Characterization of the drug resistance profiles of patients infected with CRF07-BC using phenotypic assay and ultra-deep pyrosequencing

Szu Wei Huang, Wei You Li, Wen Hung Wang, Yu Ting Lin, Chih Hung Chou, Marcelo Chen, Hsien Da Huang, Yen Hsu Chen, Po Liang Lu, Sheng Fan Wang, Shinichi Oka, Yi Ming Arthur Chen

Research output: Contribution to journalArticle

1 Citation (Scopus)

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%.

Original languageEnglish
Article numbere0170420
JournalPLoS One
Volume12
Issue number1
DOIs
Publication statusPublished - Jan 1 2017
Externally publishedYes

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Fingerprint Dive into the research topics of 'Characterization of the drug resistance profiles of patients infected with CRF07-BC using phenotypic assay and ultra-deep pyrosequencing'. Together they form a unique fingerprint.

  • Cite this

    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(1), [e0170420]. https://doi.org/10.1371/journal.pone.0170420