title: Minority variants associated with transmitted and acquired HIV-1 nonnucleoside reverse transcriptase inhibitor resistance: implications for the use of second-generation nonnucleoside reverse transcriptase inhibitors.
abstract: OBJECTIVE
  K103N, the most common nonnucleoside reverse transcriptase inhibitor (NNRTI)-resistant mutation in patients with transmitted resistance and in patients receiving a failing NNRTI-containing regimen, is fully susceptible to the new NNRTI, etravirine. Therefore, we sought to determine how often NNRTI-resistant mutations other than K103N occur as minority variants in plasma samples for which standard genotypic resistance testing detects K103N alone.
  
  
  METHODS
  We performed ultradeep pyrosequencing (UDPS; 454 Life Sciences a Roche Company, Branford, CT) of plasma virus samples from 13 treatment-naive and 20 NNRTI-experienced patients in whom standard genotypic resistance testing revealed K103N but no other major NNRTI-resistance mutations.
  
  
  RESULTS
  Samples from 0 of 13 treatment-naive patients vs. 7 of 20 patients failing an NNRTI-containing regimen had minority variants with major etravirine-associated NNRTI-resistant mutations (P = 0.03, Fisher exact test): Y181C (7.0%), Y181C (3.6%) + G190A (3.2%), L100I (14%), L100I (32%) + 190A (5.4%), K101E (3.8%) + G190A (4.9%), K101E (4.0%) + G190S (4.8%), and G190S (3.1%).
  
  
  CONCLUSIONS
  In treatment-naive patients, UDPS did not detect additional major NNRTI-resistant mutations suggesting that etravirine may be effective in patients with transmitted K103N. In NNRTI-experienced patients, UDPS often detected additional major NNRTI-resistant mutations suggesting that etravirine may not be fully active in patients with acquired K103N.
authors.affiliation: Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA. viciv@stanford.edu
authors.forename: Vici
authors.initials: V
authors.lastname: Varghese
authors.forename: Rajin
authors.initials: R
authors.lastname: Shahriar
authors.forename: Soo-Yon
authors.initials: SY
authors.lastname: Rhee
authors.forename: Tommy
authors.initials: T
authors.lastname: Liu
authors.forename: Birgitte B
authors.initials: BB
authors.lastname: Simen
authors.forename: Michael
authors.initials: M
authors.lastname: Egholm
authors.forename: Bozena
authors.initials: B
authors.lastname: Hanczaruk
authors.forename: Lisbeth A
authors.initials: LA
authors.lastname: Blake
authors.forename: Baback
authors.initials: B
authors.lastname: Gharizadeh
authors.forename: Farbod
authors.initials: F
authors.lastname: Babrzadeh
authors.forename: Michael H
authors.initials: MH
authors.lastname: Bachmann
authors.forename: W Jeffrey
authors.initials: WJ
authors.lastname: Fessel
authors.forename: Robert W
authors.initials: RW
authors.lastname: Shafer
mesh_terms: D019380:Anti-HIV Agents / Q000494:pharmacology* / Q000627:therapeutic use; D024921:Drug Resistance, Multiple, Viral; D004359:Drug Therapy, Combination; D014644:Genetic Variation; D005838:Genotype; D015658:HIV Infections / Q000097:blood / Q000188:drug therapy* / Q000821:virology; D054303:HIV Reverse Transcriptase; D015497:HIV-1 / Q000187:drug effects* / Q000235:genetics*; D006801:Humans; D009154:Mutation; D009570:Nitriles; D011724:Pyridazines / Q000494:pharmacology / Q000627:therapeutic use; D011743:Pyrimidines
chemical_list: D019380:Anti-HIV Agents; D009570:Nitriles; D011724:Pyridazines; D011743:Pyrimidines; C451734:etravirine; D054303:HIV Reverse Transcriptase