Comparative performance evaluation of hepatitis C virus genotyping based on the 5' untranslated region versus partial sequencing of the NS5B region of brazilian patients with chronic hepatitis C.

Abstract

BACKGROUND:

Genotyping of hepatitis C virus (HCV) has become an essential tool for prognosis and prediction of treatment duration. The aim of this study was to compare two HCV genotyping methods: reverse hybridization line probe assay (LiPA v.1) and partial sequencing of the NS5B region.

METHODS:

Plasma of 171 patients with chronic hepatitis C were screened using both a commercial method (LiPA HCV Versant, Siemens, Tarrytown, NY, USA) and different primers targeting the NS5B region for PCR amplification and sequencing analysis.

RESULTS:

Comparison of the HCV genotyping methods showed no difference in the classification at the genotype level. However, a total of 82/171 samples (47.9%) including misclassification, non-subtypable, discrepant and inconclusive results were not classified by LiPA at the subtype level but could be discriminated by NS5B sequencing. Of these samples, 34 samples of genotype 1a and 6 samples of genotype 1b were classified at the subtype level using sequencing of NS5B.

CONCLUSIONS:

Sequence analysis of NS5B for genotyping HCV provides precise genotype and subtype identification and an accurate epidemiological representation of circulating viral strains.

• Authors: Sueli M Nakatani, Carlos A Santos, Irina N Riediger, Marco A Krieger, Cesar A B Duarte, Maria do Carmo Debur, Flair J Carrilho, Suzane K Ono
• Journal: Virology journal (Virol J) Vol. 8 Pg. 459 (Oct 03 2011) ISSN: 1743-422X [Electronic] England
• PMID: 21967749 (Publication Type: Comparative Study, Journal Article, Research Support, Non-U.S. Gov't)

Chemical References

• 5' Untranslated Regions
• DNA Primers
• Viral Nonstructural Proteins
• NS-5 protein, hepatitis C virus

Topics

• 5' Untranslated Regions (genetics)
• Brazil
• DNA Primers (chemistry, genetics)
• Genome, Viral
• Genotype
• Hepacivirus (classification, genetics, isolation & purification)
• Hepatitis C, Chronic (blood, genetics, virology)
• Humans
• Molecular Typing (methods)
• Nucleic Acid Hybridization (methods)
• Phylogeny
• Reverse Transcriptase Polymerase Chain Reaction
• Sequence Analysis, DNA (methods)
• Viral Nonstructural Proteins (blood, genetics)