The flu shot is a muscle injection so the shot goes into the muscle.
Something to understand about the body is that internally you are basically a slightly leaky collection of tissues. Lots of transport is done by the circulatory system yes, but you are still slowly oozing fluids around outside of the circulatory system. Most of this eventually gets picked up by the lymph system and recycled.
As for moving your arm, motion or massaging helps accelerate this oozing by shifting stuff around internally and changing pressure on things. This spreads out the fluid at the injection site faster than if you were to just let it ooze around by itself. It doesn’t necessarily help so much for the shots effectiveness, but it can spread out the injection over a larger area faster and accelerate the movement of your immune cells oozing around which can help with soreness.
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