A new simian T-lymphotropic virus, STLV-PH969, was recently isolated from a wild-born Hamadryas baboon. Previous analysis had revealed that it differs sufficiently from the other HTLV/STLVs to be considered a new type, provisionally designated primate T-lymphotropic virus-L. Here we analyse a 3850 bp cDNA fragment spanning the 3′ part of the STLV-PH969 genome. The fragment encodes three major proteins: Env, Tax and Rex. Sequence comparison and phylogenetic analysis indicate that in general STLV-PH969 tends to be more closely related to HTLV-II than to HTLV-I, although separate gene regions might have evolved under different constraints. Detailed comparison of the Env, Tax and Rex proteins among the HTLV-I, -II and STLV-PH969 prototypes reveals that the amino acid sequence of each protein shows a preferential conservation of functionally important domains. RNA-PCR on cytoplasmic messengers demonstrated splicing between a splice donor site immediately downstream of the start codon, and two splice acceptor sites identified in the region. The predominant spliced messenger encodes both Tax and Rex. The other messenger potentially encodes a new viral protein from the proximal part of the region that is similar in amino acid composition to p12 and p10 of HTLV-I and HTLV-II respectively. This genomic organization of the proximal region of STLV-PH969 is different from that found in HTLV-I and HTLV-II. Therefore, the distinct classification of this virus can be justified, not only in terms of sequence divergence but also in terms of its different genomic structure.


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