title: Contribution of Gag and Protease to HIV-1 Phenotypic Drug Resistance in Pediatric Patients Failing Protease Inhibitor-Based Therapy.
abstract: Protease inhibitors (PIs) are used as a first-line regimen in HIV-1-infected children. Here we investigated the phenotypic consequences of amino acid changes in Gag and protease on lopinavir (LPV) and ritonavir (RTV) susceptibility among pediatric patients failing PI therapy. The Gag-protease from isolates from 20 HIV-1 subtype C-infected pediatric patients failing an LPV and/or RTV-based regimen was phenotyped using a nonreplicativein vitroassay. Changes in sensitivity to LPV and RTV relative to that of the matched baseline (pretherapy) sample were calculated. Gag and protease amino acid substitutions associated with PI failure were created in a reference clone by site-directed mutagenesis and assessed. Predicted phenotypes were determined using the Stanford drug resistance algorithm. Phenotypic resistance or reduced susceptibility to RTV and/or LPV was observed in isolates from 10 (50%) patients, all of whom had been treated with RTV. In most cases, this was associated with protease resistance mutations, but substitutions at Gag cleavage and noncleavage sites were also detected. Gag amino acid substitutions were also found in isolates from three patients with reduced drug susceptibilities who had wild-type protease. Site-directed mutagenesis confirmed that some amino acid changes in Gag contributed to PI resistance but only in the presence of major protease resistance-associated substitutions. The isolates from all patients who received LPV exclusively were phenotypically susceptible. Baseline isolates from the 20 patients showed a large (47-fold) range in the 50% effective concentration of LPV, which accounted for most of the discordance seen between the experimentally determined and the predicted phenotypes. Overall, the inclusion of thegaggene and the use of matched baseline samples provided a more comprehensive assessment of the effect of PI-induced amino acid changes on PI resistance. The lack of phenotypic resistance to LPV supports the continued use of this drug in pediatric patients.
authors.affiliation: Centre for HIV and STIs, National Institute for Communicable Diseases (NICD), Johannesburg, South Africa Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Giandhari
authors.affiliation: Centre for HIV and STIs, National Institute for Communicable Diseases (NICD), Johannesburg, South Africa Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
authors.forename: Adriaan E
authors.initials: AE
authors.lastname: Basson
authors.affiliation: Department of Infection, University College London, London, United Kingdom.
authors.forename: Katherine
authors.initials: K
authors.lastname: Sutherland
authors.affiliation: Public Health England, London, United Kingdom.
authors.forename: Chris M
authors.initials: CM
authors.lastname: Parry
authors.affiliation: Public Health England, London, United Kingdom.
authors.forename: Patricia A
authors.initials: PA
authors.lastname: Cane
authors.affiliation: Empilweni Services and Research Unit, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
authors.forename: Ashraf
authors.initials: A
authors.lastname: Coovadia
authors.affiliation: Gertrude H. Sergievsky Center and Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA.
authors.forename: Louise
authors.initials: L
authors.lastname: Kuhn
authors.affiliation: Centre for HIV and STIs, National Institute for Communicable Diseases (NICD), Johannesburg, South Africa Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
authors.forename: Gillian
authors.initials: G
authors.lastname: Hunt
authors.affiliation: Centre for HIV and STIs, National Institute for Communicable Diseases (NICD), Johannesburg, South Africa Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa lynnm@nicd.ac.za.
authors.forename: Lynn
authors.initials: L
authors.lastname: Morris
mesh_terms: D019943:Amino Acid Substitution; D002675:Child, Preschool; D024882:Drug Resistance, Viral / Q000235:genetics*; D005260:Female; D015870:Gene Expression; D015683:Gene Products, gag / Q000235:genetics* / Q000378:metabolism; D015658:HIV Infections / Q000188:drug therapy* / Q000821:virology; D016333:HIV Protease / Q000235:genetics* / Q000378:metabolism; D017320:HIV Protease Inhibitors / Q000627:therapeutic use*; D015497:HIV-1 / Q000187:drug effects* / Q000235:genetics / Q000254:growth & development; D006801:Humans; D007223:Infant; D061466:Lopinavir / Q000627:therapeutic use; D008297:Male; D016297:Mutagenesis, Site-Directed; D009154:Mutation; D010641:Phenotype; D019438:Ritonavir / Q000627:therapeutic use; D017211:Treatment Failure
chemical_list: D015683:Gene Products, gag; D017320:HIV Protease Inhibitors; D061466:Lopinavir; D016333:HIV Protease; D019438:Ritonavir
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