Characterization and validation of a deep sequencingbased HIV-1 genotypic and coreceptor tropism assay to simultaneously monitor susceptibility to maturation, protease, reverse transcriptase, and integrase inhibitors, and CCR5 antagonists

• Published in: Antiviral therapy 2013-01, Vol.18, p.A3-A3
• Main Authors: Gibson, R M, Meyer, A M, Winner, D, Archer, J, Feyertag, F, Robertson, D L, Ruiz-Mateos, E, Leal, M, Schmotzer, C, Quinones-Mateu, M E
• Format: Article
• Language: English
• Subjects: Human immunodeficiency virus 1
• ISSN: 1359-6535

There are 26 antiretroviral drugs, from 6 classes, approved for the treatment of HIV-1 infection. Thus, a combination of different phenotypic and genotypic tests is needed to monitor HIV-infected individuals. In this study, we developed a novel HIV-1 genotypic assay based on deep sequencing to simultaneously assess HIV-1 susceptibility to all drugs targeting the three viral enzymes as well as to quantify coreceptor tropism. Baseline samples from a cohort of antiretroviral-experienced patients on a maraviroc-based regimen were used to generate gag-p2/NCp7/p1/p6/pol- PR/RT/INT and env/C2V3 PCR products. Purified amplicons were used in the construction of barcoded libraries and sequenced on the Ion Torrent PGM. DEEPGEN(TM)HIV, our novel allinclusive HIV-1 genotypic and coreceptor tropism assay based on deep sequencing of the protease, RT, integrase and env C2V3 region, permits the multiplexed detection of low level drug-resistant and/or non-R5 viruses in up to 96 clinical samples simultaneously. This comprehensive test, the first of its class, could be instrumental in the development of new antiretroviral drugs and, more important, will aid in the treatment and management of HIV-infected individuals.