I'm comparing two AAV vectors that have the same capsid. The vectors are injected at the same dose in mice of the same age and weight. The only difference between the AAV vectors is the transgene size. When I check the transduction efficiency using qPCR, I see that the one with the larger transgene construct tends to have a higher transduction rate compared to the one with the smaller transgene size.

For the qPCR, I use primers that target a region of the transgene that is present in both constructs. As a standard I've used both plasmids that were used to create the AAVs. When analysing the data with either standard, I always end up with a higher transduction rate for the AAV with a larger transgene size.

Has anyone had this issue before? Is this caused by the difference of transgene size or should I change something in my qPCR protocol?

Thanks in advance ;)