Genetic analysis of pestiviruses at the 3' end of the genome.
Specific PCR primers were selected for each pestivirus genotype which flanked the 3'-part of the NS5B gene and more than three quarters of the 3'-UTR. PCR products were sequenced in both directions using an automatic sequencing device and analyzed by computer package program DNASTAR. A comparative analysis of the 3' untranslated region (3'-UTR) of 82 viruses, representing the four genotypes of the Pestivirus genus, provided a similar phylogenetic grouping as other genomic regions. Intertypic recombination was not observed, but Border disease virus (BDV) and Bovine viral diarrhoea virus type I (BVDV I) showed great intragenotypic variability. In most pestiviruses the stop codon is TGA, but BDV isolates were found to have either a TAG or a TAA stop codon. Various deletions and insertions were observed in the 3'-UTR region. Viruses of the BVDV lb group contained a characteristic deletion of 41 nucleotides. Compared to the 5'-UTR, the 3'-UTR was less conserved. The first 50-60 nucleotides were particularly variable, whilst the most conserved part was found at the 3' end of the studied region. All 82 viruses contained AT-rich stretches, the positions and sizes of which differed between the genotypes.
Vilcek
S
S
Department of Virology, The National Veterinary Institute, Biomedical Center, Uppsala, Sweden.
Paton
D
D
Lowings
P
P
Björklund
H
H
Nettleton
P
P
Belák
S
S
D020413:3' Untranslated Regions / Q000032:analysis; D000818:Animals; D001483:Base Sequence; D018083:Border disease virus / Q000145:classification / Q000235:genetics*; D002417:Cattle; D006692:Classical Swine Fever Virus / Q000145:classification / Q000235:genetics*; D004279:DNA, Viral; D001908:Diarrhea Viruses, Bovine Viral / Q000145:classification / Q000235:genetics*; D016679:Genome, Viral; D008969:Molecular Sequence Data; D010576:Pestivirus / Q000145:classification / Q000235:genetics; D010802:Phylogeny; D012367:RNA, Viral / Q000032:analysis; D012689:Sequence Homology, Nucleic Acid; D012756:Sheep; D013552:Swine
D020413:3' Untranslated Regions; D004279:DNA, Viral; D012367:RNA, Viral