23Well-designed viral protease inhibitors (PIs) potently inhibit replication as well as create 24 a high genetic barrier for resistance. Through in vivo selective pressure, we have generated 25 high-level resistance against ten HIV-1 PIs and their precursor, the FDA-approved drug 26 darunavir (DRV), achieving 1,000-fold resistance over the starting EC50. The accumulation of 27 mutations revealed two pathways to high-level resistance, resulting in protease variants with up 28 to 14 mutations in and outside of the active site. The two pathways demonstrate the interplay 29 between drug resistance and viral fitness. Replicate selections showed that one inhibitor could 30 select for resistance through either pathway, although subtle changes in chemical structure of 31 the inhibitors led to preferential use of one pathway over the other. Viral variants from the two 32 pathways showed differential selection of compensatory mutations in Gag cleavage sites. These 33 results reveal the high-level of selective pressure that is attainable with these fourth-generation 34 protease inhibitors, and the interplay between selection of mutations to confer resistance while 35 maintaining viral fitness. 36 37 3 Introduction 38