title: A divergent simian immunodeficiency virus from sooty mangabey with an atypical Tat-TAR structure.
abstract: SIVsm, the simian immunodeficiency virus that naturally infects sooty mangabeys in West Africa, is the closest lentiviral relative of human immunodeficiency virus type 2 (HIV-2). To determine the genetic characteristics of SIVsm in its natural host, we sequenced the full-length genome of SIVsmSL92b, a primary isolate obtained from a pet sooty mangabey in Sierra Leone. SIVsmSL92b proved to be the most divergent member of the HIV-2/SIVsm lineage found thus far, having as much as 35% nucleotide divergence from other HIV-2 genomes. A phylogenetic association between SIVsmSL92b and HIV-2 PA subtype E, which had been previously revealed by the analysis of partial gag sequences, was extended to the pol gene. SIVsmSL92b showed several divergent features, including a short Tat protein of 104 residues and an atypical TAR structure. Specifically, only one of the duplicate TAR elements contained the conserved hexanucleotide loop sequence CUGGGX important for Tat-cyclin T1 binding. These features suggested that the mechanism of SIVsmSL92b Tat and TAR interaction differed from that described for HIV-2. Taken together, these findings indicated that the structural diversity within the HIV-2/SIVsm lineage was greater than previously appreciated.
authors.affiliation: Aaron Diamond AIDS Research Center, Rockefeller University, New York, New York 10016, USAchakra@adarc.org.
authors.forename: L A
authors.initials: LA
authors.lastname: Chakrabarti
authors.forename: A
authors.initials: A
authors.lastname: Luckay
authors.forename: P A
authors.initials: PA
authors.lastname: Marx
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D016665:Cercocebus atys; D015696:Gene Products, tat / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D015756:Genes, tat; D014644:Genetic Variation / Q000235:genetics*; D016679:Genome, Viral; D015658:HIV Infections / Q000821:virology; D016325:HIV Long Terminal Repeat / Q000235:genetics*; D015498:HIV-2; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D016097:Simian Acquired Immunodeficiency Syndrome / Q000821:virology*; D015302:Simian Immunodeficiency Virus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D015533:Transcriptional Activation; D054322:tat Gene Products, Human Immunodeficiency Virus
chemical_list: D015696:Gene Products, tat; D054322:tat Gene Products, Human Immunodeficiency Virus