title: Phenotypic and genotypic analysis of clinical HIV-1 isolates reveals extensive protease inhibitor cross-resistance: a survey of over 6000 samples.
abstract: OBJECTIVE
  To evaluate in HIV-1 the extent of phenotypic and genotypic antiretroviral drug resistance and cross-resistance towards the protease inhibitors (PIs) saquinavir, ritonavir, indinavir and nelfinavir among a set of patient samples originating from European and US routine clinical practice and submitted for phenotypic drug resistance testing and/or genotypic analysis. The mutational pattern(s) underlying both resistance and cross-resistance to PIs was investigated.
  
  
  METHODS
  Over 6000 patient isolates with plasma viral load greater than 1000 copies/ml plasma were analysed. Phenotypic resistance was evaluated by a recombinant virus assay. Phenotypic resistance is expressed as the fold-increase of the 50% inhibitory concentration (IC50) value of a compound for a patient-derived recombinant virus isolate compared with that for a wild-type laboratory virus. Genotypic analysis is reported as amino acid changes at positions in the HIV-1 protease compared to a wild-type reference.
  
  
  RESULTS
  Phenotypic resistance to any single PI was observed in 17 to 25% of the clinical isolates investigated. Phenotypic cross-resistance among PIs (> 10-fold increase in IC50 value) was detected in 59 to 80% of the samples resistant (> 10-fold increase in IC50 value) to at least one PI. The prevalent mutations in PI-resistant isolates involved substitutions at codons 10, 36, 46, 54, 71, 77, 82 and 90. The most frequent mutational pattern in samples with PI cross-resistance involved combined substitutions at positions 10 and 90, extended with substitutions at positions 54, 71, 77, 82 or 84.
  
  
  CONCLUSIONS
  Extensive use of first-generation PIs leads to the emergence of HIV-1 isolates possessing cross-resistance to all members of this class. Identification of particular mutational profiles among these isolates may assist in the design of new generation inhibitors with specific activity against protease-mutant HIV strains.
authors.affiliation: Virco NV, Mechelen, Belgium. kurt.hertogs@virco.be
authors.forename: K
authors.initials: K
authors.lastname: Hertogs
authors.forename: S
authors.initials: S
authors.lastname: Bloor
authors.forename: S D
authors.initials: SD
authors.lastname: Kemp
authors.forename: C
authors.initials: C
authors.lastname: Van den Eynde
authors.forename: T M
authors.initials: TM
authors.lastname: Alcorn
authors.forename: R
authors.initials: R
authors.lastname: Pauwels
authors.forename: M
authors.initials: M
authors.lastname: Van Houtte
authors.forename: S
authors.initials: S
authors.lastname: Staszewski
authors.forename: V
authors.initials: V
authors.lastname: Miller
authors.forename: B A
authors.initials: BA
authors.lastname: Larder
mesh_terms: D019943:Amino Acid Substitution; D004352:Drug Resistance, Microbial / Q000235:genetics*; D005060:Europe; D005838:Genotype; D015658:HIV Infections / Q000097:blood / Q000821:virology; D016333:HIV Protease / Q000235:genetics*; D017320:HIV Protease Inhibitors / Q000494:pharmacology*; D015497:HIV-1 / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D009154:Mutation; D010641:Phenotype; D014481:United States; D019562:Viral Load
chemical_list: D017320:HIV Protease Inhibitors; D016333:HIV Protease