title: Study of genotypic and phenotypic HIV-1 dynamics of integrase mutations during raltegravir treatment: a refined analysis by ultra-deep 454 pyrosequencing.
abstract: BACKGROUND
  The dynamics of raltegravir-resistant variants and their impact on virologic response in 23 HIV-1-infected patients, who started a salvage raltegravir-containing regimen, were investigated.
  
  
  METHODS
  Integrase population sequencing and Ultra-Deep-454 Pyrosequencing (UDPS) were performed on plasma samples at baseline and at raltegravir failure. All integrase mutations detected at a frequency ≥1% were considered to be reliable for the UDPS analyses. Phylogenetic and phenotypic resistance analyses were also performed.
  
  
  RESULTS
  At baseline, primary resistance mutations were not detected by both population and UDPS genotypic assays; few secondary mutations (T97A-V151I-G163R) were rarely detected and did not show any statistically association either with virologic response at 24-weeks or with the development of resistant variants at failure. At UDPS, not all resistant variants appearing early during treatment evolved as major populations during failure; only specific resistance pathways (Y143R-Q148H/R-N155H) associated with an increased rate of fitness and phenotypic resistance were selected.
  
  
  CONCLUSIONS
  Resistance to raltegravir in integrase strand transfer inhibitor-naive patients remains today a rare event, which might be changed by future extensive use of such drugs. In our study, pathways of resistance at failure were not predicted by baseline mutations, suggesting that evolution plus stochastic selection plays a major role in the appearance of integrase-resistance mutations, whereas fitness and resistance are dominant factors acting for the late selection of resistant quasispecies.
authors.affiliation: University of Rome Tor Vergata, Rome, Italy.
authors.forename: Daniele
authors.initials: D
authors.lastname: Armenia
authors.forename: Ina
authors.initials: I
authors.lastname: Vandenbroucke
authors.forename: Lavinia
authors.initials: L
authors.lastname: Fabeni
authors.forename: Herwig
authors.initials: H
authors.lastname: Van Marck
authors.forename: Valeria
authors.initials: V
authors.lastname: Cento
authors.forename: Roberta
authors.initials: R
authors.lastname: D'Arrigo
authors.forename: Liesbeth
authors.initials: L
authors.lastname: Van Wesenbeeck
authors.forename: Fernanda
authors.initials: F
authors.lastname: Scopelliti
authors.forename: Valeria
authors.initials: V
authors.lastname: Micheli
authors.forename: Bianca
authors.initials: B
authors.lastname: Bruzzone
authors.forename: Sergio
authors.initials: S
authors.lastname: Lo Caputo
authors.forename: Jeroen
authors.initials: J
authors.lastname: Aerssens
authors.forename: Giuliano
authors.initials: G
authors.lastname: Rizzardini
authors.forename: Valerio
authors.initials: V
authors.lastname: Tozzi
authors.forename: Pasquale
authors.initials: P
authors.lastname: Narciso
authors.forename: Andrea
authors.initials: A
authors.lastname: Antinori
authors.forename: Lieven
authors.initials: L
authors.lastname: Stuyver
authors.forename: Carlo Federico
authors.initials: CF
authors.lastname: Perno
authors.forename: Francesca
authors.initials: F
authors.lastname: Ceccherini-Silberstein
mesh_terms: D000328:Adult; D019380:Anti-HIV Agents / Q000008:administration & dosage*; D024882:Drug Resistance, Viral; D005260:Female; D005838:Genotype; D015658:HIV Infections / Q000188:drug therapy / Q000821:virology*; D019427:HIV Integrase / Q000235:genetics*; D015497:HIV-1 / Q000145:classification / Q000201:enzymology / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D008297:Male; D008826:Microbial Sensitivity Tests; D008969:Molecular Sequence Data; D020125:Mutation, Missense; D010641:Phenotype; D010802:Phylogeny; D011760:Pyrrolidinones / Q000008:administration & dosage*; D000068898:Raltegravir Potassium; D016879:Salvage Therapy / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods
chemical_list: D019380:Anti-HIV Agents; D011760:Pyrrolidinones; D000068898:Raltegravir Potassium; D019427:HIV Integrase; C514801:p31 integrase protein, Human immunodeficiency virus 1