HIV Diversity

The genetic diversity of HIV is revealed by the tree of the main (M) group (below), which breaks into nine clades (labeled A–K) of closely related viruses. The tip of each line represents one of the hundreds of variations of the env gene, each belonging to a different viral variant. The United States epidemic is driven by B-clade viruses (blue lines); the one in South Africa is driven by those in the C-clade (red lines).

A line connects two gene sequences, with the length of the line related to the number of mutations needed to convert one sequence to the other (the genetic distance). The green circles at the B- and C-clades indicate nodal ancestral genes. In general, the genetic distance between a gene and its nodal ancestor is shorter than the distance between any two genes in the clade, so a vaccine made with the ancestral gene has a chance to immunize a person against all viruses in the clade. The middle circle represents the ancestral gene for the entire M-group. A central vaccine would use one, or all three, of the ancestral genes.

One consequence of HIV's flexible genome is that it is able to avoid a person's immune system indefinitely. The pie charts (below) show the viral diversity within a newly infected individual. After five days, this person had only two variants (blue and gray), with one (blue) completely dominating the viral load. Thirty-six days later, the immune system had successfully targeted that virus, but many new variants (colors) were generated that were not targeted by the immune response. Korber and collaborators have shown that HIV can evolve away from an immune response in as little as three weeks.