Arch Virol (1996) 141:1101-1113 _Archives Vi rology © Springer-Verlag 1996 Printed in Austria Usefulness and limitation of phylogenetic analysis for hepatitis C virus core region: application to isolates from Egyptian and Yemeni patients T. Ohno 1, M. Mizokami 2, M. G. Saleh3, E. Orito 2, K.-I. Ohbaa, R.-R. Wu2, T. Koide2, C. J. Tibbs3, K. T. Nouri-Aria 3, S. Tokudome 1, and R. Williams 3 Department of Public Health and 2Second Department of Medicine, Nagoya City University Medical School, Nagoya, Japan 3Institute of Liver Studies, King's College Hospital, London, U.K. Accepted January 17, 1996 Summary. 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 lc. 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 lc. 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. Introduction Hepatitis C virus (HCV) was identified as a major causative agent of non-A, non-B hepatitis [8, 16]. The development of several convenient methods for the detection of HCV antibodies and HCV RNA has facilitated epidemiological and molecular biological studies on HCV infection [1, 9, 20]. Especially, the nucleo- tide sequences of many HCV isolates from all over the world have been reported, and comparisons of these nucteotide sequences have revealed that the HCV genome is heterogeneous [-6, 10, 12, 15, 26, 27]. Several HCV classification