title: Identification of biased amino acid substitution patterns in human immunodeficiency virus type 1 isolates from patients treated with protease inhibitors.
abstract: Human immunodeficiency virus type 1 (HIV-1) amino acid substitutions observed during antiretroviral drug therapy may be caused by drug selection, non-drug-related evolution, or sampling error introduced by the sequencing process. We analyzed HIV-1 sequences from 371 untreated patients and from 178 patients receiving a single protease inhibitor. Amino acid substitution patterns during treatment were compared with inferred substitution patterns arising evolutionarily without treatment. Our results suggest that most treatment-associated amino acid substitutions are caused by selective drug pressure, including substitutions not previously associated with drug resistance.
authors.affiliation: Division of Infectious Diseases, Stanford University Medical Center, Stanford, California 94305, USA. rshafer@cmgm.stanford.edu
authors.forename: R W
authors.initials: RW
authors.lastname: Shafer
authors.forename: P
authors.initials: P
authors.lastname: Hsu
authors.forename: A K
authors.initials: AK
authors.lastname: Patick
authors.forename: C
authors.initials: C
authors.lastname: Craig
authors.forename: V
authors.initials: V
authors.lastname: Brendel
mesh_terms: D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D019380:Anti-HIV Agents / Q000627:therapeutic use*; D014644:Genetic Variation; D015658:HIV Infections / Q000188:drug therapy* / Q000821:virology*; D016333:HIV Protease / Q000187:drug effects / Q000235:genetics*; D017320:HIV Protease Inhibitors / Q000627:therapeutic use*; D015497:HIV-1 / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D019469:Indinavir / Q000627:therapeutic use; D008969:Molecular Sequence Data; D019888:Nelfinavir / Q000627:therapeutic use; D019438:Ritonavir / Q000627:therapeutic use; D019258:Saquinavir / Q000627:therapeutic use
chemical_list: D019380:Anti-HIV Agents; D017320:HIV Protease Inhibitors; D019469:Indinavir; D016333:HIV Protease; D019888:Nelfinavir; D019258:Saquinavir; D019438:Ritonavir