title: Secondary integrase resistance mutations found in HIV-1 minority quasispecies in integrase therapy-naive patients have little or no effect on susceptibility to integrase inhibitors.
abstract: The goal of this study was to explore the presence of integrase strand transfer inhibitor (InSTI) resistance mutations in HIV-1 quasispecies present in InSTI-naïve patients and to evaluate their in vitro effects on phenotypic susceptibility to InSTIs and their replication capacities. The RT-RNase H-IN region was PCR amplified from plasma viral RNA obtained from 49 HIV-1 subtype B-infected patients (21 drug naïve and 28 failing highly active antiretroviral therapy [HAART] not containing InSTIs) and recombined with an HXB2-based backbone with RT and IN deleted. Recombinant viruses were tested against raltegravir and elvitegravir and for replication capacity. Three-hundred forty-four recombinant viruses from 49 patients were successfully analyzed both phenotypically and genotypically. The majority of clones were not phenotypically resistant to InSTIs: 0/344 clones showed raltegravir resistance, and only 3 (0.87%) showed low-level elvitegravir resistance. No primary resistance mutations for raltegravir and elvitegravir were found as major or minor species. The majority of secondary mutations were also absent or rarely present. Secondary mutations, such as T97A and G140S, found rarely and only as minority quasispecies, were present in the elvitegravir-resistant clones. A novel mutation, E92G, although rarely found in minority quasispecies, showed elvitegravir resistance. Preexisting genotypic and phenotypic raltegravir resistance was extremely rare in InSTI-naïve patients and confined to only a restricted minority of secondary variants. Overall, these results, together with others based on population and ultradeep sequencing, suggest that at this point IN genotyping in all patients before raltegravir treatment may not be cost-effective and should not be recommended until evidence of transmitted drug resistance to InSTIs or the clinical relevance of IN minor variants/polymorphisms is determined.
authors.affiliation: Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy. ceccherini@med.uniroma2.it
authors.forename: Francesca
authors.initials: F
authors.lastname: Ceccherini-Silberstein
authors.forename: Kurt
authors.initials: K
authors.lastname: Van Baelen
authors.forename: Daniele
authors.initials: D
authors.lastname: Armenia
authors.forename: Maria
authors.initials: M
authors.lastname: Trignetti
authors.forename: Evelien
authors.initials: E
authors.lastname: Rondelez
authors.forename: Lavinia
authors.initials: L
authors.lastname: Fabeni
authors.forename: Fernanda
authors.initials: F
authors.lastname: Scopelliti
authors.forename: Michela
authors.initials: M
authors.lastname: Pollicita
authors.forename: Liesbeth
authors.initials: L
authors.lastname: Van Wesenbeeck
authors.forename: Veerle
authors.initials: V
authors.lastname: Van Eygen
authors.forename: Luca
authors.initials: L
authors.lastname: Dori
authors.forename: Loredana
authors.initials: L
authors.lastname: Sarmati
authors.forename: Stefano
authors.initials: S
authors.lastname: Aquaro
authors.forename: Guido
authors.initials: G
authors.lastname: Palamara
authors.forename: Massimo
authors.initials: M
authors.lastname: Andreoni
authors.forename: Lieven J
authors.initials: LJ
authors.lastname: Stuyver
authors.forename: Carlo Federico
authors.initials: CF
authors.lastname: Perno
mesh_terms: D024882:Drug Resistance, Viral / Q000235:genetics; D005838:Genotype; D019427:HIV Integrase / Q000235:genetics*; D019428:HIV Integrase Inhibitors / Q000627:therapeutic use*; D006801:Humans; D009154:Mutation; D010641:Phenotype; D011760:Pyrrolidinones / Q000627:therapeutic use*; D015363:Quinolones / Q000627:therapeutic use*; D000068898:Raltegravir Potassium
chemical_list: D019428:HIV Integrase Inhibitors; D011760:Pyrrolidinones; D015363:Quinolones; D000068898:Raltegravir Potassium; C509700:elvitegravir; D019427:HIV Integrase