Accumulation of integrase strand transfer inhibitor resistance mutations confers high-level resistance to dolutegravir in non-B subtype HIV-1 strains from patients failing raltegravir in Uganda

Abstract

Background: Increasing first-line treatment failures in low- and middle-income countries (LMICs) have led to increased use of integrase strand transfer inhibitors (INSTIs) such as dolutegravir. However, HIV-1 susceptibility to INSTIs in LMICs, especially with previous raltegravir exposure, is poorly understood due to infrequent reporting of INSTI failures and testing for INSTI drug resistance mutations (DRMs).

Methods: A total of 51 non-subtype B HIV-1 infected patients failing third-line (raltegravir-based) therapy in Uganda were initially selected for the study. DRMs were detected using Sanger and deep sequencing. HIV integrase genes of 13 patients were cloned and replication capacities (RCs) and phenotypic susceptibilities to dolutegravir, raltegravir and elvitegravir were determined with TZM-bl cells. Spearman's correlation coefficient was used to determine cross-resistance between INSTIs.

Results: INSTI DRMs were detected in 47% of patients. HIV integrase-recombinant virus carrying one primary INSTI DRM (N155H or Y143R/S) was susceptible to dolutegravir but highly resistant to raltegravir and elvitegravir (>50-fold change). Two patients, one with E138A/G140A/Q148R/G163R and one with E138K/G140A/S147G/Q148K, displayed the highest reported resistance to raltegravir, elvitegravir and even dolutegravir. The former multi-DRM virus had WT RC whereas the latter had lower RCs than WT.

Conclusions: In HIV-1 subtype A- and D-infected patients failing raltegravir and harbouring INSTI DRMs, there is high-level resistance to elvitegravir and raltegravir. More routine monitoring of INSTI treatment may be advised in LMICs, considering that multiple INSTI DRMs may have accumulated during prolonged exposure to raltegravir during virological failure, leading to high-level INSTI resistance, including dolutegravir resistance.

Figure 1.

The susceptibility of viruses with INSTI DRMs. The log values of drug concentrations were plotted against percentage of infections in TZM-bl cells detected by the X-gal assay. The colonies were counted using ELISpot and they were from 2–3 independent experiments, each run in quadruplicate. The change in EC₅₀ relative to WT (NL4-3) is shown. RAL, raltegravir; EVG, elvitegravir; DTG, dolutegravir. This figure appears in colour in the online version of JAC and in black and white in the print version of JAC.

Figure 2.

The susceptibility of mutants by subtype. The FC in EC₅₀ values of dolutegravir, raltegravir and elvitegravir relative to each subtype was determined by short-term infection assay in TZM-bl cells. Each value represents the mean FC of EC₅₀ from 2–3 independent experiments, each done in quadruplicate. DTG, dolutegravir; RAL, raltegravir; EVG, elvitegravir. This figure appears in colour in the online version of JAC and in black and white in the print version of JAC.

Figure 3.

Relative viral infectivity of recombinant viruses. The viral infectivity of resistant mutants compared with controls and WT was determined using short-term infection assay in TZM-bl cells. AUC was used to measure the relative decrease in infectivity. The data shown represent means and SD from independent experiments performed in triplicate. This figure appears in colour in the online version of JAC and in black and white in the print version of JAC.