title: HIV-1 integrase genotyping is reliable and reproducible for routine clinical detection of integrase resistance mutations even in patients with low-level viraemia.
abstract: OBJECTIVE
  Integrase drug resistance monitoring deserves attention because of the increasing number of patients being treated with integrase strand-transfer inhibitors. Therefore, we evaluated the integrase genotyping success rate at low-level viraemia (LLV, 51-1000 copies/mL) and resistance in raltegravir-failing patients.
  
  
  METHODS
  An integrase genotypic resistance test (GRT) was performed on 1734 HIV-1 samples collected during 2006-13. Genotyping success rate was determined according to the following viraemia levels: 51-500, 501-1000, 1001-10 000, 10 001-100 000 and >100 000 copies/mL. The reproducibility of integrase GRT was evaluated in 41 plasma samples processed in duplicate in two reference centres. The relationship between LLV and resistance prevalence was evaluated in a subset of 120 raltegravir-failing patients.
  
  
  RESULTS
  Overall, the integrase genotyping success rate was 95.7%. For viraemia levels 51-500 and 501-1000 copies/mL, the rate of success was 82.1% and 94.0%, respectively. GRT was reproducible, producing sequences with a high similarity and an equal resistance profile regardless of the sequencing centre or viraemia level. Resistance was detected both at LLV and at viraemia >1000 copies/mL (51-500 copies/mL = 18.2%; 501-1000 = 37.5%; 1001-10 000 = 53.7%; 10 001-100 000 = 30.0%; and >100 000 = 30.8%). At viraemia ≤500 copies/mL, Q148H/K/R and N155H had the same prevalence (9.1%), while the Y143C/H/R was completely absent. At early genotyping (within 3 months of raltegravir treatment), Q148H/K/R and N155H mutations were detected regardless of the viraemia level, while Y143C/H/R was observed only in samples with viraemia >1000 copies/mL.
  
  
  CONCLUSIONS
  Our findings prove the reliability of HIV-1 integrase genotyping and reinforce the concept that this assay may be useful in the management of failures even at LLV.
authors.affiliation: University of Rome Tor Vergata, Rome, Italy.
authors.forename: D
authors.initials: D
authors.lastname: Armenia
authors.affiliation: L. Spallanzani Hospital, Rome, Italy.
authors.forename: L
authors.initials: L
authors.lastname: Fabeni
authors.affiliation: University of Rome Tor Vergata, Rome, Italy.
authors.forename: C
authors.initials: C
authors.lastname: Alteri
authors.affiliation: University of Rome Tor Vergata, Rome, Italy.
authors.forename: D
authors.initials: D
authors.lastname: Di Pinto
authors.affiliation: University of Rome Tor Vergata, Rome, Italy.
authors.forename: D
authors.initials: D
authors.lastname: Di Carlo
authors.affiliation: University of Rome Tor Vergata, Rome, Italy University Hospital Tor Vergata, Rome, Italy.
authors.forename: A
authors.initials: A
authors.lastname: Bertoli
authors.affiliation: L. Spallanzani Hospital, Rome, Italy.
authors.forename: C
authors.initials: C
authors.lastname: Gori
authors.affiliation: L. Spallanzani Hospital, Rome, Italy.
authors.forename: S
authors.initials: S
authors.lastname: Carta
authors.affiliation: L. Spallanzani Hospital, Rome, Italy.
authors.forename: V
authors.initials: V
authors.lastname: Fedele
authors.affiliation: L. Spallanzani Hospital, Rome, Italy.
authors.forename: F
authors.initials: F
authors.lastname: Forbici
authors.affiliation: L. Spallanzani Hospital, Rome, Italy.
authors.forename: R
authors.initials: R
authors.lastname: D'Arrigo
authors.affiliation: University of Rome Tor Vergata, Rome, Italy.
authors.forename: V
authors.initials: V
authors.lastname: Svicher
authors.affiliation: L. Spallanzani Hospital, Rome, Italy.
authors.forename: G
authors.initials: G
authors.lastname: Berno
authors.affiliation: L. Spallanzani Hospital, Rome, Italy.
authors.forename: D
authors.initials: D
authors.lastname: Pizzi
authors.affiliation: L. Spallanzani Hospital, Rome, Italy.
authors.forename: E
authors.initials: E
authors.lastname: Nicastri
authors.affiliation: University Hospital Tor Vergata, Rome, Italy.
authors.forename: L
authors.initials: L
authors.lastname: Sarmati
authors.affiliation: L. Spallanzani Hospital, Rome, Italy.
authors.forename: C
authors.initials: C
authors.lastname: Pinnetti
authors.affiliation: L. Spallanzani Hospital, Rome, Italy.
authors.forename: A
authors.initials: A
authors.lastname: Ammassari
authors.affiliation: L. Spallanzani Hospital, Rome, Italy.
authors.forename: G
authors.initials: G
authors.lastname: D'Offizi
authors.affiliation: San Gallicano Hospital, Rome, Italy.
authors.forename: A
authors.initials: A
authors.lastname: Latini
authors.affiliation: University Hospital Tor Vergata, Rome, Italy.
authors.forename: M
authors.initials: M
authors.lastname: Andreoni
authors.affiliation: L. Spallanzani Hospital, Rome, Italy.
authors.forename: A
authors.initials: A
authors.lastname: Antinori
authors.affiliation: University of Rome Tor Vergata, Rome, Italy.
authors.forename: F
authors.initials: F
authors.lastname: Ceccherini-Silberstein
authors.affiliation: L. Spallanzani Hospital, Rome, Italy.
authors.forename: C F
authors.initials: CF
authors.lastname: Perno
authors.affiliation: University of Rome Tor Vergata, Rome, Italy santormaria@gmail.com.
authors.forename: M M
authors.initials: MM
authors.lastname: Santoro
mesh_terms: D000328:Adult; D005260:Female; D060005:Genotyping Techniques / Q000379:methods*; D015658:HIV Infections / Q000188:drug therapy / Q000821:virology*; D019427:HIV Integrase / Q000235:genetics*; D015497:HIV-1 / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D008297:Male; D008826:Microbial Sensitivity Tests / Q000379:methods*; D008875:Middle Aged; D020125:Mutation, Missense; D015203:Reproducibility of Results; D012189:Retrospective Studies; D012680:Sensitivity and Specificity; D019562:Viral Load; D014766:Viremia / Q000821:virology
chemical_list: D019427:HIV Integrase; C514801:p31 integrase protein, Human immunodeficiency virus 1
keywords: HIV-1 genotyping; INSTI; dolutegravir; drug resistance; elvitegravir; integrase; low-level viraemia; raltegravir