I dont know what to do. Normaly my Dr does not give me the flu shots because I seem to have a reaction to them that makes me sick for several days. I'm concerned about the flu this season becasue there will be so many people out there that are not getting the shots because of the shortage. Should I get the shot knowing I'll be ill for a few days and not risk a huge outbreak of a strain that might kill me?

I know my viral load and CD4 counts are not very good.. But given that there might be a huge flu season I'm worried for the first time

Your thinking is excellent, in my opinion. It is conceivable that this will be a more severe flu season, although most Americans who need the vaccine will get it, and they are the ones who would most likely get the flu anyway.

As for you, having more advanced immune disease puts you at special risk, so vaccination is all the more important. I am aware of the reactions that you report to the vaccine, but it does not sound like an allergy. Taking ibuprofen (Advil) before you get the vaccine and for the next few days thereafter could help improve your situation. As long as you and your doctor are confident you are not allergic to the vaccine, you should go ahead.