title: Evidence for Reduced Drug Susceptibility without Emergence of Major Protease Mutations following Protease Inhibitor Monotherapy Failure in the SARA Trial.
abstract: BACKGROUND
  Major protease mutations are rarely observed following failure with protease inhibitors (PI), and other viral determinants of failure to PI are poorly understood. We therefore characterized Gag-Protease phenotypic susceptibility in subtype A and D viruses circulating in East Africa following viral rebound on PIs.
  
  
  METHODS
  Samples from baseline and treatment failure in patients enrolled in the second line LPV/r trial SARA underwent phenotypic susceptibility testing. Data were expressed as fold-change in susceptibility relative to a LPV-susceptible reference strain.
  
  
  RESULTS
  We cloned 48 Gag-Protease containing sequences from seven individuals and performed drug resistance phenotyping from pre-PI and treatment failure timepoints in seven patients. For the six patients where major protease inhibitor resistance mutations did not emerge, mean fold-change EC50 to LPV was 4.07 fold (95% CI, 2.08-6.07) at the pre-PI timepoint. Following viral failure the mean fold-change in EC50 to LPV was 4.25 fold (95% CI, 1.39-7.11, p = 0.91). All viruses remained susceptible to DRV. In our assay system, the major PI resistance mutation I84V, which emerged in one individual, conferred a 10.5-fold reduction in LPV susceptibility. One of the six patients exhibited a significant reduction in susceptibility between pre-PI and failure timepoints (from 4.7 fold to 9.6 fold) in the absence of known major mutations in protease, but associated with changes in Gag: V7I, G49D, R69Q, A120D, Q127K, N375S and I462S. Phylogenetic analysis provided evidence of the emergence of genetically distinct viruses at the time of treatment failure, indicating ongoing viral evolution in Gag-protease under PI pressure.
  
  
  CONCLUSIONS
  Here we observe in one patient the development of significantly reduced susceptibility conferred by changes in Gag which may have contributed to treatment failure on a protease inhibitor containing regimen. Further phenotype-genotype studies are required to elucidate genetic determinants of protease inhibitor failure in those who fail without traditional resistance mutations whilst PI use is being scaled up globally.
authors.affiliation: University College London, London, United Kingdom.
authors.forename: Katherine A
authors.initials: KA
authors.lastname: Sutherland
authors.affiliation: Uganda Research Unit on AIDS, Medical Research Council (MRC), Uganda Virus Research Institute, Entebbe, Uganda.
authors.forename: Chris M
authors.initials: CM
authors.lastname: Parry
authors.affiliation: University College London, London, United Kingdom.
authors.forename: Adele
authors.initials: A
authors.lastname: McCormick
authors.affiliation: Uganda Research Unit on AIDS, Medical Research Council (MRC), Uganda Virus Research Institute, Entebbe, Uganda.
authors.forename: Anne
authors.initials: A
authors.lastname: Kapaata
authors.affiliation: Uganda Research Unit on AIDS, Medical Research Council (MRC), Uganda Virus Research Institute, Entebbe, Uganda.
authors.forename: Fred
authors.initials: F
authors.lastname: Lyagoba
authors.affiliation: Uganda Research Unit on AIDS, Medical Research Council (MRC), Uganda Virus Research Institute, Entebbe, Uganda.
authors.forename: Pontiano
authors.initials: P
authors.lastname: Kaleebu
authors.affiliation: School of Population Health, University of Queensland, Brisbane, Australia.
authors.forename: Charles F
authors.initials: CF
authors.lastname: Gilks
authors.affiliation: MRC Clinical Trials Unit at UCL, London, United Kingdom.
authors.forename: Ruth
authors.initials: R
authors.lastname: Goodall
authors.affiliation: MRC Clinical Trials Unit at UCL, London, United Kingdom.
authors.forename: Moira
authors.initials: M
authors.lastname: Spyer
authors.affiliation: Joint Clinical Research Centre, Kampala, Uganda.
authors.forename: Cissy
authors.initials: C
authors.lastname: Kityo
authors.affiliation: University College London, London, United Kingdom; Wellcome Trust Africa Centre for Health and Population Sciences, University of KwaZulu Natal, Mtubatuba, South Africa.
authors.forename: Deenan
authors.initials: D
authors.lastname: Pillay
authors.affiliation: University College London, London, United Kingdom.
authors.forename: Ravindra K
authors.initials: RK
authors.lastname: Gupta
mesh_terms: D024882:Drug Resistance, Viral / Q000235:genetics*; D005838:Genotype; D015658:HIV Infections / Q000188:drug therapy*; D016333:HIV Protease / Q000235:genetics*; D017320:HIV Protease Inhibitors / Q000627:therapeutic use*; D006801:Humans; D061466:Lopinavir / Q000627:therapeutic use; D009154:Mutation; D010641:Phenotype; D019438:Ritonavir / Q000627:therapeutic use; D017211:Treatment Failure; D054301:gag Gene Products, Human Immunodeficiency Virus / Q000235:genetics
chemical_list: D017320:HIV Protease Inhibitors; D054301:gag Gene Products, Human Immunodeficiency Virus; D061466:Lopinavir; D016333:HIV Protease; D019438:Ritonavir