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Hepatitis C virus (HCV) genotyping by annealing reverse transcription-PCR products with genotype-specific capture probes

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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.

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Authors and Affiliations

  1. Panbionet, Corp., POSTECH Biotech Center, Pohang, 790-784, Republic of Korea

    Jungmin Rho & Sung Key Jang

  2. Division of Molecular and Life Sciences, Pohang University of Science and Technology, Pohang, 790-784, Republic of Korea

    Sung Key Jang

  3. Division of Hepatology, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, 137-040, Republic of Korea

    Wonhee Hur, Chang Wook Kim, Jeong Won Jang, Si Hyun Bae, Jong Young Choi & Seung Kew Yoon

  4. WHO Collaborating Center on Viral Hepatitis, College of Medicine, The Catholic University of Korea, Seoul, 137-040, Republic of Korea

    Jong Soon Ryu, Chang Wook Kim, Jeong Won Jang, Si Hyun Bae, Jong Young Choi & Seung Kew Yoon

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  1. Jungmin Rho
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  2. Jong Soon Ryu
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  3. Wonhee Hur
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  4. Chang Wook Kim
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  7. Jong Young Choi
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Correspondence to Seung Kew Yoon.

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Rho, J., Ryu, J.S., Hur, W. et al. Hepatitis C virus (HCV) genotyping by annealing reverse transcription-PCR products with genotype-specific capture probes. J Microbiol. 46, 81–87 (2008). https://doi.org/10.1007/s12275-007-0121-8

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

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