Predominance of Positive Epistasis Among Resistance-Associated Mutations in HIV-1 Protease

Drug-resistant mutations often have deleterious impacts on replication fitness of viruses, posing a fitness barrier that can only be overcome by compensatory mutations. However, the importance of fitness barriers in the evolution of HIV-1 drug resistance is not evident in clinical samples or traditional in vitro selection experiments, as these data only capture the overall outcome of selection. In this study, we systematically profile the fitness effects of resistance-associated mutations in HIV-1 protease using deep mutational scanning. As expected, we find that the majority of resistance-associated mutations have significantly deleterious effects on viral replication. However, in contrast to the common belief in protein evolution that deleterious mutations tend to interact negatively, we observe the dominance of positive epistasis among resistance-associated mutations in HIV-1 protease. Furthermore, we applied the Potts model on HIV sequence data from patients to infer the genetic interactions. The Potts model also suggests that positive epistasis is significantly enriched among resistance-associated mutations. Overall, our results provide valuable insights to the role of fitness barriers and positive epistasis in the evolution of drug resistance.