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

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. (C) 1998 Elsevier Science B.V. All rights reserved.