Altered Viral Fitness and Drug Susceptibility in HIV-1 Carrying Mutations That Confer Resistance to Nonnucleoside Reverse Transcriptase and Integrase Strand Transfer Inhibitors

Abstract

Nonnucleoside reverse transcriptase (RT) inhibitors (NNRTI) and integrase (IN) strand transfer inhibitors (INSTI)are key components of antiretroviral regimens. To explore potential interactions between NNRTI and INSTI resistance mutations, we investigated the combined effects of these mutations on drug susceptibility and fitness of human immunodeficiency virus type 1 (HIV-1). In the absence of drug, single-mutant viruses were less fit than the wild type; viruses carrying multiple mutations were less fit than single-mutant viruses. These findings were explained in part by the observation that mutant viruses carrying NNRTI plus INSTI resistance mutations had reduced amounts of virion-associated RT and/or IN protein. In the presence of efavirenz (EFV), a virus carrying RT-K103N together with IN-G140S and IN-Q148H (here termed IN-G140S/Q148H) mutations was fitter than a virus with a RT-K103N mutation alone. Similarly, in the presence of EFV, the RT-E138K plus IN-G140S/Q148H mutant virus was fitter than one with the RT-E138K mutation alone. No effect of INSTI resistance mutations on the fitness of RT-Y181C mutant viruses was observed. Conversely, RT-E138K and -Y181C mutations improved the fitness of the IN-G140S/Q148H mutant virus in the presence of raltegravir (RAL); the RT-K103N mutation had no effect. The NNRTI resistance mutations had no effect on RAL susceptibility. Likewise, the IN-G140S/Q148H mutations had no effect on EFV or RPV susceptibility. However, both the RT-K103N plus IN-G140S/Q148H and the RT-E138K plus IN-G140S/Q148H mutant viruses had significantly greater fold increases in 50% inhibitory concentration (IC 50 ) of EFV than viruses carrying a single NNRTI mutation. Likewise, the RT-E138K plus IN-G140S/Q148H mutant virus had significantly greater fold increases in RAL IC 50 than that of the IN-G140S/ Q148H mutant virus. These results suggest that interactions between RT and IN mutations are important for NNRTI and INSTI resistance and viral fitness. IMPORTANCENonnucleoside reverse transcriptase inhibitors and integrase inhibitors are used to treat infection with HIV-1. Mutations that confer resistance to these drugs reduce the ability of HIV-1 to reproduce (that is, they decrease viral fitness). It is known that reverse transcriptase and integrase interact and that some mutations can disrupt their interaction, which is necessary for proper functioning of these two enzymes. To determine whether resistance mutations in these enzymes interact, we investigated their effects on drug sensitivity and viral fitness. Although individual drug resistance mutations usually reduced viral fitness, certain combinations of mutations increased fitness. When present in certain combinations, some integrase inhibitor resistance mutations increased resistance to nonnucleoside reverse transcriptase inhibitors and vice versa. Because these drugs are sometimes used together in the treatment of HIV-1 infection, these interactions could make viruses more resistant to both drugs, further limiting their clinical benefit.

HIV Genome-Wide Protein Associations: a Review of 30 Years of Research

“…It is known that drug-resistant mutations in drug-targeted proteins lead to treatment failure in HIV-infected patients (556). However, recent studies also suggest that protein-protein interactions may provide novel drug resistance mechanisms for HIV to escape the inhibition of antiviral drugs (4,85,557,558). In principle, current findings rely on the hypothesis that the drug resistance of anti-HIV inhibitors could be established by sequence changes outside druginhibited proteins, owing to the physical interactions between drug-inhibited proteins and other HIV proteins.…”

“…HIV-1 strains with RT mutations (E138K) and integrase mutations (G140S and Q148H) have significantly increased IC 50 s of raltegravir compared to those of viruses with integrase mutations alone (557). This observation is in agreement with viral fitness changes in which RT drug-resistant mutations (K103N and Y181C) rescue the replicative fitness of viruses harboring integrase drug-resistant mutations under the selective pressure of raltegravir (557). In the absence of drug pressure, protease and RT drug-resistant mutations may decrease the replica- tive fitness of viruses harboring integrase mutations (567).…”

“…HIV integrase physically interacts with viral RT (101-106), driving integrase mutations to confer resistance to RT inhibitors (RTIs) (e.g., efavirenz) (557). For instance, viruses with integrase mutations (G140S and Q148H) and the RT mutation K103N have significantly increased fold changes in 50% inhibitory concentrations (IC 50 s) of efavirenz compared to those of viruses with the RT drug-resistant mutation K103N alone (557). This finding is in agreement with data from viral fitness analyses, which suggest that integrase mutations (G140S and Q148H) rescue the replicative fitness of HIV-1 harboring RT drug-resistant mutations (K103N and E138K) under the selective pressure of efavirenz (557).…”

“…HIV RT physically interacts with viral integrase (101-106), permitting RT mutations to confer resistance to integrase inhibitors (e.g., raltegravir) (557). HIV-1 strains with RT mutations (E138K) and integrase mutations (G140S and Q148H) have significantly increased IC 50 s of raltegravir compared to those of viruses with integrase mutations alone (557).…”

“…HIV RT physically interacts with viral integrase (101-106), permitting RT mutations to confer resistance to integrase inhibitors (e.g., raltegravir) (557). HIV-1 strains with RT mutations (E138K) and integrase mutations (G140S and Q148H) have significantly increased IC 50 s of raltegravir compared to those of viruses with integrase mutations alone (557). This observation is in agreement with viral fitness changes in which RT drug-resistant mutations (K103N and Y181C) rescue the replicative fitness of viruses harboring integrase drug-resistant mutations under the selective pressure of raltegravir (557).…”