HIV-1 integrase resistance among antiretroviral treatment naive and experienced patients from Northwestern Poland

Abstract

Background: HIV integrase inhibitor use is limited by low genetic barrier to resistance and possible cross-resistance among representatives of this class of antiretrovirals. The aim of this study was to analyse integrase sequence variability among antiretroviral treatment naive and experienced patients with no prior integrase inhibitor (InI) exposure and investigate development of the InI drug resistance mutations following the virologic failure of the raltegravir containing regimen.

Methods: Sequencing of HIV-1 integrase region from plasma samples of 80 integrase treatment naive patients and serial samples from 12 patients with observed virologic failure on raltegravir containing treatment whenever plasma vireamia exceeded >50 copies/ml was performed. Drug resistance mutations were called with Stanford DB database and grouped into major and minor variants. For subtyping bootstrapped phylogenetic analysis was used; Bayesian Monte Carlo Marcov Chain (MCMC) model was implemented to infer on the phylogenetic relationships between the serial sequences from patients failing on raltegravir.

Results: Majority of the integrase region sequences were classified as subtype B; the remaining ones being subtype D, C, G, as well as CRF01_AE , CRF02_AG and CRF13_cpx recombinants. No major integrase drug resistance mutations have been observed in InI-treatment naive patients. In 30 (38.5%) cases polymorphic variation with predominance of the E157Q mutation was observed. This mutation was more common among subtype B (26 cases, 54.2%) than non-B sequences (5 cases, 16.7%), p=0.00099, OR: 5.91 (95% CI:1.77-22.63)]. Other variants included L68V, L74IL, T97A, E138D, V151I, R263K. Among 12 (26.1%) raltegravir treated patients treatment failure was observed; major InI drug resistance mutations (G140S, Q148H and N155H, V151I, E92EQ, V151I, G163R) were noted in four of these cases (8.3% of the total InI-treated patients). Time to the development of drug resistance ranged from 2.6 to 16.3 months with mean increase of HIV viral load of 4.34 (95% CI:1.86-6.84) log HIV-RNA copies/ml at the time of emergence of the major mutations. Baseline polymorphisms, including E157Q were not associated with the virologic failure on raltegravir.

Conclusions: In InI treatment naive patients polymorphic integrase sequence variation was common, with no major resistance mutants. In the treatment failing patients selection of drug resistance occurred rapidly and followed the typical drug resistance pathways. Preexisting integrase polymorphisms were not associated with the treatment failure.

Figure 1

Maximum composite likelihood inferred trees showing phylogenetic relationships of subtype B (A) and non-subtype B isolates to the HIV-1 M group reference strains. Bootstrap values, expressed as percentage, are listed at the branch nodes. Baseline integrase mutations are listed alongside patient number following an asterisk.

Figure 2

HIV-1 viral loads in the group failing raltegravir containing treatment with and without observed InI drug resistance mutations.

Figure 3

(A) Phylogenetic trees (time-annotated MCMC) of the serial sequences and (B) HIV-1 viral loads and lymphocyte CD4 counts from four patients failing raltegravir (RAL) treatment. Maximum likelihood tree with bootstrap values for 1000 replicates drawn at the tree branches. Integrase resistance mutations are marked at the tip nodes; branches with developed drug resistance are marked red. Time points in which InI drug resistance mutations were noted are indicated with red arrows, while initiation of the raltegravir containing antiretroviral treatment is indicated with green arrow. TDF – tenofovir, MVC- maraviroc, FTC – emticitabine, DRV/r – ritonavir boosted darunavir, SQV – saquinavir.