Q148N, a Novel Integrase Inhibitor Resistance Mutation Associated with Low-Level Reduction in Elvitegravir Susceptibility

A 50-year-old Hispanic homosexual man underwent HIV-1 seroconversion in August 2014. His CD4 count at the time of diagnosis was 405 cells/mm3 and his plasma HIV-1 RNA level was 3,980 copies/ml. A baseline genotypic resistance test revealed the nucleoside reverse transcriptase inhibitor-resistance mutations L210W and T215D that were interpreted as causing intermediate resistance to zidovudine and low-level resistance to tenofovir; the non-nucleoside reverse transcriptase inhibitor (NNRTI)-resistance mutations K101P and K103S that were interpreted as causing high-level resistance to each of the NNRTIs; and the protease inhibitor-resistance mutations D30N, L33F, I54V, N88D, and L90M that were interpreted as causing intermediate or high-level resistance to each of the PIs except darunavir. The patient was started on the once daily integrase strand transfer inhibitor (INSTI)-containing fixed-dose combination tenofovir/emtricitabine/elvitegravir/cobicistat. In November 2014, the patient changed clinics and an INSTI resistance test was ordered on his August 2014 sample. The test revealed G140S, a nonpolymorphic accessory INSTI-resistance mutation, and Q148N, a previously uncharacterized mutation in the INSTI-binding pocket of integrase enzyme. At the same time, the plasma HIV-1 RNA level was <50 copies/ml and CD4 count was 767 cells/mm3. Although the patient's genotypic resistance test was reported as being associated with intermediate resistance to raltegravir and elvitegravir based on the presence of G140S, no change to therapy was made because of the patient's virological and immunological response to therapy. The patient has since been monitored closely and multiple subsequent plasma HIV-1 RNA levels have been <50 copies/ml. In 2015, we created a panel of infectious molecular clones to assess the effect of the novel mutation Q148N on INSTI susceptibility. The panel included site-directed HIV-1 mutants containing G140S+Q148N, Q148N alone, G140S+Q148H, and Q148H alone. It also contained a recombinant infectious molecular clone from the patient's August 2014 sample and clones in which G140S alone and G140S and Q148N were independently mutated back to the wild type residues at these positions. These clones were subjected for phenotypic susceptibility testing using the PhenoSense assay (Monogram).1 Q148N ± G140S was associated with 2.4- to 4.5-fold reduced susceptibility to elvitegravir but not to raltegravir or dolutegravir (Table 1). This level of INSTI resistance was lower than that observed with Q148H alone (19-fold reduced raltegravir susceptibility and 5.5-fold reduced elvitegravir susceptibility) or Q148H+G140S (>150-fold reduced susceptibility to raltegravir and elvitegravir and 3.4-fold reduced dolutegravir susceptibility). Among the site-directed mutants, Q148N had a higher replication capacity than Q148H (88% vs. 27%). Table 1. Integrase Strand Transfer Inhibitor Resistance Mutations And In Vitro Susceptibility Results Of Virus Clones With And Without Q148n