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Response from Dr. Sherer

Yes, resistance to Atripla and other regimens containing an NNRTI medication such as efavirenz (Sustiva or Stocrin) or nevirapine (Viramune or Triommune)can develop quickly, even within a few weeks.
This is one of the weaknesses of these regimens; they require a high degree of adherence to the regimen, and even minor lapses in adherence, leading to prolonged times when the drug levels are sub-therapeutic, can cause resistance. Atripla contains both EFV and 3TC, and both of these drugs are associated with rapid resistance if sub-optimal drug levels result from lapses in adherence.
You and your friend should be aware also that resistance tests only reflect the majority clones in an individual's 'swarm' of HIV virus, and clones that are present at < 20% may not show up on the genotype.
Hence your friend may have acquired some 3TC or EFV resistance in 2001, and still have a genotype showing only 'wild type' virus. Hence this outcome may have occurred, even if your friend took every dose on time and maintained perfect adherence.
It seems unlikely, however, that your friend is out of all current HIV medication options, since transmission of extremely multi-ddrug resistant virus is highly unusual, though such cases have been documented. It is more likely that he has complete resistance to the NNRTIs and partial resistance to the NRTIs. From your history, I can see no reason for him to have PI resistance, unless he has received treatments that I am unaware of.
Also, your friend's doctor may want to consider obtaining a phenotype test to help to coroborate the results of the genotype test. Phenotypes can often help physicians to understand complex resistance patterns.
My advise is to take these suggestions with you to your friend's next doctor's appointment and discuss all of these questions with his or her doctor.
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