Hepatitis B virus genotype assignment using restriction fragment length polymorphism patterns

Hepatitis B virus (HBV) is classified into genotypes A-F, which is importan t for clinical and etiological investigations. To establish a simple genoty ping method, 68 full-genomic sequences and 106 S gene sequences mere analyz ed by the molecular evolutionary method. HBV genotyping with the S gene seq uence is consistent with genetic analysis using the full-genomic sequence. After alignment of the S sequences, genotype specific regions are identifie d and digested by the restriction enzymes, HphI, NciI, AlwI, EarI, and nlaI V, This HBV genotyping system using restriction fragment length polymorphis m (RFLP) was confirmed to be correct when the PCR products of the S gene in 23 isolates collected from various countries were digested with this metho d. A restriction site for EarI in genotype B was absent in spite of its pre sence in all the other genotypes and genotype C has no restriction site for AlwI. Only genotype E is digested with NciI, while only genotype F has a r estriction site for HphI. Genotype A can be distinguished by a single restr iction enzyme site for NlaIV, while genotype D digestion with this enzyme r esults in two products that migrates at 265 and 186 bp, This simple and acc urate HBV genotyping system using RFLP is considered to be useful for resea rch on HBV, (C) 1999 Federation of European Biochemical Societies.