title: Single genome sequencing of HIV-1 gag and protease resistance mutations at virologic failure during the OK04 trial of simplified versus standard maintenance therapy.
abstract: BACKGROUND
  Ritonavir-boosted lopinavir (LPV/RTV) alone has been evaluated as simplified maintenance therapy for HIV-1 infection, but there are concerns about greater potential for emergence of protease inhibitor (PI) resistance. The OK04 trial evaluated maintenance therapy with LPV/RTV alone versus standard therapy (ST) with two NRTIs plus LPV/RTV in 205 patients, of whom 15 had virological rebound by week 48 (11 versus 4 patients, respectively). We developed a single genome sequencing (SGS) assay of HIV-1 gag and protease to assess the emergence of low frequency drug-resistant variants during virological rebound.
  
  
  METHODS
  Plasma samples from 15 subjects at virological rebound were analysed by SGS of HIV-1 gag and protease genes. A total of 45 SGS sequences were planned per sample, providing 90% power to detect variants comprising >5% of the virus population.
  
  
  RESULTS
  Overall, 521 single sequences obtained from 13 patients (range 4-48 sequences/patient) revealed similar frequencies of major protease resistance mutations in samples from the LPV/RTV alone (3/11) and ST (3/4) arms (P=0.10), with a median number of minor protease resistance mutations of 3.0 versus 3.5, respectively (P=0.23). Median number of gag PI resistance mutations were similar between the LPV/RTV alone and ST arms at cleavage sites (3.0 versus 2.5; P=0.83), non-cleavage sites (21 versus 16.5; P=0.71) and the transframe protein-p6 pol region cleavage sites (4.0 versus 3.0; P=0.6).
  
  
  CONCLUSIONS
  Although more subjects with simplified maintenance therapy with LPV/RTV alone had virological rebound compared to the ST arm, this was not associated with more frequent emergence of variants encoding PI resistance mutations in gag or protease detected by SGS.
authors.affiliation: Department of Medicine, Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, PA, USA. jem44@pitt.edu
authors.forename: John E
authors.initials: JE
authors.lastname: McKinnon
authors.forename: Rafael
authors.initials: R
authors.lastname: Delgado
authors.forename: Federico
authors.initials: F
authors.lastname: Pulido
authors.forename: Wei
authors.initials: W
authors.lastname: Shao
authors.forename: Jose R
authors.initials: JR
authors.lastname: Arribas
authors.forename: John W
authors.initials: JW
authors.lastname: Mellors
mesh_terms: D002986:Clinical Trials as Topic; D024882:Drug Resistance, Viral / Q000235:genetics*; D015751:Genes, pol; D015658:HIV Infections / Q000188:drug therapy / Q000235:genetics / Q000821:virology; D016333:HIV Protease / Q000235:genetics; D017320:HIV Protease Inhibitors / Q000378:metabolism* / Q000627:therapeutic use; D015497:HIV-1 / Q000187:drug effects / Q000235:genetics; D006801:Humans; D008074:Lipoproteins / Q000235:genetics / Q000378:metabolism; D009154:Mutation; D059039:Standard of Care; D017211:Treatment Failure; D019562:Viral Load; D054301:gag Gene Products, Human Immunodeficiency Virus / Q000378:metabolism*
chemical_list: D017320:HIV Protease Inhibitors; D008074:Lipoproteins; D054301:gag Gene Products, Human Immunodeficiency Virus; C051928:lipoprotein-associated coagulation inhibitor; D016333:HIV Protease