title: Genome instability in BVDV: an examination of the sequence and structural influences on RNA recombination.
abstract: The cytopathogenic biotype of the pestivirus, bovine viral diarrhea virus, is frequently a product of nonhomologous recombination in the region of the genome encoding the viral NS2-NS3 proteins. The possibility that sequences or structures in this region contributed to a hotspot for RNA recombination was examined. A PCR-based strategy was used to examine viral genomic RNA isolated from tissue samples of cattle persistently infected with the noncytopathogenic biotype of the virus. Analysis of two different regions of the viral genome revealed that recombination was not restricted to particular sequences. Alignment of the genomic sequences undergoing recombination and examination of the predicted secondary structures of the participating RNAs revealed that the dissociation of partial, newly synthesized negative strand RNAs from the positive strand template occurred at many different sites on the molecule. Similarly, it appeared that the reassociation of the RNA polymerase complex with a second positive strand template was frequently influenced by short regions of homology between the nascent RNA strand and open secondary structures in the template molecule.
authors.affiliation: Department of Pathology and Infectious Diseases, Royal Veterinary College, Hatfield, Hertfordshire, United Kingdom.
authors.forename: M
authors.initials: M
authors.lastname: Desport
authors.forename: M E
authors.initials: ME
authors.lastname: Collins
authors.forename: J
authors.initials: J
authors.lastname: Brownlie
mesh_terms: D000818:Animals; D001912:Bovine Virus Diarrhea-Mucosal Disease / Q000821:virology*; D002417:Cattle; D001908:Diarrhea Viruses, Bovine Viral / Q000235:genetics*; D016679:Genome, Viral; D009690:Nucleic Acid Conformation; D010447:Peptide Hydrolases; D020365:RNA Helicases; D012367:RNA, Viral / Q000737:chemistry; D011995:Recombination, Genetic; D014759:Viral Envelope Proteins / Q000235:genetics*; D017361:Viral Nonstructural Proteins / Q000235:genetics*; D012697:Serine Endopeptidases; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases
chemical_list: D010447:Peptide Hydrolases; D020365:RNA Helicases; D012367:RNA, Viral; D014759:Viral Envelope Proteins; D017361:Viral Nonstructural Proteins; C076551:gp53, bovine viral diarrhea virus; C086730:p80 protein, bovine viral diarrhea virus; D012697:Serine Endopeptidases; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases