As for side effects, most people experience injection site soreness for a day or two after the first dose, and the second dose is frequently accompanied by some flu-like symptoms, such as fatigue, body aches, and low-grade fever. Though you may not experience symptoms, if you do, your immune system is behaving as it should — learning to recognize and combat the virus (though if you don’t have symptoms, it doesn’t mean that your immune system isn’t working properly).