Hepatitis B virus genotype assignment using restriction fragment length polymorphism patterns

Hepatitis B virus (HBV) is classified into genotypes A–F, which is important for clinical and etiological investigations. To establish a simple genotyping method, 68 full-genomic sequences and 106 S gene sequences were analyzed by the molecular evolutionary method. HBV genotyping with the S gene seq...

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Bibliographic Details
Published in:FEBS letters 1999-04, Vol.450 (1), p.66-71
Main Authors: Mizokami, Masashi, Nakano, Tatsunori, Orito, Etsuro, Tanaka, Yasuhito, Sakugawa, Hiroshi, Mukaide, Motokazu, Robertson, Betty H.
Format: Article
Language:English
Subjects:
Base Sequence
Databases, Factual
DNA Restriction Enzymes - metabolism
Genes, Viral
Genotype
Genotyping
Hepatitis B virus
Hepatitis B virus - classification
Hepatitis B virus - genetics
Humans
Molecular Sequence Data
Phylogeny
Polymorphism, Restriction Fragment Length
Restriction enzyme
Restriction fragment length polymorphism
S gene
Sequence Alignment
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Summary:Hepatitis B virus (HBV) is classified into genotypes A–F, which is important for clinical and etiological investigations. To establish a simple genotyping method, 68 full-genomic sequences and 106 S gene sequences were analyzed by the molecular evolutionary method. HBV genotyping with the S gene sequence is consistent with genetic analysis using the full-genomic sequence. After alignment of the S sequences, genotype specific regions are identified and digested by the restriction enzymes, HphI, NciI, AlwI, EarI, and NlaIV. This HBV genotyping system using restriction fragment length polymorphism (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 method. A restriction site for EarI in genotype B was absent in spite of its presence 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 restriction site for HphI. Genotype A can be distinguished by a single restriction enzyme site for NlaIV, while genotype D digestion with this enzyme results in two products that migrates at 265 and 186 bp. This simple and accurate HBV genotyping system using RFLP is considered to be useful for research on HBV.
ISSN:0014-5793
1873-3468
DOI:10.1016/S0014-5793(99)00471-8