Development of Hepatitis C Virus Genotyping by Real-Time PCR Based on the NS5B Region

dc.contributor.authorNakatani, Sueli M.
dc.contributor.authorSantos, Carlos A.
dc.contributor.authorRiediger, Irina N.
dc.contributor.authorKrieger, Marco A.
dc.contributor.authorDuarte, Cesar A. B.
dc.contributor.authorLacerda, Marco A.
dc.contributor.authorBiondo, Alexander W.
dc.contributor.authorCarilho, Flair J.
dc.contributor.authorOno-Nita, Suzane K.
dc.contributor.departmentMedicine, School of Medicineen_US
dc.description.abstractHepatitis C virus (HCV) genotyping is the most significant predictor of the response to antiviral therapy. The aim of this study was to develop and evaluate a novel real-time PCR method for HCV genotyping based on the NS5B region. Methodology/Principal Findings Two triplex reaction sets were designed, one to detect genotypes 1a, 1b and 3a; and another to detect genotypes 2a, 2b, and 2c. This approach had an overall sensitivity of 97.0%, detecting 295 of the 304 tested samples. All samples genotyped by real-time PCR had the same type that was assigned using LiPA version 1 (Line in Probe Assay). Although LiPA v. 1 was not able to subtype 68 of the 295 samples (23.0%) and rendered different subtype results from those assigned by real-time PCR for 12/295 samples (4.0%), NS5B sequencing and real-time PCR results agreed in all 146 tested cases. Analytical sensitivity of the real-time PCR assay was determined by end-point dilution of the 5000 IU/ml member of the OptiQuant HCV RNA panel. The lower limit of detection was estimated to be 125 IU/ml for genotype 3a, 250 IU/ml for genotypes 1b and 2b, and 500 IU/ml for genotype 1a. Conclusions/Significance The total time required for performing this assay was two hours, compared to four hours required for LiPA v. 1 after PCR-amplification. Furthermore, the estimated reaction cost was nine times lower than that of available commercial methods in Brazil. Thus, we have developed an efficient, feasible, and affordable method for HCV genotype identification.en_US
dc.eprint.versionFinal published versionen_US
dc.identifier.citationNakatani SM, Santos CA, Riediger IN, Krieger MA, Duarte CAB, Lacerda MA, et al. (2010) Development of Hepatitis C Virus Genotyping by Real-Time PCR Based on the NS5B Region. PLoS ONE 5(4): e10150.
dc.publisherPublic Library of Scienceen_US
dc.relation.journalPLoS ONEen_US
dc.rightsAttribution 4.0 International*
dc.subjectPolymerase chain reactionen_US
dc.subjectHepatitis C virusen_US
dc.subjectUntranslated regionsen_US
dc.subjectRNA extractionen_US
dc.subjectReverse transcriptionen_US
dc.subjectPhylogenetic analysisen_US
dc.titleDevelopment of Hepatitis C Virus Genotyping by Real-Time PCR Based on the NS5B Regionen_US
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