title: Full-length open reading frame of a recombinant hepatitis C virus strain from St Petersburg: proposed mechanism for its formation.
abstract: The full-length ORFs for the hepatitis C virus recombinant RF1_2k/1b (N687) and the non-recombinant 1b strain N589 were sequenced. A single recombination point was found and the sizes of the genes (C, E1, E2, p7, NS2, NS3, NS4 and NS5) were according to the parental subtypes. The PKR-eIF2alpha phosphorylation site homology domain sequence of the E2 protein was identical to those of genotype 2 strains, while the IFN-alpha-sensitivity-determining region of the NS5A protein was identical to those of interferon-resistant 1b strains. For the parental strains, two hairpin structures, HS1 and HS2, were predicted for the plus-strand up- and downstream of the crossover site, which were not present in the recombinant strain. HS2 shared similarity with the motif1 hairpin of turnip crinkle virus RNA that binds to the RNA-dependent RNA polymerase and facilitates 3'-terminal extension during recombination. This study suggests that RF1_2k/1b has emerged by homologous recombination during minus-strand synthesis via template switching because of constraints imposed by the HS1 hairpin of the 3'-parental genome.
authors.affiliation: St Petersburg Pasteur Institute, 14 Mira Street, St Petersburg 197101, Russia.|Department of Virology, Swedish Institute for Infectious Disease Control, 171 82 Solna, Sweden.
authors.forename: Olga
authors.initials: O
authors.lastname: Kalinina
authors.affiliation: Department of Virology, Swedish Institute for Infectious Disease Control, 171 82 Solna, Sweden.
authors.forename: Helene
authors.initials: H
authors.lastname: Norder
authors.affiliation: Department of Virology, Swedish Institute for Infectious Disease Control, 171 82 Solna, Sweden.
authors.forename: Lars O
authors.initials: LO
authors.lastname: Magnius
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D005814:Genes, Viral; D016174:Hepacivirus / Q000235:genetics* / Q000302:isolation & purification; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D016366:Open Reading Frames / Q000235:genetics*; D010766:Phosphorylation; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics; D011995:Recombination, Genetic; D012426:Russia; D016415:Sequence Alignment; D013698:Templates, Genetic
chemical_list: D012367:RNA, Viral