title: Inter-genotypic recombinant hepatitis C virus strains in Japan noted by discrepancies between immunoassay and sequencing.
abstract: Genetic recombination plays a significant role in the survival and evolution of hepatitis C virus (HCV), but methodological limitations have hindered the exploration of genetic recombination. HCV serotypes were evaluated in 104 patients with chronic hepatitis C when they initially presented in hospitals. Subsequently, HCV genotypes were analyzed using primers for core gene and NS5B gene. Near-complete nucleotide sequences of eight HCV isolates from two suspected patients with 2b/1b recombinant HCV were analyzed by amplification of nine overlapping regions of HCV-specific oligonucleotide primers at different time points: (i) at the first admission; (ii) before and (iii) after interferon therapy; and (iv) after development of hepatocellular carcinoma. The nucleotide sequence of eight HCV isolates obtained was 9,321-9,471 nucleotides in length, comprising a single ORF (polyprotein of 3,014 amino acids.) and segregated into discordant genotypes of 2b and 1b HCV with a recombination junction in NS2. This study highlights the need for more precise characterization of HCV in clinical samples where there is a discrepancy between immunoassays and sequencing. It also demonstrates the circulation of novel inter-genotypic recombinant HCV in Japan, because the cross over point of 2b/1b recombinant HCV in eight clinical isolates of these two patients differed from previously reported HCV recombinant from the Philippines and Japan.
authors.affiliation: Delta Clinic, Tokorozawa, Japan.
authors.forename: Hiromi
authors.initials: H
authors.lastname: Hoshino
authors.forename: Kunihiko
authors.initials: K
authors.lastname: Hino
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Miyakawa
authors.forename: Kazuaki
authors.initials: K
authors.lastname: Takahashi
authors.forename: Sheikh Mohammad Fazle
authors.initials: SM
authors.lastname: Akbar
authors.forename: Shunji
authors.initials: S
authors.lastname: Mishiro
mesh_terms: D000368:Aged; D005260:Female; D005838:Genotype; D016174:Hepacivirus / Q000235:genetics* / Q000276:immunology*; D019698:Hepatitis C, Chronic / Q000453:epidemiology* / Q000821:virology*; D006801:Humans; D007118:Immunoassay; D007564:Japan / Q000453:epidemiology; D008297:Male; D008875:Middle Aged; D017720:Molecular Epidemiology; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D014758:Viral Core Proteins / Q000235:genetics; D017361:Viral Nonstructural Proteins / Q000235:genetics; D012324:RNA-Dependent RNA Polymerase
chemical_list: D014758:Viral Core Proteins; D017361:Viral Nonstructural Proteins; C069130:nucleocapsid protein, Hepatitis C virus; C087036:NS-5 protein, hepatitis C virus; D012324:RNA-Dependent RNA Polymerase