Impact of primary elvitegravir resistance-associated mutations in HIV-1 integrase on drug susceptibility and viral replication fitness

Abstract

Elvitegravir (EVG) is an effective HIV-1 integrase (IN) strand transfer inhibitor (INSTI) in advanced clinical development. Primary INSTI resistance-associated mutations (RAMs) at six IN positions have been identified in HIV-1-infected patients failing EVG-containing regimens in clinical studies: T66I/A/K, E92Q/G, T97A, S147G, Q148R/H/K, and N155H. In this study, the effect of these primary IN mutations, alone and in combination, on susceptibility to the INSTIs EVG, raltegravir (RAL), and dolutegravir (DTG); IN enzyme activities; and viral replication fitness was characterized. Recombinant viruses containing the six most common mutations exhibited a range of reduced EVG susceptibility: 92-fold for Q148R, 30-fold for N155H, 26-fold for E92Q, 10-fold for T66I, 4-fold for S147G, and 2-fold for T97A. Less commonly observed primary IN mutations also showed a range of reduced EVG susceptibilities: 40- to 94-fold for T66K and Q148K and 5- to 10-fold for T66A, E92G, and Q148H. Some primary IN mutations exhibited broad cross-resistance between EVG and RAL (T66K, E92Q, Q148R/H/K, and N155H), while others retained susceptibility to RAL (T66I/A, E92G, T97A, and S147G). Dual combinations of primary IN mutations further reduced INSTI susceptibility, replication capacity, and viral fitness relative to either mutation alone. Susceptibility to DTG was retained by single primary IN mutations but reduced by dual mutation combinations with Q148R. Primary EVG RAMs also diminished IN enzymatic activities, concordant with their structural proximity to the active site. Greater reductions in viral fitness of dual mutation combinations may explain why some primary INSTI RAMs do not readily coexist on the same HIV-1 genome but rather establish independent pathways of resistance to EVG.

Fig 1

Clinical development of EVG primary INSTI RAMs. Most commonly observed IN mutations are indicated above the dotted line, while less commonly observed mutations are indicated below. *, T97A may require additional mutations for reduced phenotypic susceptibility.

Fig 2

Correlation between phenotypic EVG resistance determined by the PhenoSense IN HIV assay and relative viral replication fitness.

Fig 3

Relative catalytic activities of HIV-1 IN enzymes. IN-mediated 3′-processing (A) and strand transfer (B) activities were determined by using unprocessed and preprocessed donor DNA substrates, respectively. Data shown represent the means and standard deviations of data from an independent experiment performed in triplicate.

Fig 4

Proximal location of EVG primary INSTI RAMs in a homology model of the HIV-1 IN active site. Amino acid residues of HIV-1 IN were substituted in a crystal structure model of PFV IN with bound EVG and its cognate DNA substrate (PDB accession number 3L2U) (29). The protein backbone in a ribbon representation is shown in green. The viral DNA substrate sugar-phosphate backbone and nitrogenous bases are shown in brown and blue, respectively. Residues associated with primary EVG RAMs are shown as light blue spheres, and Mg²⁺ ions are shown as pink spheres. Elvitegravir (EVG) is labeled and shown as yellow spheres. White labels indicate HIV-1 IN residue numbers and mutations.