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Göteborgs universitets publikationer

Genotyping of hepatitis C virus by Taqman real-time PCR.

Författare och institution:
Magnus Lindh (Institutionen för laboratoriemedicin, Avdelningen för klinisk virologi); Charles Hannoun (Institutionen för laboratoriemedicin, Avdelningen för klinisk virologi)
Publicerad i:
Journal of clinical virology, 34 ( 2 ) s. 108-114
Artikel, refereegranskad vetenskaplig
Sammanfattning (abstract):
BACKGROUND: Genotype of hepatitis C virus (HCV) is of major importance for the outcome of treatment. The response rate is considerably lower for genotype 1, the predominant genotype in western countries. OBJECTIVES: To develop and evaluate a new, simple method for genotyping of HCV based on real-time polymerase chain reaction (PCR) and Taqman probes targeting the 5' non-coding region. STUDY DESIGN: The method was compared with Innolipa on 220 serum samples representing genotypes 1-4, and was applied on a further 614 clinical samples. RESULTS: Taqman typing of the 220 samples showed genotype 1 in 69, genotype 2 in 58, genotype 3 in 57 and genotype 4 in 19, while 17 were non-reactive. There was a complete concordance with Innolipa with the exception of seven samples, which were of genotype 1 by Taqman, but genotype 4 by Innolipa. Sequencing of these samples showed a subtype 4 variant which differed at two positions compared with subtypes 4b/c/d, which are targeted by the probe. By adding a modified probe, these genotype 4 variants could also be identified. Out of 614 consecutive clinical samples, 524 could be typed by the Taqman assay; 45.2% were genotype 1, 19.3% genotype 2, 33.8% genotype 3 and 1.7%, genotype 4. CONCLUSION: The method was overall accurate and provides an attractive alternative for genotyping because processing time and costs are significantly reduced. Inclusion of probes targeting genotypes 5 and 6 is required for the method to be useful in areas where these genotypes are present.
Ämne (baseras på Högskoleverkets indelning av forskningsämnen):
5' Untranslated Regions, genetics, DNA Primers, Genotype, Hepacivirus, classification, genetics, Humans, Phylogeny, Polymerase Chain Reaction, methods, RNA, Messenger, genetics, RNA, Viral, genetics, Sensitivity and Specificity, Sequence Analysis, DNA
Postens nummer:
Posten skapad:
2007-10-22 13:11
Posten ändrad:
2012-01-27 10:16

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