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Reverse transcription of retroviral genomes is primed by a tRNA molecule that anneals to an 18 nt primer binding site (PBS) on the viral RNA genome. Additional base pair interactions between the tRNA primer and the viral RNA have been proposed. In particular, base pairing was proposed between the anticodon loop of tRNALys3 and the 'A-rich' loop of a hairpin located immediately upstream of the PBS site in HIV-1 RNA. In order to judge the importance of this sequence/structure motif, we performed an extensive phylogenetic analysis of this genomic region in a variety of simian and human immunodeficiency viruses (SIV and HIV). Both the phylogeny of natural HIV/SIV sequences and the behaviour of U5-PBS mutant/revertant viruses support the idea that this RNA structure is critical for virus replication. Although this hairpin may play a role in tRNA annealing and/or initiation of reverse transcription, the proposed base pairing interaction between the A-rich loop of the HIV-1 hairpin and the anticodon of the initiator tRNA is not directly supported by this analysis.

Background Live-attenuated SIV can induce superinfection resistance; however, the mechanism of this effect is not understood and may have implications for HIV vaccine development. To further investigate the role of virus replication in conferring protection we have analysed T cell phenotype and responses in gut tissue following infection of macaques with either SIVmac239Δnef or a doxycycline-dependent replication variant of SIVmac239 Δnef designated SIVrtTA.

Background In the SIV/macaque model of HIV in man, live attenuated virus confers the most potent protection against wild-type virus challenge. We have developed a novel live attenuated (nef deleted) vaccine SIVmac239 (SIVrtTA) that is dependent on doxycycline for replication in vivo. Withdrawal of doxycycline prevents replication of SIVrtTA. We used this virus to vaccinate rhesus macaques to investigate the role of virus replication and persistence in protection against SIVmac239 challenge.

Publisher Summary This chapter deals with the structure and function of the leader transcript of human immunodeficiency virus (HIV-1) and HIV-2. Most of the RNA signals encoded by the untranslated leader RNA have specific nucleotide sequences critical for recognition and function, but there is accumulating evidence that their structural context can also be important. There is an intense effort to analyze the secondary structure of retroviral leader RNAs using a variety of methods, including biochemical analysis, free-energy minimization, sequence comparison, and mutant analysis. The chapter focuses primarily on the relationships between the structure of specific leader RNA motifs and their function in the retroviral life cycle. Among retroviruses, the lentiviruses have the most complex genome structure and expression strategy. The primate lentiviruses include the human and simian immunodeficiency viruses (SIV). Understanding the three-dimensional structure formed by the HIV leader RNA molecule, both free and in the ribonucleoprotein complex of virion, is crucial for analyzing its specific recognition by proteins and its interaction by other RNA molecules during virus replication. The number of HIV–SIV sequences now known is sufficiently large; hence, comparative analysis can be used effectively to deduce some of the basic design principles underlying HIV RNA structure. By understanding the molecular basis of the interactions that govern critical steps in the retroviral replication cycle, it may be possible to develop methods to intervene therapeutically in the process.