title: Usefulness and limitation of phylogenetic analysis for hepatitis C virus core region: application to isolates from Egyptian and Yemeni patients.
abstract: We report here the nucleotide sequences of the core region of HCV isolates from Egyptian and Yemeni patients and the method for classifying these HCV isolates by phylogenetic analysis. Sequence comparison suggested that the genotypes of these isolates were the same. Preliminary phylogenetic analysis of the HCV core region indicated that the genotypes of both isolates were 1c. However, an additional phylogenetic tree of the HCV core region constructed using a greater number of HCV isolates than that used in the preliminary analysis and on the basis of alignment of nucleotide sequences in an appropriate length indicated that the genotypes of these isolates were 4 and not 1c. For a more detailed analysis, the nucleotide sequences of the HCV E1 region as well as the core region for the same Yemeni patient were determined. A phylogenetic tree of the E1 region confirmed that the genotype of the HCV isolate from the Yemeni patient was 4. These data indicate that even when classifying HCV isolates using phylogenetic analysis, the misclassification would occur if care is not taken regarding the number and sequence lengths of the isolates included in the analysis.
authors.affiliation: Department of Public Health, Nagoya City University Medical School, Japan.
authors.forename: T
authors.initials: T
authors.lastname: Ohno
authors.forename: M
authors.initials: M
authors.lastname: Mizokami
authors.forename: M G
authors.initials: MG
authors.lastname: Saleh
authors.forename: E
authors.initials: E
authors.lastname: Orito
authors.forename: K I
authors.initials: KI
authors.lastname: Ohba
authors.forename: R R
authors.initials: RR
authors.lastname: Wu
authors.forename: T
authors.initials: T
authors.lastname: Koide
authors.forename: C J
authors.initials: CJ
authors.lastname: Tibbs
authors.forename: K T
authors.initials: KT
authors.lastname: Nouri-Aria
authors.forename: S
authors.initials: S
authors.lastname: Tokudome
authors.forename: R
authors.initials: R
authors.lastname: Williams
mesh_terms: D001483:Base Sequence; D004279:DNA, Viral; D004534:Egypt; D005838:Genotype; D016174:Hepacivirus / Q000145:classification* / Q000235:genetics; D006526:Hepatitis C / Q000821:virology; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D012689:Sequence Homology, Nucleic Acid; D014758:Viral Core Proteins / Q000235:genetics*; D014759:Viral Envelope Proteins / Q000235:genetics*; D015006:Yemen
chemical_list: D004279:DNA, Viral; C087035:E1 protein, Hepatitis C virus; D014758:Viral Core Proteins; D014759:Viral Envelope Proteins; C069130:nucleocapsid protein, Hepatitis C virus