title: Oligonucleotide ligation assay detects HIV drug resistance associated with virologic failure among antiretroviral-naive adults in Kenya.
abstract: BACKGROUND
  Transmitted drug resistance (TDR) is increasing in some areas of Africa. Detection of TDR may predict virologic failure of first-line nonnucleoside reverse transcriptase inhibitor (NNRTI)-based antiretroviral therapy (ART). We evaluated the utility of a relatively inexpensive oligonucleotide ligation assay (OLA) to detect clinically relevant TDR at the time of ART initiation.
  
  
  METHODS
  Pre-ART plasmas from ART-naive Kenyans initiating an NNRTI-based fixed-dose combination ART in a randomized adherence trial conducted in 2006 were retrospectively analyzed by OLA for mutations conferring resistance to NNRTI (K103N, Y181C, and G190A) and lamivudine (M184V). Post-ART plasmas were analyzed for virologic failure (≥1000 copies/mL) at 6-month intervals over 18-month follow-up. Pre-ART plasmas of those with virologic failure were evaluated for drug resistance by consensus and 454-pyrosequencing.
  
  
  RESULTS
  Among 386 participants, TDR was detected by OLA in 3.89% (95% confidence interval: 2.19 to 6.33) and was associated with a 10-fold higher rate of virologic failure (hazard ratio: 10.39; 95% confidence interval: 3.23 to 32.41; P < 0.001) compared with those without TDR. OLA detected 24 TDR mutations (K103N: n = 13; Y181C: n = 5; G190A: n = 3; M184V: n = 3) in 15 subjects (NNRTI: n = 15; 3TC: n = 3). Among 51 participants who developed virologic failure, consensus sequencing did not detect additional TDR mutations conferring high-level resistance, and pyrosequencing only detected additional mutations at frequencies <2%. Mutant frequencies <2% at ART initiation were significantly less likely to be found at the time of virologic failure compared with frequencies ≥2% (22% vs. 63%; P < 0.001).
  
  
  CONCLUSIONS
  Detection of TDR by a point mutation assay may prevent the use of suboptimal ART.
authors.affiliation: Departments of *Global Health; †Medicine; ‡Epidemiology, University of Washington, Seattle, WA; §Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA; ‖Department of Obstetrics and Gynaecology, University of Nairobi, Nairobi, Kenya; ¶Department of Biostatistics, University of Washington, Seattle, WA; #Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA; **Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA; ††Coptic Hospital, Nairobi, Kenya; Departments of ‡‡Pediatrics; and §§Laboratory Medicine, University of Washington, Seattle, WA.
authors.forename: Michael H
authors.initials: MH
authors.lastname: Chung
authors.forename: Ingrid A
authors.initials: IA
authors.lastname: Beck
authors.forename: Sandra
authors.initials: S
authors.lastname: Dross
authors.forename: Kenneth
authors.initials: K
authors.lastname: Tapia
authors.forename: James N
authors.initials: JN
authors.lastname: Kiarie
authors.forename: Barbra A
authors.initials: BA
authors.lastname: Richardson
authors.forename: Julie
authors.initials: J
authors.lastname: Overbaugh
authors.forename: Samah R
authors.initials: SR
authors.lastname: Sakr
authors.forename: Grace C
authors.initials: GC
authors.lastname: John-Stewart
authors.forename: Lisa M
authors.initials: LM
authors.lastname: Frenkel
mesh_terms: D000328:Adult; D019380:Anti-HIV Agents / Q000627:therapeutic use*; D023241:Antiretroviral Therapy, Highly Active; D004279:DNA, Viral / Q000032:analysis; D024882:Drug Resistance, Viral; D005260:Female; D015658:HIV Infections / Q000188:drug therapy* / Q000821:virology; D015497:HIV-1 / Q000187:drug effects* / Q000235:genetics / Q000302:isolation & purification; D006801:Humans; D007630:Kenya; D022521:Ligase Chain Reaction / Q000379:methods; D008297:Male; D008875:Middle Aged; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D009154:Mutation; D015345:Oligonucleotide Probes / Q000235:genetics; D012189:Retrospective Studies; D018894:Reverse Transcriptase Inhibitors / Q000627:therapeutic use*; D017211:Treatment Failure; D019562:Viral Load
chemical_list: D019380:Anti-HIV Agents; D004279:DNA, Viral; D015345:Oligonucleotide Probes; D018894:Reverse Transcriptase Inhibitors