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There are a variety of trackers available in After Effects, but if I were doing this, I'd probably look first at Boris FX Mocha, which has a version included for free with AE.
The character elements would need to be designed and layered properly, then animated in AE.
For example, for the eyes you would want the following layers, likely in this order:
- (Optional) outer stroke around base shape
- Top Lid (matted to base shape)
- Bottom Lid (matted to base shape)
- Pupil (matted to base shape)
- Base white shape
You may be able to create both eyes together, or may want individual control.
Eyebrows would be separate from the eyes and separate from one another.
Mouths would require a handful of different mouth shapes being drawn, some with individually-animated elements (such as the tongue)
It may be helpful to take a look at Character Animator and some of the example puppets included with the program. That will give you a great breakdown on the kind of layering required. You also may be able to create the facial animations directly in Character, then track them onto footage in After Effects.
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3d camera tracker or mocha tracking (both available in after effects) could do the tracking. the animation is rather simple 2d animation. I recommend you start here to learn how to animate layers in after effects look for the animation part.