title: Comparative study of three methods for genotyping hepatitis C virus strains in samples from Spanish patients.
abstract: Hepatitis C virus (HCV) genotypes may be investigated by a variety of laboratory methods that target different parts of the HCV genome and have various degrees of technical difficulty. Since the choice of a particular method is difficult, we compared the performance of (i) a type-specific PCR with type-specific primers from the core region, (ii) molecular hybridization of the PCR-amplified 5' noncoding region to type-specific probes, and (iii) identification of type-specific antibodies against epitopes of nonstructural region 4 by enzyme-linked immunosorbent assay (ELISA). One hundred fifty-one patients with biopsy-proved chronic hepatitis and HCV RNA in serum were investigated. The HCV genotype was identified in 99%, 100%, and 85% of the cases by type-specific PCR, probe hybridization, and ELISA, respectively. The type-specific PCR disclosed infection with type 1a in 3%, type 1b in 74%, and type 3a in 4% of the cases and suggested infection with two or more HCV types, including 2a/2c and 2b, in the remaining 18%. Apparently mixed infections were more prevalent in patients with past intravenous drug use (P < 0.001), but cloning and sequencing of PCR products did not confirm a mixed infection in any of the four cases investigated. Concordant results were obtained by the three procedures with virtually all of the samples in which the type-specific PCR revealed a single HCV genotype. Type-specific hybridization and ELISA usually recognized the genotype producing the strongest DNA band in samples in which type-specific PCR suggested a mixed infection. In conclusion, the three procedures evaluated in this study are reliable for investigation of HCV genotype. Type-specific PCR provides information about HCV subtypes, but a mixed infection detected with this method should be interpreted with caution.
authors.affiliation: Liver Unit, University of Barcelona, Catalonia, Spain.
authors.forename: X
authors.initials: X
authors.lastname: Forns
authors.forename: M D
authors.initials: MD
authors.lastname: Maluenda
authors.forename: F X
authors.initials: FX
authors.lastname: López-Labrador
authors.forename: S
authors.initials: S
authors.lastname: Ampurdanès
authors.forename: E
authors.initials: E
authors.lastname: Olmedo
authors.forename: J
authors.initials: J
authors.lastname: Costa
authors.forename: P
authors.initials: P
authors.lastname: Simmonds
authors.forename: J M
authors.initials: JM
authors.lastname: Sánchez-Tapias
authors.forename: M T
authors.initials: MT
authors.lastname: Jimenez De Anta
authors.forename: J
authors.initials: J
authors.lastname: Rodés
mesh_terms: D004797:Enzyme-Linked Immunosorbent Assay; D016679:Genome, Viral; D016174:Hepacivirus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D016133:Polymerase Chain Reaction; D013030:Spain