HIV-1 integrase genotyping is reliable and reproducible for routine clinical detection of integrase resistance mutations even in patients with low-level viraemia

• Published in: Journal of antimicrobial chemotherapy 2015-06, Vol.70 (6), p.1865-1873
• Main Authors: Armenia, D, Fabeni, L, Alteri, C, Di Pinto, D, Di Carlo, D, Bertoli, A, Gori, C, Carta, S, Fedele, V, Forbici, F, D'Arrigo, R, Svicher, V, Berno, G, Pizzi, D, Nicastri, E, Sarmati, L, Pinnetti, C, Ammassari, A, D'Offizi, G, Latini, A, Andreoni, M, Antinori, A, Ceccherini-Silberstein, F, Perno, C F, Santoro, M M
• Format: Article
• Language: English
• Subjects: Adult; Antiretroviral drugs; Drug resistance; Female; Genotype & phenotype; Genotyping Techniques - methods; HIV; HIV Infections - drug therapy; HIV Infections - virology; HIV Integrase - genetics; HIV-1 - genetics; HIV-1 - isolation & purification; Human immunodeficiency virus; Humans; Male; Microbial Sensitivity Tests - methods; Middle Aged; Mutation; Mutation, Missense; Reproducibility of Results; Retrospective Studies; Sensitivity and Specificity; Viral Load; Viremia - virology
• ISSN: 0305-7453; 1460-2091
• DOI: 10.1093/jac/dkv029

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. 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. 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. 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.