THE NUCLEOTIDE-SEQUENCE AND SPLICED POL MESSENGER-RNA LEVELS OF THE NONPRIMATE SPUMAVIRUS BOVINE FOAMY VIRUS

We have determined the complete nucleotide sequence of a replication-c ompetent clone of bovine foamy virus (BFV) and have quantitated the am ount of splice pol mRNA processed early in infection. The 544-amino-ac id Gag protein precursor has little sequence similarity with its prima te foamy virus homologs, but the putative nucleocapsid (NC) protein, l ike the primate NCs, contains the three glycine-arginine-rich regions that are postulated to bind genomic RNA during virion assembly. The BF V gag and pol open reading frames overlap, with pro and pol in the sam e translational frame. As with the human foamy virus (HEV) and feline foamy virus, we have detected a spliced pol mRNA by PCR. Quantitativel y, this mRNA approximates the level of full-length genomic RNA early i n infection. The integrase (IN) domain of reverse transcriptase does n ot contain the canonical HH-CC zinc finger motif present in all charac terized retroviral INs, but it does contain a nearby histidine residue that could conceivably participate as a member of the zinc finger. Th e env gene encodes a protein that is over 40% identical in sequence to the HFV Env. By comparison, the Gag precursor of BFV is predicted to be only 28% identical to the HFV protein.