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Journal of Clinical Microbiology, November 2006, p. 3969-3974, Vol. 44, No. 11
0095-1137/06/$08.00+0     doi:10.1128/JCM.01122-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Genotyping Hepatitis C Viruses from Southeast Asia by a Novel Line Probe Assay That Simultaneously Detects Core and 5' Untranslated Regions{triangledown}

Suwanna Noppornpanth,1 Erwin Sablon,2 Kathy De Nys,1,2 Truong Xuan Lien,3 Jan Brouwer,1 Marianne Van Brussel,2 Saskia L. Smits,1 Yong Poovorawan,4 Albert D. M. E. Osterhaus,1 and Bart L. Haagmans1*

Department of Virology, Erasmus Medical Center, Rotterdam, The Netherlands,1 Innogenetics, N.V., Ghent, Belgium,2 Department of Biological Analysis, Pasteur Institute Ho Chi Minh City, Ho Chi Minh City, Vietnam,3 Center of Excellence in Viral Hepatitis Research, Department of Pediatrics, Chulalongkorn Hospital, Bangkok, Thailand4

Received 1 June 2006/ Returned for modification 23 July 2006/ Accepted 28 August 2006

Hepatitis C viruses (HCVs) display a high level of sequence diversity and are currently divided into six genotypes. A line probe assay (LiPA), which targets the 5' untranslated region (5'UTR) of the HCV genome, is widely used for genotyping. However, this assay cannot distinguish many genotype 6 subtypes from genotype 1 due to high sequence similarity in the 5'UTR. We investigated the accuracy of a new generation LiPA (VERSANT HCV genotype 2.0 assay), in which genotyping is based on 5'UTR and core sequences, by testing 75 selected HCV RNA-positive sera from Southeast Asia (Vietnam and Thailand). For comparison, sera were tested on the 5'UTR based VERSANT HCV genotype assay and processed for sequence analysis of the 5'UTR-to-core and NS5b regions as well. Phylogenetic analysis of both regions revealed the presence of genotype 1, 2, 3, and 6 viruses. Using the new LiPA assay, genotypes 6c to 6l and 1a/b samples were more accurately genotyped than with the previous test only targeting the 5'UTR (96% versus 71%, respectively). These results indicate that the VERSANT HCV genotype 2.0 assay is able to discriminate genotypes 6c to 6l from genotype 1 and allows a more accurate identification of genotype 1a from 1b by using the genotype-specific core information.

* Corresponding author. Mailing address: Department of Virology, Erasmus Medical Center, P.O. Box 1738, 3000 DR, Rotterdam, The Netherlands. Phone: (31) 10-4088066. Fax: (31) 10-4089485. E-mail: b.haagmans{at}erasmusmc.nl.

{triangledown} Published ahead of print on 6 September 2006.

Journal of Clinical Microbiology, November 2006, p. 3969-3974, Vol. 44, No. 11
0095-1137/06/$08.00+0     doi:10.1128/JCM.01122-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.



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