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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

Sueli M Nakatani14, Carlos A Santos2, Irina N Riediger1, Marco A Krieger3, Cesar AB Duarte3, Maria do Carmo Debur1, Flair J Carrilho4 and Suzane K Ono4*

Author Affiliations

1 Laboratório Central do Estado do Paraná, LACEN-PR, São José dos Pinhais, Paraná, Brazil

2 Centro de Genomas, São Paulo, São Paulo, Brazil

3 Instituto Carlos Chagas (ICC) FioCruz, Curitiba, Paraná, Brazil

4 Department of Gastroenterology, São Paulo University School of Medicine, São Paulo, Brazil

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Virology Journal 2011, 8:459  doi:10.1186/1743-422X-8-459

Published: 3 October 2011



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.


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.


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.


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

HCV; genotyping; NS5B region; 5'UTR