I'm assuming the virtual DOM, and that React takes care of it with diff'ing. But I had a recruiter say that ref's affect the actual DOM, I can't see how this can be. I assume that they were just mistaken.
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Refs should reference the actual DOM. One usage of Refs is integrating with third-party DOM libraries, so you can directly modify the DOM using Refs. If Refs reference the virtual DOM, I don't think the demand can be meet. You modify a virtual DOM, but you can't make sure the modification would be synchronized to the actual DOM. Besides, if you want to modify actual DOM when using react, you should always modify the state of components instead of modifying the DOM by Refs.