Genotyping of hepatitis B virus by restriction pattern analysis of a pre-S amplicon

J Virol Methods. 1998 Jun;72(2):163-74. doi: 10.1016/s0166-0934(98)00026-3.


A method is described for genotyping of hepatitis B virus (HBV), based on the restriction fragment length polymorphism (RFLP) created by Ava2 and Dpn2 action on an amplified segment of the pre-S region. Analysing 51 database sequences by phylogenetic tree construction and RFLP prediction, the method was shown to be capable of detecting all known genotypes (A-F). The method was applied to 99 serum samples from hepatitis B e antigen (HBeAg)-positive chronic carriers, comparing observed agarose gel patterns with the RFLP predicted from the database sequences. In 95 typable samples the following genotypes were observed; 23 A, 20 B, 20 C, 22 D, 5 E and 5 F. Phylogenetic grouping of the 51 database sequences and RFLP genotyping of the 99 patient samples were compared with typing based on S gene analysis, showing disagreement in only one case, a database sequence of ayw subtype which was classified as genotype D by pre-S region and genotype A by S region analysis. This method should be useful for epidemiological investigations and for studying the potential influence of genotype on the course of infection.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Genotype
  • Hepatitis B virus / classification*
  • Hepatitis B virus / genetics*
  • Humans
  • Phylogeny
  • Polymerase Chain Reaction
  • Polymorphism, Restriction Fragment Length*
  • Virology / methods