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How do we ever manage medical issues at a regional or national level, then?

This is a solved problem. Where I live, my journal is kept in an online computer system accessible to all, but my journal itself can only be read and written to by those medical practitioners that I explicitly give consent to. There are exceptions for emergencies and it can be overridden by the authorities. That's it. Problem solved.

What is a "journal" in this case?

I meant more from a public health perspective, like how CDCs and other agencies are able to collect enough population-level data to work on regional/national health issues (COVID or otherwise) when there are privacy concerns.

Do they have to do anonymization and aggregation the way we do for web analytics?

Patent data collection is very sensitive (I happen to work in an area that deals with it) and yes it has to have multiple layers of security, only approved access, and if used in research anonymised.

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