Title: Characterization of the Drug Resistance Profiles of Patients Infected with CRF07_BC Using Phenotypic Assay and Ultra-Deep Pyrosequencing
Authors: Huang, Szu-Wei
Li, Wei-You
Wang, Wen-Hung
Lin, Yu-Ting
Chou, Chih-Hung
Chen, Marcelo
Huang, Hsien-Da
Chen, Yen-Hsu
Lu, Po-Liang
Wang, Sheng-Fan
Oka, Shinichi
Chen, Yi-Ming Arthur
Department of Biological Science and Technology
Institude of Bioinformatics and Systems Biology
Issue Date: 20-Jan-2017
Abstract: The usefulness of ultra-deep pyrosequencing (UDPS) for the diagnosis of HIV-1 drug resistance (DR) remains to be determined. Previously, we reported an explosive outbreak of HIV-1 circulating recombinant form (CRF) 07_BC among injection drug users (IDUs) in Taiwan in 2004. The goal of this study was to characterize the DR of CRF07_BC strains using different assays including UDPS. Seven CRF07_BC isolates including 4 from early epidemic (collected in 2004 - 2005) and 3 from late epidemic (collected in 2008) were obtained from treatment-naive patient\'s peripheral blood mononuclear cells. Viral RNA was extracted directly from patient\'s plasma or from cultural supernatant and the pol sequences were determined using RT-PCR sequencing or UDPS. For comparison, phenotypic drug susceptibility assay using MAGIC-5 cells (in-house phenotypic assay) and Antivirogram were performed. In-house phenotypic assay showed that all the early epidemic and none of the late epidemic CRF07_BC isolates were resistant to most protease inhibitors (PIs) (4.4 - 47.3 fold). Neither genotypic assay nor Antivirogram detected any DR mutations. UDPS showed that early epidemic isolates contained 0.01 +/- 0.08% of PI DR major mutations. Furthermore, the combinations of major and accessory PI DR mutations significantly correlated with the phenotypic DR. The in-house phenotypic assay is superior to other conventional phenotypic assays in the detection of DR variants with a frequency as low as 0.01%.
URI: http://dx.doi.org/10.1371/journal.pone.0170420
ISSN: 1932-6203
DOI: 10.1371/journal.pone.0170420
Journal: PLOS ONE
Volume: 12
Issue: 1
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