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I can only speak for TNG, but in all of the missions to uncontacted worlds, no new civilizations have ever gotten sick. When the Europeans made first contact the Native Americans, the Native Americans were ravaged with myriad Europian plagues.

Does any episode/book in the Star Trek universe discuss how this is handled during first contact? Especially given the episode Journey's End it seems like European-Native relations were on the writers' minds, so I'm curious if any sort of preventative measure was ever mentioned.

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    In the 24th century, common diseases have been eradicated. – Rebel-Scum Feb 3 at 7:23
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    The transporter can be tuned not to transport disease organisms (source?), but evidently it has to recognize them. Presumably, the human symbiont E. coli is left untouched. Disease could still be introduced by shuttle. Unfamiliar disease-causing organisms might be passed to the crew of a starship more easily than the reverse! – Invisible Trihedron Feb 3 at 13:28
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    In one TNG episode ("Thine Own Self"), a memory-impaired Data inadvertently helps to spread radiation sickness via debris from a crashed space probe. Does that count (first contact happens, but was not intended). – Eike Pierstorff Feb 3 at 16:10
  • Eike Pierstorff that's an excellent point. I forgot about that episode. I suppose that sort of counts, in the sense that uncontacted peoples were in danger of getting sick due to the Federation, but I'm really looking for a pathogen. I think @Rebel-Scum makes the best point here; in the future there just aren't any diseases left to spread. At least, not in the Federation (plasma plague notwithstanding) – Zaya Feb 3 at 21:01
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Miri, in the original series, where a deadly bioengineered pathogen killed off all the adults beyond a certain age. There is every indication that it could have been carried back to the Enterprise (and beyond). Indeed, much of the plot revolves around them being trapped in quarantine on the planet surface. That was probably the earliest example of infectious disease, establishing that it’s clearly a thing.

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    I'll have to check this episode out. But this is sort of the reverse of what I was wondering about. It seems with all of the Federation's advanced technology, and all of the new species they've come into contact with they would have higher immunity than an uncontacted world. But I'll be sure to watch this episode, thank you! – Zaya Feb 9 at 17:11

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