Background: HIV replication results in a high mutation rate that permits rapid generation of viruses that can escape immune recognition. HIV sequences sampled from a population of infected individuals recapitulate a star burst-like evolutionary tree pattern; most of the variants sampled at the same time are positioned roughly equidistant from the center of the tree, and thus also approximately twice this distance from any other circulating strain. A primary concern in designing protective AIDS vaccines, then, is the choice of strains likely to best provide protection against the ever expanding population of HIV-1 variants. We have proposed and are evaluating the use of an HIV population ancestral sequence as a vaccine candidate, since it is expected to recapitulate a functional state and is found near the center of the evolutionary tree.

Methods: Ancestral viral sequences were reconstructed from a phylogenetic tree describing the relationships between available sequences from the population of interest, and is thus expected to correspond to the most recent common ancestor of the viral strains sampled from the targeted epidemic. To evaluate our ability to accurately predict an ancestral sequence through phylogenetic reconstruction, we used viral gene sequences taken from rhesus macaques infected with a molecularly defined strain of SIV. Next, we evaluated prototype HIV clade B and C Env proteins.

Results: We accurately predicted > 90% of the ancestral SIV sequences, including variable sites. Most of the differences corresponded to mutations resulting from parallel evolutionary changes that occurred in all infected animals. The deduced ancestral HIV-1 clade env genes were found to encode more of the known recognition sites of HIV-1 Env-specific human cytotoxic T-cells than any natural strain except that used to define epitope reactivity. Similarly, all deduced ancestors were highly enriched for potential N- and O-linked glycosylation sites. Thus ancestral reconstructions reflect features of founder strains as well as parallel evolutionary changes that occur upon growth in host populations.

Conclusions: Ancestor protein immunogens are likely to focus immunologic reactivity onto sites that are important to viral fitness. Hence, their use in candidate vaccines provides a promising new approach for the formulation of broadly protective HIV vaccines.