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The bottom line: Drugs that attack the HIV virus are a huge benefit when used properly. Failure to use these drugs properly causes the virus to become resistant to them.
I like that summary (I wish it would get me through immunology/pharmacology

)
I think this does bring an interesting point to debate - but it often gets lost in all the technical language. Even my eyes glaze over at times! The drugs used to treat HIV can be very expensive, even if a single drug costs a reasonable amount, the combination of drugs required is daunting. And the schedule to take the drugs would be difficult for the most regemented individual (imagine some of us complain about remembering just one pill a day). This leads to a dangerous situation - a situation in which it is easy for an individual to begin the therapy but not follow through properly - either through lack of medicine when funding dries up or through simple human error. And this creates the prime environment for the mutants to proliferate.
This leads to a question about current treatment plans pursued by doctors. THe idea would be to treat everyone with the cocktail - but should the doctors be assessing the individual ability/willingness to comply first? If the person has a history of being actively hostile to doctor's orders, or has shown past inability to follow schedules or simpler drug regimens (even as simple as finishing all ten days of antibiotics post-infection), does the doctor still have an obligation to treat this patient using the cocktail? Or is the doctor acting in the best interest of the greater good by denying them access to the drugs which lead to greater mutagenesis (those which create more mutants more quickly) and simply treat this patient with other therapies that may not have as good an outcome, yet would not create as many potentially harmful mutated HIV strains?
I have heard a similar argument in regards to ability to pay. In this case, the discussion centered on the African epidemic - but a doctor (actual practicing MD) argued we should not be treating any indigenous patient in Africa with the cocktail because the drug supply was not guaranteed to be continuous - mostly from money concerns and also due to logistics concerns (actually being able to get the drugs to remote locations, etc). While this might seem heartless, in the end we would be protecting more people by preventing a larger pool of individuals from becoming essentially HIV mutant factories.
Now, I was outraged by these types of argument, because my first instinct is to treat and support the patient in any way possible. But then, I probably will not be an immunologist working for the CDC trying to make these difficult decisions.
One final note - from the last study link:
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However, increased mutagenesis of HIV by NRTIs could be viewed as an advantage in therapies directed at extinguishing virus infectivity by lethal mutagenesis.
Which translates to: not all viral mutations are bad for the patient - some kill the virus or render it inert. A fact that many of our earlier vaccines relied on. This could almost be an argument to reverse the ones I pointed out above - treat as many people as possible (to maximize number of mutations), and maybe we'll find a type of mutation that kills HIV all together.