The AIDS researchers reasoned that if they had correctly understood the course of infection, then the diversity and number of viruses within a given patient would map to the progress of the disease. First, for a variable period of weeks to months, high levels of the virus would show up in the bloodstream of someone recently infected. Then the fully roused immune system would do its virus-control work, so that peak would be followed by a long period when virus numbers would be low. The immune system would be keeping up with the viruses, but they would be constantly mutating, so the number of subspecies would keep increasing. Theoretically, after the victim showed signs of full-blown AIDS, the number of subspecies should decrease.
Preliminary results support the theory.
It explains the unpredictable length of the incubation period between entrance of the virus and development of disease symptoms. Decades may pass before the virus mutates in just the right way to confuse the immune system, or the key mutations could appear within months. The theory also explains why medical scientists are having so little luck developing vaccines or cures for this modern plague. The virus is actually an enormous, ever-changing family of targets, too shifty for any medical magic bullet found so far.