Genotyping of hepatitis C virus based on NS5B region sequence analysis

Objective: To establish a method of genotyping for HCV based on NS5B region sequence analysis. Methods:Serum HCV RNA levels in 41 patients with chronic hepatit is C in Shanghai area were determined using the real time fluorescent quantitat ive polymerase chain reaction (PCR) assay. Part of HCV NS5B region was amplified by RT PCR and nested PCR, the PCR products were subjected to direct sequencing. A 222 bp segment of the HCV NS5B region was used to construct phylogenetic trees for analyzing the relationships between the amplified NS5B region sequences and 25 published proto type sequences retrieved from the GenBank data base.Results:Genotype classification based on phylogenetic analysis o f the commonly used 222 bp long NS5B region was possible for all serum samples tested in this study. Among the 41 samples tested 35(85.4%) were 1b subtype, 5( 12.2%)and 1(2.4%) were 2a subtype and 3a subtype respectively. Other genotypes a nd subtypes were not detected. Conclusions:Phylogenetic analysis based on the NS5B region was a reliable and convenient method for HCV genotyping. 1b subtype seemed to be the dominant genotype of HCV in Shanghai area.