>Viruses
That is how the vaccine works. It is the most vital ingredient.
>Other things

Again, back to the chemistry, these are not pure elemental things. To put it this way, your body needs iron. Iron is necessary for your red blood cells to move blood. Without it you are a dead man. That doesn't mean you just have iron bars moving around your system.
I'll once again use the classic sodium chloride example. Alone, chlorine is a poisonous gas. Ingesting it will kill you. Sodium is a metal that would literally explode if you try to eat it. Sodium chloride doesn't have either of these properties, and is necessary for proper biological function.

Dead or inactive elements of a disease (or even just proteins) to train the ommune system to kill it