Although they are designed to be selective for viral enzymes and pathways, its likely that the HIV drugs are affecting normal cellular systems that are needed for healthy cellular repair/function and over time they damage normal cells. Most drugs such as antibiotics and antivirals do this to some degree, the ones that do it less are usually "less toxic". Also, insomuch as aging is dependent on antioxidant status, having an chronic infection causing inflamation and also taking drugs that put a heavy load on the body's detoxifying/antioxidant systems probably accelerates the aging process as well.
This whole area is the reason why chronic long term supressive therapy is really unsustainable with HIV and or XMRV (if it ends up being causual for CFS). Not only is it expensive to keep developing and taking multiple supressive drugs for decades, it likely causes long term effects that are not able to be tested for during the drug trials. Also, in the case of HIV the virus mutates so quickly that its really unreasonable to think that we will be able to keep up with it forever and develop drugs that work to keep it from replicating.
They need to focus on developing a vaccine, but also on eradication therapies that will put HIV and other retroviruses under completely. Unfortunately for the currently infected, I think like with smallpox, polio, etc... public health authorities probably look at the situation such that if they can come up with a vaccine and halt the spread, the epidemic will take care of itself because the non infected population will be immune and when all of the people who have the diease die, there will be nobody left to spread it. The one silver lining (if you can call it that) is that it appears to be *so hard* to make a vaccine for HIV that they might be actually easier to eradicate it. Sorry for the diversion, sobering to think about though...
