Drug Susceptibility and Viral Fitness of HIV-1 with Integrase Strand Transfer Inhibitor Resistance Substitution Q148R or N155H in Combination with Nucleoside/Nucleotide Reverse Transcriptase Inhibitor Resistance Substitutions

Abstract

In clinical trials of coformulated elvitegravir (EVG), cobicistat (COBI), emtricitabine (FTC), and tenofovir disoproxil fumarate (TDF), emergent drug resistance predominantly involved the FTC resistance substitution M184V/I in reverse transcriptase (RT), with or without the tenofovir (TFV) resistance substitution K65R, accompanied by a primary EVG resistance substitution (E92Q, N155H, or Q148R) in integrase (IN). We previously reported that the RT-K65R, RT-M184V, and IN-E92Q substitutions lacked cross-class phenotypic resistance and replicative fitness compensation. As a follow-up, the in vitro characteristics of mutant HIV-1 containing RT-K65R and/or RT-M184V with IN-Q148R or IN-N155H were also evaluated, alone and in combination, for potential interactions. Single mutants displayed reduced susceptibility to their corresponding inhibitor classes, with no cross-class resistance. Viruses with IN-Q148R or IN-N155H exhibited reduced susceptibility to EVG (137- and 40-fold, respectively) that was not affected by the addition of RT-M184V or RT-K65R/M184V. All viruses containing RT-M184V were resistant to FTC (>1,000-fold). Mutants with RT-K65R had reduced susceptibility to TFV (3.3- to 3.6-fold). Without drugs present, the viral fitness of RT and/or IN mutants was diminished relative to that of the wild type in the following genotypic order: wild type > RT-M184V ≥ IN-N155H ≈ IN-Q148R ≥ RT-M184V + IN-N155H ≥ RT-M184V + IN-Q148R ≥ RT-K65R/M184V + IN-Q148R ≈ RT-K65R/M184V + IN-N155H. In the presence of drug concentrations approaching physiologic levels, drug resistance counteracted replication defects, allowing single mutants to outcompete the wild type with one drug present and double mutants to outcompete single mutants with two drugs present. These results suggest that during antiretroviral treatment with multiple drugs, the development of viruses with combinations of resistance substitutions may be favored despite diminished viral fitness.

FIG 1

Growth competitions of wild-type HIV-1 (WT; open circles) versus the RT-M184V (A), IN-N155H (B), IN-Q148R (C), RT-M184V + IN-N155H (D), RT-M184V + IN-Q148R (E), RT-K65R/M184V + IN-Q148R (F), and RT-K65R/M184V + IN-N155H (G) mutants (closed circles). Data are averages from 3 independent competition experiments, with standard deviations. (H) Mean relative fitness (RF; 1 + s) values of viruses (genotype indicated) in competition with the WT. Asterisks indicate statistically significant differences for the mutant-versus-WT competitions compared to the WT-versus-WT control competitions using a two-tailed Student's t test (P < 0.01).

FIG 2

Growth competitions of the IN-N155H mutant (open circles) versus the IN-Q148R mutant (closed circles) in the presence of no drug (A), 1 nM EVG (B), 10 nM EVG (C), 50 nM EVG (D), and 100 nM EVG (E). Data are averages from 3 independent competition experiments, with standard deviations. Mean relative fitness (RF) values for the IN-Q148R mutant compared to the IN-N155H mutant are shown in Table 2.

FIG 3

(A to F) Growth competitions of the RT-M184V mutant versus the RT-M184V + IN-Q148R and RT-M184V + IN-N155H mutants in the presence of no drug (A and D, respectively), 0.5 nM EVG + 1 nM FTC (B and E, respectively), and 10 nM EVG + 100 nM FTC (C and F, respectively). (G to L) Growth competitions of the IN-Q148R mutant versus the RT-M184V + IN-Q148R mutant and the IN-N155H versus RT-M184V + IN-N155H mutant in the presence of no drug (G and J, respectively), 1 nM EVG plus 1 nM FTC (H and K, respectively), and 100 nM EVG plus 100 nM FTC (I and L, respectively) Data are averages from 3 independent competition experiments, with standard deviations. Mean relative fitness (RF) values for the double mutants (closed circles) compared to the single mutants (open circles) are shown in Table 2.

FIG 4

Relative fitness (RF) values of wild-type and mutant HIV-1 in competition with the wild type in the absence and presence of increasing EVG concentrations (0.5 nM, 2 nM, and 10 nM). Asterisks indicate statistically significant differences for the mutant-versus-WT competitions compared to the WT-versus-WT control competitions using a two-tailed Student's t test (P < 0.01).