Designing HIV-1 vaccines to reflect viral diversity and the global context of HIV / AIDS.

One of the greatest barriers to developing an effective HIV-1 vaccine is the diversity of HIV-1 viral strains and clades. The number of unique HIV-1 sequences in public databases has been steadily increasing every year with no end in sight. The most effective type of vaccine in the global context of the HIV epidemic would include immunogenic regions or epitopes of the HIV-1 genome that are highly conserved across clades and strains of HIV-1. Until recently discovery of conserved epitopes in the HIV-1 genome has been hampered by a lack of effective tools that would enable researchers to mine large HIV-1 protein sequence databases for vaccine components. This article reviews the current status of bioinformatics tools for HIV-1 sequence database mining and concludes that the necessary tools for attempting to prepare "cross-clade" vaccines are at hand. (authors)