Hepatitis C Virus (HCV) Genotyping by Annealing Reverse Transcription-PCR Products with Genotype-Specific Capture Probes

Jungmin Rho; Jong Soon Ryu; Wonhee Hur; Chang Wook Kim; Jeong Won Jang; Si Hyun Bae; Jong Young Choi; Sung Key Jang; Seung Kew Yoon

doi:10.1007/s12275-007-0121-8

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Hepatitis C Virus (HCV) Genotyping by Annealing Reverse Transcription-PCR Products with Genotype-Specific Capture Probes: Jungmin Rho ¹, Jong Soon Ryu ², Wonhee Hur ³, Chang Wook Kim ^2,3, Jeong Won Jang ^2,3, Si Hyun Bae ^2,3, Jong Young Choi ^2,3, Sung Key Jang ^1,4, Seung Kew Yoon ^2,3; Journal of Microbiology 2008;46(1):81-87.
DOI: https://doi.org/10.1007/s12275-007-0121-8

Author Affiliations

¹Panbionet, Corp., POSTECH Biotech Center, Pohang 790-784, Republic of Korea, ²WHO Collaborating Center on Viral Hepatitis, College of Medicine, The Catholic University of Korea, Seoul 137-040, Republic of Korea, ³Division of Hepatology, Department of Internal Medicine, The Catholic University of Korea, Seoul 137-040, Republic of Korea, ⁴Division of Molecular and Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea

Corresponding author: Seung Kew Yoon , Tel: 82-2-590-2622,

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Abstract

The genotype of the hepatitis C virus (HCV) strain infecting a given patient is an important predictive factor for the clinical outcome of chronic liver disease and its response to anti-viral therapeutic agents. We herein sought to develop a new easy, sensitive and accurate HCV genotyping method using annealing genotype- specific capture probes (AGSCP) in an automation-friendly 96-well plate format. The validation of our new AGSCP was performed using the Standard HCV Genotype Panel. We then used both our AGSCP and the commercially available INNO-LiPA assay to analyze the HCV genotypes from 111 Korean patients. Discordant results were analyzed by direct sequencing. AGSCP successfully genotyped the standard panel. The genotypes of 111 patient samples were also obtained successfully by AGSCP and INNO-LiPA. We observed a high concordance rate (93 matched samples, 83.8%) between the two assays. Sequencing analysis of the 18 discordant results revealed that the AGSCP had correctly identified 12 samples, whereas the INNO- LiPA had correctly identified only 6. These results collectively indicate that AGSCP assay is a convenient and sensitive method for large-scale genotyping, and it may be a promising tool for the determination of HCV and other genotypes in clinical settings.

Keywords: hepatitis C virus;genotype;reverse-hybridization

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Hepatitis C Virus (HCV) Genotyping by Annealing Reverse Transcription-PCR Products with Genotype-Specific Capture Probes

J. Microbiol. 2008;46(1):81-87.

DOI: https://doi.org/10.1007/s12275-007-0121-8

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