Cooperation between HIV-1 integrase natural polymorphism K156N and 3'PPT mutations in dolutegravir monotherapy failure

Objectives: Mutations in the 3'-polypurine tract (3'PPT) of HIV-1 have been observed under pressure with two integrase strand transfer inhibitors, dolutegravir and cabotegravir. In the DOMONO randomized clinical trial, 3'PPT mutations emerged in a participant who experienced treatment failure under dolutegravir monotherapy. To understand the basis for this rare mutational pathway, we examined baseline viral sequences and identified the K156N natural polymorphism. Given the role of K156 in viral DNA binding, the potential relationship between K156N and 3'PPT mutations was further investigated.

Methods: We assessed the impact of K156N on integrase using in silico modelling and biochemical assays with recombinant proteins. Infectivity, replicative capacity, and drug susceptibility of viruses carrying K156N, 3'PPT mutations, or both were measured. Viral evolution was assessed in Cell Culture.

Results: Structural models indicated that K156N altered viral DNA binding. K156N reduced strand transfer activity through decreased affinity for the LTR but increased 3'-processing. The K156N virus had normal infectivity, whereas the 3'PPT mutations decreased infectiousness sixfold and lowered maximal infectivity. K156N partially compensated for this defect, but maximal infectivity remained diminished. K156N also partially compensated for defects in replicative capacity imposed by 3'PPT mutations. K156N alone did not confer resistance against dolutegravir, nor did it increase the modest (2.5-fold) resistance conferred by the 3'PPT mutations. K156N alone promoted the spontaneous emergence of 3'PPT mutations distinct from those seen in DOMONO.

Conclusions: These findings establish a direct functional relationship between natural variation in HIV-1 integrase and the emergence of 3'PPT mutations. People harbouring a virus with the K156N natural polymorphism may be predisposed to developing 3'PPT mutations upon failure with DTG. However, the clinical relevance of this association remains to be established.