Response from Dr. Sherer

Yes, any time there is a disruption in a continuous dosing of antiretroviral therapy, there is a small risk of drug resistance to members of that class. The NNRTIs, i.e. Sustiva and Viramune, are vulnerable to such interruptions, because only one amino acid change is needed to develop complete resistance to the entire class, and this can happen rapidly, i.e. in a matter of hours or days.
It is recommended that, when NNRTI-based regimens need to be discontinued, the NNRTI drug be stopped first, and the nucleosides like AZT or tenofovir (Viread) be stopped after one week. This is because the NNRTIs have much longer half lives in the blood, in the range of days to a week or more, compared to the other drugs.
Your doctor was trying to accomplish this when he advised you to stop taking the Sustiva first, and then the Epzicom. He was also probably trying to establish whether your symptoms might be related to a hypresensitivity rash to abacavir, which is one of the drugs in the co-formulated epzicom (the other is lamivudine or 3TC). This is important because abacavir is a very useful drug, and before a physician diagnoses this HSR, he or she wants to be sure before the use of that drug is eliminated.
Whether or not you did suffer an abacavir HSR is for you and your doctor to determine; there are elements in your history that are consistent with that diagnosis.
To return to your main question, the best way to test this question will be to resume a Sustiva-baed regimen (with the NRTI backbone that you and your physician choose) and closely follow your response.
If the response is sub-optimal, then your doctor can obtain a genotype resistance test to see if Sustiva resistance has occurred.
Even if that is the case, there remain good ART options for you that can be expected to fully suppress your viral load.
I urge you to talk to your doctor about your concerns, and these responses.
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