HIV-1 drug-resistance genotyping by ultra-deep sequencing increases the sensitivity of detection of minor and intermediate resistant viral populations

HIV-1 resistance genotyping is recommended prior to and during HAART therapy to detect the presence of resistant viral populations associated with treatment failure. The recently developed ultra-deep sequencing technology (UDS) is claimed to be able to detect such variants with a sensitivity cutoff of 1%, which appears to be clinically relevant. The goal of this study was to compare the results of UDSbased genotyping of the HIV-1 protease (Pr) and reverse transcriptase (RT) genotyping. We compared the new kit developed by Roche Diagnostics on GS Junior Sequencer to two bulk sequencing methods: ViroSeq HIV-1 Genotyping System (Abbott Molecular) on ABI Prism 3130XL sequencer (Life Technologies) and TRUGENE HIV-1 (Siemens Healthcare). The UDS-based method developed by Roche was less efficient than the other methods in amplifying samples with a low viral load. However, UDS was substantially more sensitive than bulk sequencing methods and could detect mutations that represented as few as 1% of the viral quasispecies. Thus, UDS appears as a promising method for HIV resistance genotyping and prediction of resistance emergence.