Abstract

The HIV Gag polyprotein has been demonstrated to modulate HIV resistance. The aim of our project was use Ultra Deep Sequencing (UDS) to identify novel Gag mutations and changes in the 5’ UTR sequences when protease inhibitor resistance occurs. Samples were chosen from patients on protease inhibitor (PI) treatment and with PI mutations who had had an HIV genotyping test in the past 12 months. Eight sequences were obtained from twelve patient samples using primers for the UTR. The potential RNA secondary structures of each were obtained and folded using Mfold version 3.5. None of the associated RNA structures deviated significantly from the wild type virus. However, in 4/8 RNA sequences it was possible to demonstrate that multiple RNA structures could potentially exist simultaneously. This might indicate evolution of RNA structure over time. Ten Gag sequences were generated and in the protease cleavage sites the following mutations were found: MA/CA = I138L, CA/p2 = N372 K/G/A. In addition, 65 mutations were found in Matrix, 36 mutations in Capsid, 20 in Nucleocapsid, 3 in p1 and 46 in p6. We successfully demonstrated the use of UDS for the discovery of both novel resistance mutations and RNA secondary structures in HIV sequences.