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%.
- IMMUNODEFICIENCY-VIRUS TYPE-1; HIV-1 SUBTYPE B; REVERSE-TRANSCRIPTASE; MOLECULAR EPIDEMIOLOGY; IN-VITRO; ANTIRETROVIRAL THERAPY; COMBINATION THERAPIES; CLINICAL-SIGNIFICANCE; REPLICATION CAPACITY; PROTEASE INHIBITORS
Huang, S-W., Li, W-Y., Wang, W-H., Lin, Y-T., Chou, C-H., Chen, M., Huang, H-D., Chen, Y-H., Lu, P-L., Wang, S-F., Oka, S., & Chen, Y-M. A. (2017). Characterization of the Drug Resistance Profiles of Patients Infected with CRF07_BC Using Phenotypic Assay and Ultra-Deep Pyrosequencing. PLoS ONE, 12, [e0170420]. https://doi.org/10.1371/journal.pone.0170420