COMPLETE NUCLEOTIDE-SEQUENCE OF THE NEW SIMIAN T-LYMPHOTROPIC VIRUS, STLV-PH969 FROM A HAMADRYAS BABOON, AND UNUSUAL FEATURES OF ITS LONG TERMINAL REPEAT

A third type of primate T-lymphotropic virus, PTLV-L, with STLV-PH969 as a prototype, has recently been isolated from an African baboon (Pap io hamadryas). Classification of this virus has been based on partial sequence analysis of cDNA from a virus-producing cell line, PH969. We obtained the complete nucleotide sequence of this virus with a provira l genome of 8,916 bp. All major gents, homologous in all human T-cell lymphotropic virus (HTLV)-related viruses, and their corresponding mRN As, including appropriate splicing, were identified. One additional no nhomologous open reading frame in the proximal pX region is accessible for translation through alternative splicing, Sequence comparison sho ws that STLV-PH969 is equidistantly related to HTLV type 1 (HTLV-1) an d HTLV-2. In all coding regions, the similarity tends to be the lowest between STLV-PH969 and HTLV-1. However, in the long terminal repeat ( LTR) region, the lowest similarity was found between STLV-PH969 and HT LV-2, The U3-R and R-U5 boundaries of the STLV-PH969 LTR were experime ntally determined at nucleotides 268 and 524, respectively. This 695-b p LTR is 60 and 73 bp shorter than the LTRs of HTLV-1 and HTLV-2, resp ectively, but its general organization is similar to the one found in the HTLV-bovine leukemia virus genus, In the long region between the p olyadenylation signal and the poly(A) site, sequence similarity with t he HTLV-1 Rex-responsive element (RexRE) core and secondary structure prediction suggest the presence of a RexRE. The presence of three 21-b p repeats is conserved within the US region of HTLV-1, HTLV-2, and BLV . Only two direct repeats with similarity to these Tax-responsive elem ents were found in the STLV-PH969 LTR, which might suggest differences in the Tax-mediated transactivation of this virus. We conclude that S TLV-PH969 has all the genes and genomic regions to suggest a replicati on cycle comparable to that of HTLV-1 and HTLV-2.