title: Optimization of the oligonucleotide ligation assay, a rapid and inexpensive test for detection of HIV-1 drug resistance mutations, for non-North American variants.
abstract: OBJECTIVE
  We evaluated the feasibility of the oligonucleotide ligation assay (OLA), a specific, sensitive, and economical ligase-based point mutation assay designed to detect HIV-1 drug-resistance mutations at 12 codons of HIV-1 subtype B pol, for potential use in resource-poor settings.
  
  
  METHODS
  Specimens from HIV-1-infected individuals collected by 7 international laboratories, including subtypes A, B, C, D, F, G, J, and recombinants AE and AG, were tested by the OLA developed for HIV-1 subtype B. Common polymorphisms that interfered with reactivity of the OLA were identified and modified probes designed and evaluated.
  
  
  RESULTS
  92.5% (2,410) of 2,604 codons in specimens from 217 individuals were successfully genotyped by the subtype B OLA. A high rate (range 8.3%-31.2%) of indeterminate results (negative OLA reaction for both mutant and wild type) was observed for 5 codons. Modified probes at reverse transcriptase codons 151 and 184 and protease codon 90 increased the rate of valid OLA to 96.1%.
  
  
  CONCLUSIONS
  The OLA designed for HIV-1 subtype B genotyped most pol codons in non-B subtypes from Asia and Africa but was improved by addition of several modified probes. International laboratories experienced in molecular techniques were able to perform the OLA.
authors.affiliation: Division of Infectious Diseases and Virology, University of Washington, Seattle, WA, USA.
authors.forename: Ingrid A
authors.initials: IA
authors.lastname: Beck
authors.forename: Claudia
authors.initials: C
authors.lastname: Crowell
authors.forename: Robin
authors.initials: R
authors.lastname: Kittoe
authors.forename: Helba
authors.initials: H
authors.lastname: Bredell
authors.forename: Molefe
authors.initials: M
authors.lastname: Machaba
authors.forename: Carolyn
authors.initials: C
authors.lastname: Willamson
authors.forename: Wouter
authors.initials: W
authors.lastname: Janssens
authors.forename: Sabelle
authors.initials: S
authors.lastname: Jallow
authors.forename: Guido
authors.initials: G
authors.lastname: van der Groen
authors.forename: Yiming
authors.initials: Y
authors.lastname: Shao
authors.forename: Mini
authors.initials: M
authors.lastname: Jacob
authors.forename: N M
authors.initials: NM
authors.lastname: Samuel
authors.forename: Ivette Lorenzana
authors.initials: IL
authors.lastname: de Rivera
authors.forename: Nicole
authors.initials: N
authors.lastname: Ngo-Giang-Huong
authors.forename: Sharon
authors.initials: S
authors.lastname: Cassol
authors.forename: George
authors.initials: G
authors.lastname: Alemnji
authors.forename: Lisa M
authors.initials: LM
authors.lastname: Frenkel
mesh_terms: D019380:Anti-HIV Agents / Q000494:pharmacology*; D003062:Codon; D011088:DNA Ligases; D018076:DNA, Complementary / Q000235:genetics; D024882:Drug Resistance, Viral; D005240:Feasibility Studies; D015751:Genes, pol / Q000235:genetics; D015658:HIV Infections / Q000821:virology*; D016333:HIV Protease / Q000235:genetics; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D015345:Oligonucleotide Probes; D009841:Oligonucleotides; D017354:Point Mutation; D016133:Polymerase Chain Reaction / Q000379:methods*; D012194:RNA-Directed DNA Polymerase / Q000235:genetics; D012680:Sensitivity and Specificity
chemical_list: D019380:Anti-HIV Agents; D003062:Codon; D018076:DNA, Complementary; D015345:Oligonucleotide Probes; D009841:Oligonucleotides; D012194:RNA-Directed DNA Polymerase; D016333:HIV Protease; D011088:DNA Ligases