The categorization of HCV isolates into genotypes occurred during the characterization of HCV clones in different laboratories by sequencing. This has led to the establishment of extensive phylogenetic trees, which are usually based upon comparative sequence analysis of subgenomic regions, such as those spanning core, E1, or NS5B (Bukh et al., 1995) (Section 3.2). Given the high sequence diversity of HCV, sequence analysis of these short regions has often provided enough information for definitive genotyping and, in many cases, subtyping as well (Bukh et al., 1993). Although sequencing is the “gold standard” for genotyping and subtyping, several faster methods have been designed to provide the same information. For example, RT/PCR products from different subgenomic regions of the viral genome have been generated using universal primers that presumably permit amplification of viral RNA from all genotypes and subtypes (Ch. 19). Following amplification using universal primers, one approach then uses genotype-specific primers for further (nested) amplification of only targets with the corresponding sequences (Kato et al., 1991; Okamoto et al., 1994, 1996). Genotype-specific core region primers could distinguish between 1a, 1b, 1c, 2a, 2b, and 3a sequences in the nested amplification step (Okamoto et al., 1992c, 1994). Alternatively, the RT/PCR products resulting from amplification using universal primers have been tested for hybridization to genotype-specific probes (Li et al., 1991, 1994; Takada et al., 1993) or have been digested with one or more restriction endonucleases to permit identification of digestion fragments that are genotype specific (Nakao et al., 1991; Murphy, Willems ' Delage, 1994).