title: Collinearity of protease mutations in HIV-1 samples with high-level protease inhibitor class resistance.
abstract: OBJECTIVE
  To determine whether pan-protease inhibitor (PI)-resistant virus populations are composed predominantly of viruses with resistance to all PIs or of diverse virus populations with resistance to different subsets of PIs.
  
  
  METHODS
  We performed deep sequencing of plasma virus samples from nine patients with high-level genotypic and/or phenotypic resistance to all licensed PIs. The nine virus samples had a median of 12 PI resistance mutations by direct PCR Sanger sequencing.
  
  
  RESULTS
  For each of the nine virus samples, deep sequencing showed that each of the individual viruses within a sample contained nearly all of the mutations detected by Sanger sequencing. Indeed, a median of 94.9% of deep sequence reads had each of the PI resistance mutations present as a single chromatographic peak in the Sanger sequence. A median of 5.0% of reads had all but one of the Sanger mutations that were not part of an electrophoretic mixture.
  
  
  CONCLUSIONS
  The collinearity of PI resistance mutations in the nine virus samples demonstrated that pan-PI-resistant viruses are able to replicate in vivo despite their highly mutated protease enzymes. We hypothesize that the marked collinearity of PI resistance mutations in pan-PI-resistant virus populations results from the unique requirements for multi-PI resistance and the extensive cross-resistance conferred by many of the accessory PI resistance mutations.
authors.affiliation: Stanford Genome Technology Center, Stanford University, Stanford, CA 94305, USA.
authors.forename: Farbod
authors.initials: F
authors.lastname: Babrzadeh
authors.forename: Vici
authors.initials: V
authors.lastname: Varghese
authors.forename: Mary
authors.initials: M
authors.lastname: Pacold
authors.forename: Tommy F
authors.initials: TF
authors.lastname: Liu
authors.forename: Pål
authors.initials: P
authors.lastname: Nyrén
authors.forename: Celia
authors.initials: C
authors.lastname: Schiffer
authors.forename: W Jeffrey
authors.initials: WJ
authors.lastname: Fessel
authors.forename: Robert W
authors.initials: RW
authors.lastname: Shafer
mesh_terms: D024882:Drug Resistance, Viral; D016333:HIV Protease / Q000235:genetics*; D017320:HIV Protease Inhibitors / Q000494:pharmacology*; D015497:HIV-1 / Q000187:drug effects* / Q000235:genetics* / Q000302:isolation & purification; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008826:Microbial Sensitivity Tests; D020125:Mutation, Missense; D010949:Plasma / Q000821:virology; D012367:RNA, Viral / Q000235:genetics
chemical_list: D017320:HIV Protease Inhibitors; D012367:RNA, Viral; D016333:HIV Protease