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The recipient of the transplant now will have two variants of the virus -- which may significantly increase resistance to HIV meds. That's why even couples who are both HIV+ are recommended to have protected sex.
Let's say that one person's virus is currently being treated well with Combivir and Sustiva (a very common first-line treatment regimen consisting of AZT, 3TC, and EVF). The other person has been treated with AZT in the past as a single-drug, and has developed resistance to it, and is now on Truvada and Kaletra (a common second-line treatment consisting of TDF, FTC, and the protease inhibitor LPV). They think that since both of them have HIV that they don't have to use condoms, but now both are infected with both virus strains, and they merge to some degree.
The Combivir/Sustiva work fairly well at first because at least two of the three drugs are active, but the virus from the partner that is being treated with Truvada/Kaletra gets into the first person's blood, and is no longer getting the Truvada/Kaletra. Just like bacteria, the virus that survives treatment is at least somewhat resistant to the drugs it's being given, and once it stops getting those drugs it will reproduce and flourish, spreading those resistance genes.
When the Combivir/Sustiva regimen fails (as it seems eventually every regimen does), the person goes to their doctor. The doctor, under the impression that his virus has only been exposed to one regimen of drugs, tries a second level treatment. He decides on Atriplia and a protease inhibitor. Atriplia contains EFV (Sustiva), but it also has two other drugs that the doctor thinks he shouldn't have resistance to -- TDF and FTC, so he thinks it will work. Alas, his virus is already resistant to all three, so this regimen is doomed to fail quickly, and will also make the virus resistant to whatever protease inhibitor he gives with it, because the protease inhibitor will be working alone... whatever virus it doesn't kill will be resistant (whereas in a normal second-line regimen, whatever virus isn't killed by the protease inhibitor will usually be killed by the other antiretrovirals).
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