Hepatitis B virus genotyping based on cluster analysis of the region involved in lamivudine resistance.
Hepatitis B virus (HBV) genotyping and treatment resistances analysis provide key information for the study of infected patients. Among the existing HBV genotyping methods, restriction fragment length polymorphism (RFLP) based methods are used widely, but HBV genetic variability may lead to wrong results. A simple method for HBV genotyping is described. This single assay provides information related to both genotyping and lamivudine resistance. measuring genotyping reliability. A short region including the YMDD motif of the polymerase gene was analyzed using cluster analysis of 55 isolates. To discriminate the seven HBV genotypes, a selected fragment was used as representative of each genotype (consensus sequences). Comparison between complete genomes from GenBank and from the YMDD analysis using PHILIP package was used for method testing. Sequencing of 102 different serum samples was carried out, and the results were compared with representative sequences. Consensus sequences were chosen corresponding to the different HBV genotypes. Statistical comparison between our method and others gives more than 90% of coincidences with a critical level of 0.056. Comparison between RFLP and the method described gives 3% of discordance results and 3% of untypables samples by RFLP. All the discordant results observed had a change in the pre-S sequence which introduced a new restriction site.
Rodríguez-Nóvoa
Sonia
S
Hospital Provincial de Conxo, Servicio de Microbiologi;a, Complejo Hospitalario Universitario de Santiago de Compostela, C/Ramón Baltar sn, Santiago de Compostela, La Coruña, Spain.
Gómez-Tato
Antonio
A
Aguilera-Guirao
Antonio
A
Castroagudín
Javier
J
González-Quintela
Arturo
A
Garcia-Riestra
Carlos
C
Regueiro
Benito J
BJ
D020816:Amino Acid Motifs; D001483:Base Sequence; D016000:Cluster Analysis; D004259:DNA-Directed DNA Polymerase / Q000737:chemistry* / Q000235:genetics; D024882:Drug Resistance, Viral / Q000235:genetics*; D005838:Genotype; D006515:Hepatitis B virus / Q000145:classification* / Q000187:drug effects* / Q000235:genetics; D019694:Hepatitis B, Chronic / Q000188:drug therapy / Q000821:virology; D006801:Humans; D019259:Lamivudine / Q000494:pharmacology*; D008969:Molecular Sequence Data; D012150:Polymorphism, Restriction Fragment Length; D018894:Reverse Transcriptase Inhibitors / Q000494:pharmacology*; D017422:Sequence Analysis, DNA
D018894:Reverse Transcriptase Inhibitors; D019259:Lamivudine; D004259:DNA-Directed DNA Polymerase