Molecular cloning and nucleotide sequence of hog cholera virus strain Brescia and mapping of the genomic region encoding envelope protein E1.

Genomic RNA of hog cholera virus (HCV) strain Brescia was cloned and sequenced. The nucleotide sequence was deduced from overlapping cDNA clones and comprises 12,283 nucleotides. We cloned the complete 3' end of the HCV genome, but could not unequivocally prove that the cDNA sequence also completely covers HCV RNA at the 5' end. The HCV genome contained one large open reading frame, which spans the viral plus strand RNA and encodes an amino acid sequence of 3898 residues with a calculated molecular weight of 438,300. To identify structural HCV glycoproteins, we prepared rabbit antisera against three synthetic peptides deduced from the sequence. Because one of these antisera reacted with a 51- to 54-kDa glycoprotein (envelope protein E1 of HCV) on Western blot, the genomic position of the sequence encoding gp51-54 could be clearly established. The amino acid sequence of Brescia was compared with that of HCV strain Alfort and that of BVDV strains NADL and Osloss. The degree of homology between the two HCV strains was 93%, and between Brescia and the BVDV strains about 70%. NADL contained an inserted sequence of 90 amino acids that was absent from the sequences of Brescia, Alfort, and Osloss, whereas Osloss contained an inserted sequence of 76 amino acids that was absent from the sequences of Brescia, Alfort, and NADL. Sequences in p80, the most homologous protein among pestiviruses, showed similarity to six sequence motifs found conserved in helicase-like proteins represented by eIF-4A. Furthermore, a trypsin-like serine protease domain detected in p80 of BVDV was also found conserved in HCV, suggesting that pestivirus p80 may be bifunctional.