The primer binding site on the RNA genome of human and simian immunodeficiency viruses is flanked by an upstream hairpin structure.

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.