Discrepant results of hepatitis B virus genotype determination by PCR and DNA sequencing

Currently, multiplex-PCR with genotype-specific primers is widely used for preliminary screening of hepatitis B virus (HBV) genotypes, despite its relatively lower accuracy compared with whole genome sequencing. Here, we present the discrepant results of HBV genotyping by PCR and full-length sequencing. HBV DNA was isolated from chronic hepatitis B serum and the HBV genotype was detected by PCR using genotype-specific primers and full-length genome sequencing. As a result, the determination of genotype B by the PCR method was consistent with the DNA sequencing results; however, PCR revealed that genotype C showed a mix of B and C genotypes in the current study. In conclusion, the PCR-based genotyping may not provide accurate information of the HBV genotype and whole genome sequencing remains the "gold standard" for HBV genotyping.