The tests could be false positives caused by contamination. It's also possible that these are just residual bits of HIV being detected because the tests are so effective, but the infection is still effectively eradicated. Those would be the best outcomes for those people who want to believe that marrow transplantation could be a cure.
A less thrilling possibility is that the virus has been slowly mutating around its new obstacles and his infection has resumed. That would be a far more devastating blow to researchers who, although they knew widespread marrow transplantation weren't a practical cure, were looking towards this technique for new treatment ideas.
There is, of course, one final possibility. The patient in question could have become re-infected with the virus. What an irony that would be, if the person who demonstrated that there might be a cure went right back out and got infected again.
Personally, I'm hoping for the one of the first two explanations to be true. A false positive test, or residual bits of viral genome being detected, are a lot more pleasant to consider than either of the other alternatives. They're also the most likely explanation, since the patient in question has been off ART for 5 years, and there's no detectable virus in his blood. The doctors had to go hunting to find the signals they did.
Source: http://std.about.com/b/2012/06/27/so-much-for-a-cure.htm
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