HIV-1 sub-subtype A6 remains susceptible to second-generation integrase inhibitors with limited emergence of resistance in vitro

Background HIV-1 sub-subtype A6 is predominant in Eastern Europe and was associated with increased risk of treatment failure with the long-acting cabotegravir plus rilpivirine regimen. In this study we aimed to evaluate the in vitro susceptibility and the genetic barrier to resistance to INSTI in recombinant viruses harbouring clinically derived A6 integrase coding regions. Methods We generated 23 NL4-3 strain-based recombinant viruses harboring clinically derived integrase coding region. We measured their susceptibility to second generation INSTI dolutegravir, bictegravir and cabotegravir in a TZM-bl cell-based phenotypic assay. The genetic barrier to resistance was evaluated by exposing MT-2 cell cultures infected with four A6 integrase recombinant viruses, as well as the NL4-3 and HXB2 subtype B reference strains. Results All 23 recombinant viruses generated with clinically derived A6 integrase displayed full susceptibility to dolutegravir, bictegravir, and cabotegravir, showing median fold-change values of 1.2 (IQR 0.9-1.5), 1.1 (0.7-1.5) and 0.9 (0.6-1.1), respectively. Of four A6 viruses assessed for their genetic barrier to resistance in vitro, only one showed emerging integrase mutations E138K or Q148R at sub-inhibitory concentrations of dolutegravir or cabotegravir, respectively. Conclusions These data suggest that sub-subtype A6 integrase has full susceptibility and largely maintains a high genetic barrier to resistance to second-generation integrase strand transfer inhibitors.