We've been having an issue with endotoxin contamination in our AAV preps. A few months ago we had a very bad bacterial contamination which we have since addressed. Our preps are clean of bacteria, fungus, and mycoplasma, but we still have high endotoxin levels (>500EU/mL). We have had success using an endotoxin removal column to get the endotoxin levels to below 10EU/mL.
We are still getting high endotoxin contamination in all of our AAV preps and are looking for recommendations on how to address this issue in our upstream purification process. This is how we package and purify our AAV:
Check the endotoxin levels in all your starting material, including the plasmids and the media. Other source of contamination could be the dishes and other consumables. Besides those aseptic technique is the way to go. It might be helpful to track the endotoxin levels at each step of AAV purification, starting from crude lysate.
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