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PLoS One. 2017 Jan 20;12(1):e0170420. doi: 10.1371/journal.pone.0170420. eCollection 2017.

Characterization of the Drug Resistance Profiles of Patients Infected with CRF07_BC Using Phenotypic Assay and Ultra-Deep Pyrosequencing.

Huang SW1, Li WY1,2, Wang WH1,3, Lin YT1, Chou CH4, Chen M5,6,7, Huang HD4,8, Chen YH1,2,9, Lu PL1,2,10, Wang SF1,11, Oka S12,13, Chen YA1,2.

Author information

1
Center for Infectious Disease and Cancer Research (CICAR), Kaohsiung Medical University, Kaohsiung, Taiwan.
2
Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.
3
Departments of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.
4
Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan.
5
Department of Urology, Mackay Memorial Hospital, Taipei, Taiwan.
6
Department of Cosmetic Applications and Management, Mackay Junior College of Medicine, Nursing and Management, Taipei, Taiwan.
7
School of Medicine, Mackay Medical College, New Taipei City, Taiwan.
8
Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan.
9
Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.
10
Department of Laboratory Medicine, and Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.
11
Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan.
12
AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan.
13
Center for AIDS Research, Kumamoto University, Kumamoto, Japan.

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-naïve 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%.

PMID:
28107423
PMCID:
PMC5249062
DOI:
10.1371/journal.pone.0170420
[Indexed for MEDLINE]
Free PMC Article

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