLUSIONS
  TDR is stable in this cohort and remains a significant concern to both individual patient management and the public health.
authors.affiliation: The Aaron Diamond AIDS Research Center, Rockefeller University, New York, NY 10016, USA.
authors.forename: Delivette
authors.initials: D
authors.lastname: Castor
authors.forename: Andrea
authors.initials: A
authors.lastname: Low
authors.forename: Teresa
authors.initials: T
authors.lastname: Evering
authors.forename: Sharon
authors.initials: S
authors.lastname: Karmon
authors.forename: Brandi
authors.initials: B
authors.lastname: Davis
authors.forename: Amir
authors.initials: A
authors.lastname: Figueroa
authors.forename: Melissa
authors.initials: M
authors.lastname: LaMar
authors.forename: Donald
authors.initials: D
authors.lastname: Garmon
authors.forename: Saurabh
authors.initials: S
authors.lastname: Mehandru
authors.forename: Martin
authors.initials: M
authors.lastname: Markowitz
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D024882:Drug Resistance, Viral; D005260:Female; D005838:Genotype; D015658:HIV Infections / Q000453:epidemiology* / Q000635:transmission* / Q000821:virology; D015497:HIV-1 / Q000145:classification* / Q000187:drug effects* / Q000235:genetics / Q000302:isolation & purification; D018451:Homosexuality, Male; D006801:Humans; D015994:Incidence; D008297:Male; D008875:Middle Aged; D009519:New York City / Q000453:epidemiology; D010802:Phylogeny; D015995:Prevalence; D017422:Sequence Analysis, DNA; D055815:Young Adult