Nucleotide Similarity Approach The Notion of Genotypes

Although HDV was expected, like many RNA viruses, to exhibit considerable genetic variability, only three HDV genotypes (labelled genotype I, II and III) have been characterized on the basis of a small number of complete genome sequences (Casey et al. 1993; Imazeki et al. 1991; Wang et al. 1986). In 1993, J. Casey and coworkers identified strains from Columbia and Peru that have the lowest similarity score when compared with all identified HDV strains of other lineages (range, 67.5%-69.4%) (Casey et al. 1993).

Therefore, the definition of 'genotype' is based on the comparison of nu-cleotide sequence similarity between pairs of sequences that have been discovered and characterized at the time. A nucleotide similarity percentage corresponds directly to the number of positions bearing identical nucleotides between pairs of sequences, divided by the length of the alignment. For HDV genomes that are known at present, with regards to the region studied, the divergence in nucleotide sequence (= 100% - similarity score) is less than 14%-15.7% among different isolates of the same genotype and ranges from 19% to 38% between sequences from different genotypes (Casey et al. 1993; Imazeki et al. 1991; Shakil et al. 1997; Wu et al. 1998). Table 1 indicates the nucleotide similarity of the sHD coding gene.

Genotype I includes the European, Mediterranean, North American, and some Russian, African and Asian HDV isolates (Makino et al. 1987; Chao et al. 1990; Shakil et al. 1997); it was also described in the Pacific island of Nauru (Chao et al. 1990). Genotype II was initially found in Japan and Taiwan (Imazeki et al. 1990; Lee et al. 1996); some sequences from Taiwan and Okinawa islands were tentatively assigned to a subtype of genotype II (i.e., genotype IIb, see below) (Wu et al. 1998; Sakugawa et al. 1999). However, addition to the data set of sequences from Yakutia (Sakha republic, Russia), which were clearly identified as a subclade of genotype II strains, suggested that the IIb strain TW-2b (genotype IIb) might not be affiliated with HDV-IIa (HDV-2) (Ivaniushina et al. 2001). Therefore Ivaniushina et al. suggested that TW-2b might be the prototype of a new clade. Genotype III has been exclusively found in the Amazonian part of South America (Peru, Colombia, Equator, Brazil and Venezuela) (Casey et al. 1993; Nakano et al. 2001; A Kay, personal communication).

These studies on HDV genome variability have been performed in non-African countries except for the description of two sequences (assigned to genotype I) from Ethiopia and Somalia (Zhang et al. 1996). The existence of different subclades among genotype I sequences have been proposed but dismissed (Zhang et al. 1996; Shakil et al. 1997). On studying African HDV sequences (Radjef et al. 2004 and unpublished data from our laboratory), our phylogenetic analyses indicated that, in addition to genotype I-like sequences, approximately 70% of the characterized African isolates (mostly from West and Central Africa) form highly divergent groups (see the score of similarity in Table 1). These results (1) suggest a possible ancient African radiation, and (2) extend the known HDV genetic variability to probably eight major monophyletic groups or 'clades', thus bringing this satellite variability closer to human HBV genetic variability. In the following section of this review, we shall focus on these different HDV clades and shall make a proposal to suggest an updating of the classification among the Deltavirus genus.

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