Response from Dr. Sherer

You ask a good question. It is possible that your viral infection caused a short term increase in your viral load. Unfortunately, the magnitude of the viral load increase and the associated drop in the CD4 cell count suggest a more serious problem, i.e. drug resistance.
Unfortunately, drug resistance mutations and virologic failure can occur, even in the presence of excellent adherence. While it is uncommon, occuring in <10% of people on Atripla in the first year of treatment in clinical trials, it does occur.
There are several possible answers as to why it happens. One is that your virus may have had one or more resistance mutations when you acquired it. You and your doctor can answer these questions - did you have a resistance test done before you started this regimen?
If so, was it consistent with a wild-type virus, i.e. with no significant primary resistance mutations?
Even if that were the case, your virus may still have had significant resistance mutations in a percentage of clones, i.e. < 20%, which would have escaped detection due to the sensitivity of the resistance test, but which still could have led to drug resistance and virologic failure.
Other factors that might contribute to this outcome could include other illnesses (like your 'flu') or vaccinations at the time of the last blood test, or other medications that might have interfered with the absorption or action of your ART medications. You and your doctor will need to review all of this clinical information and assess your current situation, as well as repeat the viral load and CD4 cell count and obtain a resistance test, in order to plan for the next best action in your management. Even if this IS virologic failure and drug resistance, there are second line options available to you that should achieve full viral suppression and rising CD4 cells, as you initially had with this regimen.
I urge you not to be overly discouraged and to see your doctor promptly to undergo this assessment, get these next blood tests, and figure out your next best course of action.
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