Genotyping of hepatitis C virus by sequencing of 5' non coding region

Abstract

The reliable method for determining the HCV genotype was developed and evaluated by following the reference standard and most definitive method for HCV genotyping which is sequencing of a specific PCR amplification portion of the HCV genome, followed by phylogenetic analysis. In this study, in-house 5' NCR amplification product obtained from the HCV RNA positive cases were subjected to direct sequencing and genotyping by phylogenetic analysis of Clustal W program. This reliable genotyping method, compared with commercial kit, is a modification of TRUGENE HCV 5' NC genotyping kit with the improve efficiency for genotyping. All specimens were successfully classified the HCV genotype and subtype. Moreover, the HCV genotype 6 variants, which are common in Southeast Asia, can be classified. This genotyping method was used to study the prevalence of HCV genotype in the patients from King Chulalongkorn Memorial Hospital. HCV genotype 3a was the most prevalent genotype (44%), followed by genotype 1b (21%) and 1a (16%). HCV genotype 6 variants were identified among 7%. The genotype data will be useful in the clinical management and treatment.