Genotyping hepatitis C viruses from Southeast Asia by a novel line probe assay that simultaneously detects core and 5' untranslated regions.
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.
Noppornpanth
Suwanna
S
Department of Virology, Erasmus Medical Center, P.O. Box 1738, 3000 DR, Rotterdam, The Netherlands.
Sablon
Erwin
E
De Nys
Kathy
K
Truong
Xuan Lien
XL
Brouwer
Jan
J
Van Brussel
Marianne
M
Smits
Saskia L
SL
Poovorawan
Yong
Y
Osterhaus
Albert D M E
AD
Haagmans
Bart L
BL
D020121:5' Untranslated Regions / Q000235:genetics*; D001483:Base Sequence; D005838:Genotype; D016174:Hepacivirus / Q000145:classification* / Q000235:genetics; D008969:Molecular Sequence Data; D009693:Nucleic Acid Hybridization / Q000379:methods*; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D014758:Viral Core Proteins / Q000235:genetics*
D020121:5' Untranslated Regions; D014758:Viral Core Proteins