Sequence comparison of JSRV with endogenous proviruses: Envelope genotypesand a novel ORF with similarity to a G-protein-coupled receptor

Ovine pulmonary carcinoma, a contagious lung cancer of sheep, is caused by the oncogenic jaagsiekte sheep retrovirus (JSRV) that is closely related to a family of endogenous sheep retroviral sequences (ESRVs). By using exogen ous virus-specific U3 oligonucleotide primers, the entire JSRV proviral gen ome or its 3' part was amplified from tumor DNA. Analysis of these proviral sequences revealed a novel open reading frame (ORF) within the pol coding region, designated ORF X, which was well conserved in ESRV and JSRV sequenc es. Deduced amino acids of ORF X showed similarity to a portion of the mamm alian adenosine receptor subtype 3, a member of the G-protein-coupled recep tor family. Comparison of deduced env amino acids of six JSRV strains from three continents identified 15 residues that defined two distinct genotypes of JSRVs. Sequence analysis identified two highly variable regions between JSRV and ESRV in the transmembrane domain of env (TM) and the 3' unique se quence (U3) of the long terminal repeat, from which JSRV-specific DNA probe s were derived. By using these DNA probes in Southern hybridization, for th e first time we successfully identified JSRV proviral sequences in tumor ge nomic DNA in the presence of multiple ESRV loci, validating the use of exog enous virus-specific DNA probes in the analysis of oncogenic proviral integ ration sites and identification of integrated exogenous proviral sequences, (C) 1999 Academic Press.