Background: Bictegravir (BIC) and cabotegravir (CAB) are novel HIV integrase inhibitors currently in clinical trials. Descriptions of clinically relevant resistance to these newest inhibitors are still relatively limited. Dolutegravir (DTG) response in vivo in the VIKING study was reduced in patient viruses with Q148H±G140S and/or additional mutations, with 2-fold increases in IC50 considered clinically relevant. Reduced in vitro susceptibility to viruses with these mutations has also been observed with BIC and CAB. Here, we compare the phenotypic susceptibility to all five available HIV integrase inhibitors of a panel of fourteen viruses derived from patients having integrase inhibitor resistance.
Methods: Initially clonal recombinant viruses were produced by PCR amplification under conditions where single copies of integrase were amplified. This was followed by co-transfection of integrase amplicons and linearized integrase-deleted pNL4.3 plasmid into CEM-GXR cells. Subsequent titering and phenotyping were performed in MT4-LTR-EGFP cells, where infectivity data was collected using a Spectra-max i3 Minimax 300 microplate reader. Recombinant viruses were grown under a range of concentrations of raltegravir, elvitegravir, DTG, BIC and CAB. EC50 fold-changes (FC) relative to a NL4.3 control were determined on day 3 post-infection.
Results: Viruses with the combination of G140S and Q148H substitutions alone had >100-fold increases in EC50 to raltegravir and elvitegravir, but relatively small changes (2-4-fold) in DTG, BIC or CAB susceptibility (Table 1). Viruses with progressively more substitutions showed extensive high level cross resistance to all five drugs (increases >50-fold). Viruses with T97A and L74M substitutions exhibited 6-fold greater increases in IC50 (67 to 456-fold change to DTG, BIC or CAB) compared to viruses which had only a T97A substitution (11 to 80-fold change). Phenotypic resistance values were strongly correlated between DTG, BIC, and CAB, with correlation coefficients ranging from 0.96 to 0.98.
Conclusions: Accumulation of multiple mutations in HIV integrase led to high level phenotypic resistance to all five HIV integrase inhibitors in patient-derived samples. Increases in phenotypic resistance values for DTG, BIC and CAB were almost co-linear.

Key Mutations (Stanford HIV DB)G140S + Q148HG140S + Q148HG140S + Q148H
Additional mutations-+ T97A+ T97A + L74M
EVG>100(>100 - >100)>100(>100 - >100)>100(>100 - >100)
[Median Fold Change in EC50 (IQR) of recombinant viruses with G140S and Q148H mutations and additional mutations for RAL, EVG, DTG, BIC and CAB.]