Abstract
HIV-1 Gag and protease are both involved in protease inhibitor resistance, where Gag mutations alone were reported to be able to compensate for protease inhibition. These resistance mutations arise as a result of the error-prone HIV-1 reverse transcriptase. To study if such mutations were incorporated randomly, we investigated the mutations generated in our HIV-RT cDNA synthesis PCR assay that is devoid of selection pressures involving protein fitness and immune surveillance. Studying a total of 269 one-generation sequences using HIV-1 RT, we calculated an error rate of about 8.7 × 10−5/bp with a bias towards transition mutations. We found previously reported mutations as well as unreported novel mutations in our system. Computational structural analysis showed that the novel mutations had varying effects on the thermostability of the capsid linker and the first Gag cleavage site. In this work, we showed that our platform can be used for mutation generation that could aid in the design of pre-emptive interventions, and give us an insight to the effects of emerging mutations in HIV-1 Gag.