Selection of Mutations in HIV-1 Nucleocapsid and Integrase in Individuals Living with HIV Experiencing Virologic Failure After Initiating or Switching to Tenofovir-Lamivudine-Dolutegravir

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ABSTRACT Background Tenofovir-lamivudine-dolutegravir (TLD) is an effective, single-tablet ART regimen but the causes of virologic failure that can occur despite adherence to TLD are incompletely understood, especially when resistance mutations in integrase (IN) are absent. Noncanonical resistance mutations in nucleocapsid (NC) have been selected in cell culture and are associated with decreased dolutegravir (DTG) susceptibility in vitro . Samples from the ACTG A5381-Hakim study were examined to assess the potential contribution of NC mutations to virologic failure on TLD. Methods A5381-Hakim was an observational cohort study that enrolled individuals with HIV-1 RNA >1000 copies/mL when initiating TLD as first line ART or switching from failing non-nucleoside reverse transcriptase inhibitor (NNRTI)-based or protease inhibitor (PI)-based ART. Whole HIV RNA genome next generation sequencing was performed on paired plasma samples from study entry and confirmed virologic failure in 56 participants receiving TLD for ≥six months. Mutations relative to the HIV HXB2 reference genome were identified with DeepChek® software using a mutation reporting threshold of five percent mixed-base frequency. Canonical drug resistance mutations (DRMs) were identified within the DeepChek® software using Stanford’s HIVdb v9.8 algorithm. Site-directed NC and IN mutants were tested for susceptibility to DTG, raltegravir and cabotegravir in the TZM-bl HIV-1 indicator cell line and evaluated for infectivity and replication in multi-round assays. Results Mutations in NC that emerged between TLD initiation and virologic failure were identified in 11 of 56 (20%) participants. Of these 11, three participants also had IN mutations at virologic failure but not at study entry, suggesting dual selection. Selected mutations in the NC zinc-finger domain included V13I, K20R, E21V, N27I/S, A30T, K34R, K38R, K41G/R/N, Q45R and/or M46I, alone or in combination with other NC and/or IN mutations. Specific NC mutations (K20R, N27I, A30T, K41N, M46I) conferred a significant decrease in DTG susceptibility. The combination of certain NC with IN mutations (e.g. NC N27I and IN R263K) conferred greater reduction in susceptibility to DTG in vitro than either mutation alone. Conclusions This work provides the first clinical evidence of NC mutation selection in individuals on failing TLD ART and shows that NC mutations, combined with IN mutations, can further decrease susceptibility to DTG. Our findings support additional investigations of the contributions of mutations outside of IN to virologic failure of integrase inhibitor-containing ART regimens.

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