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

被引:15
作者
Nakatani, Sueli M. [1 ,2 ]
Santos, Carlos A. [3 ]
Riediger, Irina N. [2 ]
Krieger, Marco A. [4 ]
Duarte, Cesar A. B. [4 ]
Debur, Maria do Carmo [2 ]
Carrilho, Flair J. [1 ]
Ono, Suzane K. [1 ]
机构
[1] Univ Sao Paulo, Sch Med, Dept Gastroenterol, Sao Paulo, Brazil
[2] LACEN PR, Lab Cent Estado Parana, Sao Jose Dos Pinhais, Parana, Brazil
[3] Ctr Genomas, Sao Paulo, Brazil
[4] ICC FioCruz, Curitiba, Parana, Brazil
关键词
HCV; genotyping; NS5B region; 5 ' UTR; MAJOR GENOTYPES; ASSAY; NOMENCLATURE; SUBTYPES; SYSTEM;
D O I
10.1186/1743-422X-8-459
中图分类号
Q93 [微生物学];
学科分类号
071005 ; 100705 ;
摘要
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.
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