Identification of minority resistance mutations in the HIV-1 integrase gene using Next Generation Sequencing. HIV integrase deep sequencing.

The current widely applied standard method to screen for HIV-1 genotypic resistance is based on Sanger population sequencing. This method does not allow for the identification of low-level minority variants (MVs) (i.e. below the limit of detection for the Sanger-method) in patients receiving integrase strand-transfer inhibitors (INSTI). Next Generation Sequencing (NGS) has facilitated the detection of MVs at a much deeper level than traditional Sanger population sequencing. Here we used the Illumina MiSeq sequencing approach to evaluate the presence of MVs involved in resistance to the three commonly used INSTI: RAL, EVG and DTG.